50 results on '"Fan, Yang"'
Search Results
2. Single-cell profiling of African swine fever virus disease in the pig spleen reveals viral and host dynamics.
- Author
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Zixiang Zhu, Ruoqing Mao, Baohong Liu, Huanan Liu, Zhengwang Shi, Kunpeng Zhang, Huisheng Liu, Danyang Zhang, Jia Liu, Zhenxiang Zhao, Kangli Li, Fan Yang, Weijun Cao, Xiangle Zhang, Chaochao Shen, Dehui Sun, Liyuan Wang, Hong Tian, Yi Ru, and Tao Feng
- Subjects
AFRICAN swine fever virus ,VIRUS diseases ,AFRICAN swine fever ,CLASSICAL swine fever ,SPLEEN ,SWINE farms - Abstract
African swine fever, one of the major viral diseases of swine, poses an imminent threat to the global pig industry. The high-efficient replication of the causative agent .African swine fever virus (ASFV) in various organs in pigs greatly contributes to the disease. However, how ASFV manipulates the cell population to drive high-efficient replication of the virus in vivo remains unclear. Here, we found that the spleen reveals the most severe pathological manifestation with the highest viral loads among various organs in pigs during ASFV infection. By using single-cell-RNA-sequencing technology and multiple methods, we determined that macrophages and monocytes are the major cell types infected by ASFV in the spleen, showing high viral-load heterogeneity. A rare subpopulation of immature monocytes represents the major population infected at late infection stage. ASFV causes massive death of macrophages, but shifts its infection into these monocytes which significantly arise after the infection. The apoptosis, interferon response, and antigen-presentation capacity are inhibited in these monocytes which benefits prolonged infection of ASFV in vivo. Until now, the role of immature monocytes as an important target by ASFV has been overlooked due to that they do not express classical monocyte marker CD14. The present study indicates that the shift of viral infection from macrophages to the immature monocytes is critical for maintaining prolonged ASFV infection in vivo. This study sheds light on ASFV tropism, replica-tion, and infection dynamics, and elicited immune response, which may instruct future research on antiviral strategies. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Cloud microphysical response to entrainment and mixing is locally inhomogeneous and globally homogeneous: Evidence from the lab.
- Author
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Jae Min Yeom, Helman, Ian, Prabhakaran, Prasanth, Anderson, Jesse C., Fan Yang, Shaw, Raymond A., and Cantrell, Will
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CLOUD droplets ,ATMOSPHERIC temperature ,CEMENT mixing ,OPTICAL properties ,MICROPHYSICS ,AEROSOLS ,GAS industry - Abstract
Entrainment of dry air into clouds strongly influences cloud optical and precipitation properties and the response of clouds to aerosol perturbations. The response of cloud droplet size distributions to entrainment-mixing is examined in the Pi convection-cloud chamber that creates a turbulent, steady-state cloud. The experiments are conducted by injecting dry air with temperature (T
e ) and flow rate (Qe ) through a flange in the top boundary, into the otherwise well-mixed cloud, to mimic the entrainment-mixing process. Due to the large-scale circulation, the downwind region is directly affected by entrained dry air, whereas the upwind region is representative of the background conditions. Droplet concentration (Cn ) and liquid water content (L) decrease in the downwind region, but the difference in the mean diameter of droplets (Dm ) is small. The shape of cloud droplet size distributions relative to the injection point is unchanged, to within statistical uncertainty, resulting in a signature of inhomogeneous mixing, as expected for droplet evaporation times small compared to mixing time scales. As Te and Qe of entrained air increase, however, Cn, L, and Dm of the whole cloud system decrease, resulting in a signature of homogeneous mixing. The apparent contradiction is understood as the cloud microphysical responses to entrainment and mixing differing on local and global scales: locally inhomogeneous and globally homogeneous. This implies that global versus local sampling of clouds can lead to seemingly contradictory results for mixing, which informs the long-standing debate about the microphysical response to entrainment and the parameterization of this process for coarse-resolution models. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
4. Structural basis and molecular mechanism of biased GPBAR signaling in regulating NSCLC cell growth via YAP activity
- Author
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Lijuan Ma, Fan Yang, Xiang Wu, Chunyou Mao, Lulu Guo, Tianshu Miao, Shao-Kun Zang, Xiaoyu Jiang, Dan-Dan Shen, Tianhui Wei, Hengxing Zhou, Qin Wei, Shiyang Li, Qiang Shu, Shiqing Feng, Changtao Jiang, Bo Chu, Lutao Du, Jin-Peng Sun, Xiao Yu, Yan Zhang, and Pengju Zhang
- Subjects
Bile Acids and Salts ,Multidisciplinary ,Lung Neoplasms ,beta-Arrestin 1 ,Carcinoma, Non-Small-Cell Lung ,Cryoelectron Microscopy ,Humans ,Cell Cycle Proteins ,Cholic Acids ,Receptors, G-Protein-Coupled ,Transcription Factors - Abstract
The G protein–coupled bile acid receptor (GPBAR) is the membrane receptor for bile acids and a driving force of the liver–bile acid–microbiota–organ axis to regulate metabolism and other pathophysiological processes. Although GPBAR is an important therapeutic target for a spectrum of metabolic and neurodegenerative diseases, its activation has also been found to be linked to carcinogenesis, leading to potential side effects. Here, via functional screening, we found that two specific GPBAR agonists, R399 and INT-777, demonstrated strikingly different regulatory effects on the growth and apoptosis of non–small cell lung cancer (NSCLC) cells both in vitro and in vivo. Further mechanistic investigation showed that R399-induced GPBAR activation displayed an obvious bias for β-arrestin 1 signaling, thus promoting YAP signaling activation to stimulate cell proliferation. Conversely, INT-777 preferentially activated GPBAR-Gs signaling, thus inactivating YAP to inhibit cell proliferation and induce apoptosis. Phosphorylation of GPBAR by GRK2 at S310/S321/S323/S324 sites contributed to R399-induced GPBAR–β-arrestin 1 association. The cryoelectron microscopy (cryo-EM) structure of the R399-bound GPBAR-Gs complex enabled us to identify key interaction residues and pivotal conformational changes in GPBAR responsible for the arrestin signaling bias and cancer cell proliferation. In summary, we demonstrate that different agonists can regulate distinct functions of cell growth and apoptosis through biased GPBAR signaling and control of YAP activity in a NSCLC cell model. The delineated mechanism and structural basis may facilitate the rational design of GPBAR-targeting drugs with both metabolic and anticancer benefits.
- Published
- 2023
5. Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors
- Author
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Jiayue Su, Desheng Liu, Fan Yang, Mei-Qing Zuo, Chang Li, Meng-Qiu Dong, Shan Sun, and Sen-Fang Sui
- Subjects
Multidisciplinary ,Protein Domains ,Cryoelectron Microscopy ,Mitochondrial Precursor Protein Import Complex Proteins ,Humans ,Receptors, Cytoplasmic and Nuclear - Abstract
Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence and further guide the protein translocation. Their deficiency has been linked with neurodegenerative diseases and cardiac pathology. Although several structures of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and captured the structure of the TOM complex containing Tom22 and Tom20 cytosolic domains at 3.74 Å. Structural analysis indicates that Tom20 and Tom22 share a similar three-helix bundle structural feature in the cytosolic domain. Further structure-guided biochemical analysis reveals that the Tom22 cytosolic domain is responsible for binding to the presequence, and the helix H1 is critical for this binding. Altogether, our results provide insights into the functional mechanism of the TOM complex recognizing and transferring preproteins across the mitochondrial membrane.
- Published
- 2022
6. A thermal receptor for nonvisual sunlight detection in myriapods.
- Author
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Zhihao Yao, Licheng Yuan, Xiaoying Chen, Qian Wang, Longhui Chai, Xiancui Lu, Fan Yang, Yunfei Wang, and Shilong Yang
- Subjects
MYRIAPODA ,SUNSHINE ,PHOTOTHERMAL effect ,PHOTOTHERMAL conversion ,SODIUM channels - Abstract
Organisms from cyanobacteria to humans have evolved a wide array of photoreceptive strategies to detect light. Sunlight avoidance behavior is common in animals without vision or known photosensory genes. While indirect light perception via photothermal conversion is a possible scenario, there is no experimental evidence for this hypothesis. Here, we show a nonvisual and extraocular sunlight detection mechanism by identifying the broad-range thermal receptor 1 (BRTNaC1, temperature range = 33 to 48 °C) in centipede antennae. BRTNaC1, a heat-activated cation-permeable ion channel, is structurally related to members of the epithelial sodium channel family. At the molecular level, heat activation of BRTNaC1 exhibits strong pH dependence controlled by two protonatable sites. Physiologically, temperature-dependent activation of BRTNaC1 upon sunlight exposure comes from a striking photothermal effect on the antennae, where a slightly acidic environment (pH 6.1) of the body fluid leads to the protonation of BRTNaC1 and switches on its high thermal sensitivity. Furthermore, testosterone potently inhibits heat activation of BRTNaC1 and the sunlight avoidance behavior of centipedes. Taken together, our study suggests a sophisticated strategy for nonvisual sunlight detection in myriapods. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
7. A paradigm of thermal adaptation in penguins and elephants by tuning cold activation in TRPM8
- Author
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Xiancui Lu, Shilong Yang, Yunfei Wang, Ren Lai, Lizhen Xu, Xiaoying Chen, and Fan Yang
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TRPM8 ,side-chain hydrophobicity ,Physiology ,Elephants ,Sequence Homology ,TRPM Cation Channels ,cold activation ,Transient receptor potential channel ,Mice ,thermal adaptation ,Animals ,Humans ,Thermosensing ,Amino Acid Sequence ,Ion channel ,Multidisciplinary ,Chemistry ,Membrane Proteins ,Biological Sciences ,Solvent accessibility ,Adaptation, Physiological ,Spheniscidae ,pore domain ,Cold Temperature ,Menthol ,Biophysics ,Adaptation ,Ion Channel Gating - Abstract
Significance Sensing temperature is critical for the survival of all living beings. Here, we show that during cold-induced activation of the archetypical temperature-sensitive TRPM8 ion channel, there are hydrophobic residues in the pore domain stabilized in the exposed state. Tuning hydrophobicity of these residues specifically alters cold response in TRPM8. Furthermore, TRPM8 orthologs in vertebrates evolved to employ such a mechanism, which physiologically tunes cold tolerance for better thermal adaptation. Our findings not only advance the understanding of the cold-induced activation mechanism of TRPM8 but also bring insights to the molecular evolution strategy for ambient-temperature adaptation in vertebrates., To adapt to habitat temperature, vertebrates have developed sophisticated physiological and ecological mechanisms through evolution. Transient receptor potential melastatin 8 (TRPM8) serves as the primary sensor for cold. However, how cold activates TRPM8 and how this sensor is tuned for thermal adaptation remain largely unknown. Here we established a molecular framework of how cold is sensed in TRPM8 with a combination of patch-clamp recording, unnatural amino acid imaging, and structural modeling. We first observed that the maximum cold activation of TRPM8 in eight different vertebrates (i.e., African elephant and emperor penguin) with distinct side-chain hydrophobicity (SCH) in the pore domain (PD) is tuned to match their habitat temperature. We further showed that altering SCH for residues in the PD with solvent-accessibility changes leads to specific tuning of the cold response in TRPM8. We also observed that knockin mice expressing the penguin’s TRPM8 exhibited remarkable tolerance to cold. Together, our findings suggest a paradigm of thermal adaptation in vertebrates, where the evolutionary tuning of the cold activation in the TRPM8 ion channel through altering SCH and solvent accessibility in its PD largely contributes to the setting of the cold-sensitive/tolerant phenotype.
- Published
- 2020
8. Tuning protein half-life in mouse using sequence-defined biopolymers functionalized with lipids
- Author
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Koen Vanderschuren, Pol Arranz-Gibert, Minsoo Khang, Dagan Hadar, Alice Gaudin, Fan Yang, Ewa Folta-Stogniew, W. Mark Saltzman, Miriam Amiram, and Farren J. Isaacs
- Subjects
Multidisciplinary ,Proteins ,serum protein half-life extension ,protein engineering ,Biological Sciences ,Lipids ,Mice ,Biopolymers ,Engineering ,genome recoding ,Physical Sciences ,Animals ,Synthetic Biology ,Applied Biological Sciences ,Amino Acids ,Peptides ,Half-Life ,noncanonical amino acids - Abstract
Significance Functionalization of proteins and biopolymers with chemical modifications can be utilized to alter their chemical and biophysical properties. In contrast to traditional chemical functionalization strategies, the use of nonstandard amino acids enables precise positioning of functional groups. Here, we report that multisite conjugation of fatty acids, at precise sites harboring genetically encoded nonstandard amino acids with bioorthogonal chemical handles, can be employed to tune the half-life of proteins in a mouse model. This programmable approach could offer a technical foundation for the modification of protein and peptide therapeutics to improve their efficacy or pharmacokinetic profile (e.g., to prevent rapid clearance and reduce frequency of administration)., The use of biologics in the treatment of numerous diseases has increased steadily over the past decade due to their high specificities, low toxicity, and limited side effects. Despite this success, peptide- and protein-based drugs are limited by short half-lives and immunogenicity. To address these challenges, we use a genomically recoded organism to produce genetically encoded elastin-like polypeptide–protein fusions containing multiple instances of para-azidophenylalanine (pAzF). Precise lipidation of these pAzF residues generated a set of sequence-defined synthetic biopolymers with programmable binding affinity to albumin without ablating the activity of model fusion proteins, and with tunable blood serum half-lives spanning 5 to 94% of albumin’s half-life in a mouse model. Our findings present a proof of concept for the use of genetically encoded bioorthogonal conjugation sites for multisite lipidation to tune protein stability in mouse serum. This work establishes a programmable approach to extend and tune the half-life of protein or peptide therapeutics and a technical foundation to produce functionalized biopolymers endowed with programmable chemical and biophysical properties with broad applications in medicine, materials science, and biotechnology.
- Published
- 2021
9. Mec1 regulates PAS recruitment of Atg13 via direct binding with Atg13 during glucose starvation-induced autophagy.
- Author
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Weijing Yao, Yixing Li, Yingcong Chen, Yuting Chen, Pengwei Zhao, Yi Zhang, Qiang Jiang, Yuyao Feng, Fan Yang, Choufei Wu, Huiming Zhong, Yiting Zhou, Qiming Sun, Liqin Zhang, Wei Liu, and Cong Yi
- Subjects
DNA repair ,AUTOPHAGY ,GLUCOSE ,ADAPTOR proteins - Abstract
Mec1 is a DNA damage sensor, which performs an essential role in the DNA damage response pathway and glucose starvation-induced autophagy. However, the functions of Mec1 in autophagy remain unclear. In response to glucose starvation, Mec1 forms puncta, which are recruited to mitochondria through the adaptor protein Ggc1. Here, we show that Mec1 puncta also contact the phagophore assembly site (PAS) via direct binding with Atg13. Functional analysis of the Atg13-Mec1 interaction revealed two previously unrecognized protein regions, the Mec1-Binding Region (MBR) on Atg13 and the Atg13-Binding Region (ABR) on Mec1, which mediate their mutual association under glucose starvation conditions. Disruption of the MBR or ABR impairs the recruitment of Mec1 puncta and Atg13 to the PAS, consequently blocking glucose starvation-induced autophagy. Additionally, the MBR and ABR regions are also crucial for DNA damage-induced autophagy. We thus propose that Mec1 regulates glucose starvation-induced autophagy by controlling Atg13 recruitment to the PAS. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
10. Super-enhancers conserved within placental mammals maintain stem cell pluripotency.
- Author
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Juqing Zhang, Yaqi Zhou, Wei Yue, Zhenshuo Zhu, Xiaolong Wu, Shuai Yu, Qiaoyan Shen, Qin Pan, Wenjing Xu, Rui Zhang, Xiaojie Wu, Xinmei Li, Yayu Li, Yunxiang Li, Yu Wang, Sha Peng, Shiqiang Zhang, Anmin Lei, Xinbao Ding, and Fan Yang
- Subjects
STEM cells ,PLURIPOTENT stem cells ,MAMMALS ,MAMMAL conservation ,TRANSCRIPTION factors ,SUPER enhancers - Abstract
Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
11. Structural basis and molecular mechanism of biased GPBAR signaling in regulating NSCLC cell growth via YAP activity.
- Author
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Lijuan Ma, Fan Yang, Xiang Wu, Chunyou Mao, Lulu Guo, Tianshu Miao, Shao-Kun Zang, Xiaoyu Jiang, Dan-Dan Shen, Tianhui Wei, Hengxing Zhou, Qin Wei, Shiyang Li, Qiang Shu, Shiqing Feng, Changtao Jiang, Bo Chu, Lutao Du, Jin-Peng Sun, and Xiao Yu
- Subjects
- *
YAP signaling proteins , *FARNESOID X receptor , *CELL growth , *NON-small-cell lung carcinoma , *CANCER cell proliferation , *CURCUMIN - Abstract
The G protein-coupled bile acid receptor (GPBAR) is the membrane receptor for bile acids and a driving force of the liver-bile acid-microbiota-organ axis to regulate metabolism and other pathophysiological processes. Although GPBAR is an important therapeutic target for a spectrum of metabolic and neurodegenerative diseases, its activation has also been found to be linked to carcinogenesis, leading to potential side effects. Here, via functional screening, we found that two specific GPBAR agonists, R399 and INT-777, demonstrated strikingly different regulatory effects on the growth and apoptosis of non-small cell lung cancer (NSCLC) cells both in vitro and in vivo. Further mechanistic investigation showed that R399-induced GPBAR activation displayed an obvious bias for ß-arrestin 1 signaling, thus promoting YAP signaling activation to stimulate cell proliferation. Conversely, INT-777 preferentially activated GPBAR-Gs signaling, thus inactivating YAP to inhibit cell proliferation and induce apoptosis. Phosphorylation of GPBAR by GRK2 at S310/S321/S323/S324 sites contributed to R399-induced GPBAR-ß-arrestin 1 association. The cryoelectron microscopy (cryo-EM) structure of the R399-bound GPBAR-Gs complex enabled us to identify key interaction residues and pivotal conformational changes in GPBAR responsible for the arrestin signaling bias and cancer cell proliferation. In summary, we demonstrate that different agonists can regulate distinct functions of cell growth and apoptosis through biased GPBAR signaling and control of YAP activity in a NSCLC cell model. The delineated mechanism and structural basis may facilitate the rational design of GPBAR-targeting drugs with both metabolic and anticancer benefits. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
12. Continuous topological transition from metal to dielectric
- Author
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Shaojie Ma, Shuang Zhang, Kun Ding, Fan Yang, and John B. Pendry
- Subjects
Permittivity ,Materials science ,topology ,Physics::Optics ,02 engineering and technology ,Dielectric ,Topology ,01 natural sciences ,Electromagnetic radiation ,plasmonics ,Condensed Matter::Materials Science ,0103 physical sciences ,Topological order ,010306 general physics ,Plasmon ,Multidisciplinary ,Metamaterial ,021001 nanoscience & nanotechnology ,Surface plasmon polariton ,Applied Physical Sciences ,metamaterials ,Zak phase ,Physical Sciences ,State of matter ,Condensed Matter::Strongly Correlated Electrons ,0210 nano-technology - Abstract
Significance We extend the concept of metals and dielectrics to the “generalized metal/dielectric” by treating a pure metal or dielectric as the limiting case of a metal–dielectric layered metamaterial. Specifically, the metamaterial with metal filling ratio larger than one-half shares the same topological invariant as a pure metal and thus exhibits some metallic behaviors. In contrast, the dielectric-rich metamaterial and a pure dielectric are topologically equivalent and display dielectric properties. The topological edge state exists between the generalized metal and dielectric, giving the surface plasmon polariton (SPP) an additional physical meaning: the limiting case of a topological edge state., Metal and dielectric have long been thought as two different states of matter possessing highly contrasting electric and optical properties. A metal is a material highly reflective to electromagnetic waves for frequencies up to the optical region. In contrast, a dielectric is transparent to electromagnetic waves. These two different classical electrodynamic properties are distinguished by different signs of the real part of permittivity: The metal has a negative sign while the dielectric has a positive one. Here, we propose a different topological understanding of metal and dielectric. By considering metal and dielectric as just two limiting cases of a periodic metal–dielectric layered metamaterial, from which a metal can continuously transform into a dielectric by varying the metal filling ratio from 1 to 0, we further demonstrate the abrupt change of a topological invariant at a certain point during this transition, classifying the metamaterials into metallic state and dielectric state. The topological phase transition from the metallic state to the dielectric state occurs when the filling ratio is one-half. These two states generalize our previous understanding of metal and dielectric: The metamaterial with metal filling ratio larger/smaller than one-half is named as the “generalized metal/dielectric.” Interestingly, the surface plasmon polariton (SPP) at a metal/dielectric interface can be understood as the limiting case of a topological edge state.
- Published
- 2020
13. Progesterone activates GPR126 to promote breast cancer development via the Gi pathway.
- Author
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Wentao An, Hui Lin, Lijuan Ma, Chao Zhang, Yuan Zheng, Qiuxia Cheng, Chuanshun Ma, Xiang Wu, Zihao Zhang, Yani Zhong, Menghui Wang, Dongfang He, Zhao Yang, Lutao Du, Shiqing Feng, Chuanxin Wang, Fan Yang, Peng Xiao, Pengju Zhang, and Xiao Yu
- Subjects
PROGESTERONE ,TRIPLE-negative breast cancer ,BREAST cancer ,CARCINOGENESIS ,G protein coupled receptors - Abstract
GPR126 is a member of the adhesion G protein-coupled receptors (aGPCRs) that is essential for the normal development of diverse tissues, and its mutations are implicated in various pathological processes. Here, through screening 34 steroid hormones and their derivatives for cAMP production, we found that progesterone (P4) and 17-hydroxyprogesterone (17OHP) could specifically activate GPR126 and trigger its downstream Gi signaling by binding to the ligand pocket in the seven-transmembrane domain of the C-terminal fragment of GPR126. A detailed mutagenesis screening according to a computational simulated structure model indicated that K1001
ECL2 and F1012ECL2 are key residues that specifically recognize 17OHP but not progesterone. Finally, functional analysis revealed that progesterone-triggered GPR126 activation promoted cell growth in vitro and tumorigenesis in vivo, which involved Gi-SRC pathways in a triple-negative breast cancer model. Collectively, our work identified a membrane receptor for progesterone/17OHP and delineated the mechanisms by which GPR126 participated in potential tumor progression in triple-negative breast cancer, which will enrich our understanding of the functions and working mechanisms of both the aGPCR member GPR126 and the steroid hormone progesterone. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
14. Tuning protein half-life in mouse using sequence-defined biopolymers functionalized with lipids.
- Author
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Vanderschuren, Koen, Arranz-Gibert, Pol, Minsoo Khang, Hadar, Dagan, Gaudin, Alice, Fan Yang, Folta-Stogniew, Ewa, Saltzman, W. Mark, Amiram, Miriam, and Isaacs, Farren J.
- Subjects
BIOPOLYMERS ,CHIMERIC proteins ,MATERIALS science ,PEPTIDES ,LIPIDS ,FIREPROOFING agents ,COMMERCIAL products - Abstract
The use of biologics in the treatment of numerous diseases has increased steadily over the past decade due to their high specificities, low toxicity, and limited side effects. Despite this success, peptide- and protein-based drugs are limited by short half-lives and immunogenicity. To address these challenges, we use a genomically recoded organism to produce genetically encoded elastin-like polypeptide-protein fusions containing multiple instances of para-azidophenylalanine (pAzF). Precise lipidation of these pAzF residues generated a set of sequence-defined synthetic biopolymers with programmable binding affinity to albumin without ablating the activity of model fusion proteins, and with tunable blood serum half-lives spanning 5 to 94% of albumin's half-life in a mouse model. Our findings present a proof of concept for the use of genetically encoded bioorthogonal conjugation sites for multisite lipidation to tune protein stability in mouse serum. This work establishes a programmable approach to extend and tune the half-life of protein or peptide therapeutics and a technical foundation to produce functionalized biopolymers endowed with programmable chemical and biophysical properties with broad applications in medicine, materials science, and biotechnology. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
15. Structural and functional studies of TBC1D23 C-terminal domain provide a link between endosomal trafficking and PCH
- Author
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Dingdong Liu, Huan Zhou, Yifei Zhou, Wentong Meng, Xiaoyu Yang, Daniel D. Billadeau, Xin Yong, Fan Yang, Li Li, Xianming Mo, Xiaofei Shen, Yihong Zhang, Lijia Xue, Wenjie Huang, Wenming Zhang, Yuquan Wei, Da Jia, Xiaohu Zhang, Cong Ma, Qingxiang Sun, and Zhe Liu
- Subjects
Endosome ,Mutant ,Pontocerebellar hypoplasia ,Endosomes ,medicine.disease_cause ,Protein Domains ,Cerebellar Diseases ,medicine ,Animals ,Humans ,Zebrafish ,Mutation ,Multidisciplinary ,biology ,Chemistry ,C-terminus ,GTPase-Activating Proteins ,Phosphate-Binding Proteins ,medicine.disease ,biology.organism_classification ,Cell biology ,Transport protein ,Pleckstrin homology domain ,Protein Transport ,PNAS Plus ,HeLa Cells ,Protein Binding ,trans-Golgi Network - Abstract
Pontocerebellar hypoplasia (PCH) is a group of neurological disorders that affect the development of the brain, in particular, the pons and cerebellum. Homozygous mutations of TBC1D23 have been found recently to lead to PCH; however, the underlying molecular mechanisms remain unclear. Here, we show that the crystal structure of the TBC1D23 C-terminal domain adopts a Pleckstrin homology domain fold and selectively binds to phosphoinositides, in particular, PtdIns(4)P, through one surface while binding FAM21 via the opposite surface. Mutation of key residues of TBC1D23 or FAM21 selectively disrupts the endosomal vesicular trafficking toward the Trans-Golgi Network. Finally, using the zebrafish model, we show that PCH patient-derived mutants, impacting either phosphoinositide binding or FAM21 binding, lead to abnormal neuronal growth and brain development. Taken together, our data provide a molecular basis for the interaction between TBC1D23 and FAM21, and suggest a plausible role for PtdIns(4)P in the TBC1D23-mediating endosome-to-TGN trafficking pathway. Defects in this trafficking pathway are, at least partially, responsible for the pathogenesis of certain types of PCH.
- Published
- 2019
16. Dietary ω-3 polyunsaturated fatty acids are protective for myopia.
- Author
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Miaozhen Pan, Fei Zhao, Bintao Xie, Hao Wu, Sen Zhang, Cong Ye, Zhenqi Guan, Lin Kang, Yuqing Zhang, Xuan Zhou, Yi Lei, Qi Wang, Li Wang, Fan Yang, Chenchen Zhao, Jia Qu, and Xiangtian Zhou
- Subjects
UNSATURATED fatty acids ,MYOPIA ,OMEGA-3 fatty acids ,EICOSAPENTAENOIC acid ,GUINEA pigs - Abstract
Myopia is a leading cause of visual impairment and blindness worldwide. However, a safe and accessible approach for myopia control and prevention is currently unavailable. Here, we investigated the therapeutic effect of dietary supplements of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) on myopia progression in animal models and on decreases in choroidal blood perfusion (ChBP) caused by near work, a risk factor for myopia in young adults. We demonstrated that daily gavage of ω-3 PUFAs (300 mg docosahexaenoic acid [DHA] plus 60 mg eicosapentaenoic acid [EPA]) significantly attenuated the development of form deprivation myopia in guinea pigs and mice, as well as of lens-induced myopia in guinea pigs. Peribulbar injections of DHA also inhibited myopia progression in form-deprived guinea pigs. The suppression of myopia in guinea pigs was accompanied by inhibition of the "ChBP reduction-scleral hypoxia cascade." Additionally, treatment with DHA or EPA antagonized hypoxia-induced myofibroblast transdifferentiation in cultured human scleral fibroblasts. In human subjects, oral administration of ω-3 PUFAs partially alleviated the near-work-induced decreases in ChBP. Therefore, evidence from these animal and human studies suggests ω-3 PUFAs are potential and readily available candidates for myopia control. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
17. Structural changes in bacteriophage T7 upon receptor-induced genome ejection.
- Author
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Wenyuan Chen, Hao Xiao, Li Wang, Xurong Wang, Zhixue Tan, Zhen Han, Xiaowu Li, Fan Yang, Zhonghua Liu, Jingdong Song, Hongrong Liu, and Lingpeng Cheng
- Subjects
CELL receptors ,BACTERIOPHAGES ,LIPOPOLYSACCHARIDES ,GENOMES ,PERIPLASM ,COMMERCIAL products - Abstract
Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near-atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
18. Scaffolding mechanism of arrestin-2 in the cRaf/MEK1/ERK signaling cascade.
- Author
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Changxiu Qu, Ji Young Park, Min Woo Yun, Qing-tao He, Fan Yang, Kiae Kim, Donghee Ham, Rui-rui Li, Iverson, T. M., Gurevich, Vsevolod V., Jin-Peng Sun, and Ka Young Chung
- Subjects
G protein coupled receptors ,ARRESTINS ,FLUORESCENCE quenching ,MITOGEN-activated protein kinases - Abstract
Arrestins were initially identified for their role in homologous desensitization and internalization of G protein-coupled receptors. Receptor-bound arrestins also initiate signaling by interacting with other signaling proteins. Arrestins scaffold MAPK signaling cascades, MAPK kinase kinase (MAP3K), MAPK kinase (MAP2K), and MAPK. In particular, arrestins facilitate ERK1/2 activation by scaffolding ERK1/2 (MAPK), MEK1 (MAP2K), and Raf (MAPK3). However, the structural mechanism underlying this scaffolding remains unknown. Here, we investigated the mechanism of arrestin-2 scaffolding of cRaf, MEK1, and ERK2 using hydrogen/deuterium exchange-mass spectrometry, tryptophan-induced bimane fluorescence quenching, and NMR. We found that basal and active arrestin-2 interacted with cRaf, while only active arrestin-2 interacted with MEK1 and ERK2. The ATP binding status of MEK1 or ERK2 affected arrestin-2 binding; ATP-bound MEK1 interacted with arrestin-2, whereas only empty ERK2 bound arrestin-2. Analysis of the binding interfaces suggested that the relative positions of cRaf, MEK1, and ERK2 on arrestin-2 likely facilitate sequential phosphorylation in the signal transduction cascade. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
19. New insights into ice multiplication using remote-sensing observations of slightly supercooled mixed-phase clouds in the Arctic.
- Author
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Lukea, Edward P., Fan Yang, Kollias, Pavlos, Vogelmann, Andrew M., and Maahn, Maximilian
- Subjects
- *
SUPERCOOLING , *RADIO networks , *MULTIPLICATION , *ICE crystals , *ATMOSPHERIC radiation measurement , *DROP size distribution , *AIRCRAFT cabins - Abstract
However, recent in situ measurements show that substantial numbers of needles and columns (signs of splintering) are observed in mixed-phase clouds without the presence of rimers (i.e., fast Significance During secondary ice events, ice particle number concentrations in mixed-phase clouds can increase by orders of magnitude with profound implications for the cloud evolution. EARTH, ATMOSPHERIC, AND PLANETARY SCIENCES New insights into ice multiplication using remote-sensing observations of slightly supercooled mixed-phase clouds in the Arctic Edward P. Luke a,1, Fan Yang a,1, Pavlos Kollias a,b, Andrew M. Vogelmann a, and Maximilian Maahn c,d,2 a Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973; b School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794; c Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80305; and d Physical Sciences Laboratory, National Oceanic and Atmospheric Administration, Boulder, CO 80305 Edited by John H. Seinfeld, California Institute of Technology, Pasadena, CA, and approved February 1, 2021 (received for review October 17, 2020) Secondary ice production (SIP) can significantly enhance ice particle number concentrations in mixed-phase clouds, resulting in a substantial impact on ice mass flux and evolution of cold cloud systems. Results show that the occurrence of secondary ice events is higher when only drizzle exists compared to when only rimer exists, and the event occurrence is highest when both rimer and drizzle exist. [Extracted from the article]
- Published
- 2021
- Full Text
- View/download PDF
20. Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner
- Author
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Audrey P. Gasch, Gabriele Varani, Aseem Z. Ansari, Corinna Hintermair, Laurence Florens, Ying Zhang, Yi-Hsuan Ho, Dirk Eick, Corey M. Nemec, Sandra C. Tseng, Michael P. Washburn, Fan Yang, Joshua M. Gilmore, and Martin Heidemann
- Subjects
0301 basic medicine ,Threonine ,RNA, Untranslated ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,Termination factor ,Protein subunit ,RNA polymerase II ,Saccharomyces cerevisiae ,03 medical and health sciences ,Protein Domains ,Transcription (biology) ,Serine ,Protein Isoforms ,RNA, Small Nucleolar ,Amino Acid Sequence ,Small nucleolar RNA ,Phosphorylation ,Gene ,Genetics ,Multidisciplinary ,biology ,Non-coding RNA ,Cell biology ,030104 developmental biology ,PNAS Plus ,biology.protein ,RNA, Small Untranslated ,CTD ,RNA Polymerase II ,Ctd Code ,Ctd Interactome ,Nmr ,Noncoding Rna ,Phosphothreonine ,Peptide Termination Factors ,Transcription Factors - Abstract
The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar RNA (snoRNA) genes. Quantitative proteomics reveals an interactome of known readers as well as protein complexes that were not known to rely on Thr4 for association with Pol II. The data indicate a key role for Thr4 in engaging the machinery used for transcription elongation and termination. We focus on Rtt103, a protein that binds phospho-Ser2 and phospho-Thr4 marks and facilitates transcription termination at protein-coding genes. To elucidate how Rtt103 engages two distinct CTD modifications that are differentially enriched at noncoding genes, we relied on NMR analysis of Rtt103 in complex with phospho-Thr4- or phospho-Ser2-bearing CTD peptides. The structural data reveal that Rtt103 interacts with phospho-Thr4 in a manner analogous to its interaction with phospho-Ser2-modified CTD. The same set of hydrogen bonds involving either the oxygen on phospho-Thr4 and the hydroxyl on Ser2, or the phosphate on Ser2 and the Thr4 hydroxyl, can be formed by rotation of an arginine side chain, leaving the intermolecular interface otherwise unperturbed. This economy of design enables Rtt103 to engage Pol II at distinct sets of genes with differentially enriched CTD marks.
- Published
- 2017
21. Aerosol indirect effect from turbulence-induced broadening of cloud-droplet size distributions
- Author
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Kelken Chang, Raymond A. Shaw, Dennis Niedermeier, Will Cantrell, Kamal Kant Chandrakar, David Ciochetto, Mikhail Ovchinnikov, and Fan Yang
- Subjects
Supersaturation ,Multidisciplinary ,010504 meteorology & atmospheric sciences ,Microphysics ,Turbulence ,Chemistry ,Radius ,respiratory system ,Albedo ,Atmospheric sciences ,01 natural sciences ,complex mixtures ,Standard deviation ,Computational physics ,Aerosol ,0103 physical sciences ,Physical Sciences ,sense organs ,010306 general physics ,Dispersion (chemistry) ,Astrophysics::Galaxy Astrophysics ,Physics::Atmospheric and Oceanic Physics ,0105 earth and related environmental sciences - Abstract
The influence of aerosol concentration on the cloud-droplet size distribution is investigated in a laboratory chamber that enables turbulent cloud formation through moist convection. The experiments allow steady-state microphysics to be achieved, with aerosol input balanced by cloud-droplet growth and fallout. As aerosol concentration is increased, the cloud-droplet mean diameter decreases, as expected, but the width of the size distribution also decreases sharply. The aerosol input allows for cloud generation in the limiting regimes of fast microphysics ([Formula: see text]) for high aerosol concentration, and slow microphysics ([Formula: see text]) for low aerosol concentration; here, [Formula: see text] is the phase-relaxation time and [Formula: see text] is the turbulence-correlation time. The increase in the width of the droplet size distribution for the low aerosol limit is consistent with larger variability of supersaturation due to the slow microphysical response. A stochastic differential equation for supersaturation predicts that the standard deviation of the squared droplet radius should increase linearly with a system time scale defined as [Formula: see text], and the measurements are in excellent agreement with this finding. The result underscores the importance of droplet size dispersion for aerosol indirect effects: increasing aerosol concentration changes the albedo and suppresses precipitation formation not only through reduction of the mean droplet diameter but also by narrowing of the droplet size distribution due to reduced supersaturation fluctuations. Supersaturation fluctuations in the low aerosol/slow microphysics limit are likely of leading importance for precipitation formation.
- Published
- 2016
22. Speech can produce jet-like transport relevant to asymptomatic spreading of virus.
- Author
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Abkarian, Manouk, Mendez, Simon, Nan Xue, Fan Yang, and Stone, Howard A.
- Subjects
COVID-19 ,AIR flow ,INFECTIOUS disease transmission ,TECHNICAL reports - Abstract
Many scientific reports document that asymptomatic and presymptomatic individuals contribute to the spread of COVID-19, probably during conversations in social interactions. Droplet emission occurs during speech, yet few studies document the flow to provide the transport mechanism. This lack of understanding prevents informed public health guidance for risk reduction and mitigation strategies, e.g., the "6-foot rule." Here we analyze flows during breathing and speaking, including phonetic features, using orders-of-magnitude estimates, numerical simulations, and laboratory experiments. We document the spatiotemporal structure of the expelled airflow. Phonetic characteristics of plosive sounds like "P" lead to enhanced directed transport, including jet-like flows that entrain the surrounding air. We highlight three distinct temporal scaling laws for the transport distance of exhaled material including 1) transport over a short distance (<0.5 m) in a fraction of a second, with large angular variations due to the complexity of speech; 2) a longer distance, ~1 m, where directed transport is driven by individual vortical puffs corresponding to plosive sounds; and 3) a distance out to about 2 m, or even farther, where sequential plosives in a sentence, corresponding effectively to a train of puffs, create conical, jet-like flows. The latter dictates the long-time transport in a conversation. We believe that this work will inform thinking about the role of ventilation, aerosol transport in disease transmission for humans and other animals, and yield a better understanding of linguistic aerodynamics, i.e., aerophonetics. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
23. Hemolymph protease-5 links the melanization and Toll immune pathways in the tobacco hornworm, Manduca sexta.
- Author
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Yang Wang, Fan Yang, Xiaolong Cao, Zhen Zou, Zhiqiang Lu, Michael R. Kanost, and Haobo Jiang
- Subjects
- *
MANDUCA , *HEMOLYMPH , *SERINE proteinases , *PEPTIDE antibiotics , *IMMUNE response - Abstract
Proteolytic activation of phenoloxidase (PO) and the cytokine Spätzle during immune responses of insects is mediated by a network of hemolymph serine proteases (HPs) and noncatalytic serine protease homologs (SPHs) and inhibited by serpins. However, integration and conservation of the system and its control mechanisms are not fully understood. Here we present biochemical evidence that PO-catalyzed melanin formation, Spätzle-triggered Toll activation, and induced synthesis of antimicrobial peptides are stimulated via hemolymph (serine) protease 5 (HP5) in Manduca sexta. Previous studies have demonstrated a protease cascade pathway in which HP14 activates proHP21; HP21 activates proPAP2 and proPAP3, which then activate proPO in the presence of a complex of SPH1 and SPH2. We found that both HP21 and PAP3 activate proHP5 by cleavage at ESDR176*IIGG. HP5 then cleaves proHP6 at a unique site of LDLH112*ILGG. HP6, an ortholog of Drosophila Persephone, activates both proHP8 and proPAP1. HP8 activates proSpätzle-1, whereas PAP1 cleaves and activates proPO. HP5 is inhibited by Manduca sexta serpin-4, serpin-1A, and serpin-1J to regulate its activity. In summary, we have elucidated the physiological roles of HP5, a CLIPB with unique cleavage specificity (cutting after His) that coordinates immune responses in the caterpillar. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
24. Continuous topological transition from metal to dielectric.
- Author
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Fan Yang, Shaojie Ma, Kun Ding, Shuang Zhang, and Pendry, J. B.
- Subjects
- *
TRANSITION metals , *DIELECTRICS , *ELECTROMAGNETIC waves , *ELECTRIC properties , *REFLECTIVE materials - Abstract
Metal and dielectric have long been thought as two different states of matter possessing highly contrasting electric and optical properties. A metal is a material highly reflective to electromagnetic waves for frequencies up to the optical region. In contrast, a dielectric is transparent to electromagnetic waves. These two different classical electrodynamic properties are distinguished by different signs of the real part of permittivity: The metal has a negative sign while the dielectric has a positive one. Here, we propose a different topological understanding of metal and dielectric. By considering metal and dielectric as just two limiting cases of a periodic metal-dielectric layered metamaterial, from which a metal can continuously transform into a dielectric by varying the metal filling ratio from 1 to 0, we further demonstrate the abrupt change of a topological invariant at a certain point during this transition, classifying the metamaterials into metallic state and dielectric state. The topological phase transition from the metallic state to the dielectric state occurs when the filling ratio is one-half. These two states generalize our previous understanding of metal and dielectric: The metamaterial with metal filling ratio larger/smaller than one-half is named as the "generalized metal/dielectric." Interestingly, the surface plasmon polariton (SPP) at a metal/dielectric interface can be understood as the limiting case of a topological edge state. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
25. A paradigm of thermal adaptation in penguins and elephants by tuning cold activation in TRPM8.
- Author
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Shilong Yang, Xiancui Lu, Yunfei Wang, Lizhen Xu, Xiaoying Chen, Fan Yang, and Lai, Ren
- Subjects
AFRICAN elephant ,PENGUINS ,ION channels ,ELEPHANTS ,PHYSIOLOGICAL adaptation - Abstract
To adapt to habitat temperature, vertebrates have developed sophisticated physiological and ecological mechanisms through evolution. Transient receptor potential melastatin 8 (TRPM8) serves as the primary sensor for cold. However, how cold activates TRPM8 and how this sensor is tuned for thermal adaptation remain largely unknown. Here we established a molecular framework of how cold is sensed in TRPM8 with a combination of patch-clamp recording, unnatural amino acid imaging, and structural modeling. We first observed that the maximum cold activation of TRPM8 in eight different vertebrates (i.e., African elephant and emperor penguin) with distinct side-chain hydrophobicity (SCH) in the pore domain (PD) is tuned to match their habitat temperature. We further showed that altering SCH for residues in the PD with solventaccessibility changes leads to specific tuning of the cold response in TRPM8. We also observed that knockin mice expressing the penguin's TRPM8 exhibited remarkable tolerance to cold. Together, our findings suggest a paradigm of thermal adaptation in vertebrates, where the evolutionary tuning of the cold activation in the TRPM8 ion channel through altering SCH and solvent accessibility in its PD largely contributes to the setting of the cold-sensitive/tolerant phenotype. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
26. Structural and functional studies of TBC1D23 Cterminal domain provide a link between endosomal trafficking and PCH.
- Author
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Wenjie Huang, Zhe Liu, Fan Yang, Huan Zhou, Xin Yong, Xiaoyu Yang, Yifei Zhou, Lijia Xue, Yihong Zhang, Dingdong Liu, Wentong Meng, Wenming Zhang, Xiaohu Zhang, Xiaofei Shen, Qingxiang Sun, Li Li, Cong Ma, Yuquan Wei, Billadeau, Daniel D., and Xianming Mo
- Subjects
NEURAL development ,NEUROLOGICAL disorders ,MOLECULAR interactions ,CRYSTAL structure ,CEREBELLUM - Abstract
Pontocerebellar hypoplasia (PCH) is a group of neurological disorders that affect the development of the brain, in particular, the pons and cerebellum. Homozygous mutations of TBC1D23 have been found recently to lead to PCH; however, the underlying molecular mechanisms remain unclear. Here, we show that the crystal structure of the TBC1D23 C-terminal domain adopts a Pleckstrin homology domain fold and selectively binds to phosphoinositides, in particular, PtdIns(4)P, through one surface while binding FAM21 via the opposite surface. Mutation of key residues of TBC1D23 or FAM21 selectively disrupts the endosomal vesicular trafficking toward the Trans-Golgi Network. Finally, using the zebrafish model, we show that PCH patient-derived mutants, impacting either phosphoinositide binding or FAM21 binding, lead to abnormal neuronal growth and brain development. Taken together, our data provide a molecular basis for the interaction between TBC1D23 and FAM21, and suggest a plausible role for PtdIns(4)P in the TBC1D23-mediating endosome-to-TGN trafficking pathway. Defects in this trafficking pathway are, at least partially, responsible for the pathogenesis of certain types of PCH. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
27. Simple yet functional phosphate-loop proteins.
- Author
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Romero Romero, Maria Luisa, Fan Yang, Yu-Ru Lin, Toth-Petroczy, Agnes, Berezovsky, Igor N., Goncearenco, Alexander, Wen Yang, Wellner, Alon, Kumar-Deshmukh, Fanindra, Sharon, Michal, Baker, David, Varani, Gabriele, and Tawfik, Dan S.
- Subjects
- *
AMINO acid sequence , *PROTEIN structure , *CARRIER proteins , *BIOINFORMATICS , *OLIGOMERIZATION - Abstract
Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein's scaffold. Can motifs such as P-loops confer function in a simpler context?We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop's key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
28. Mechanism of inhibition of retromer transport by the bacterial effector RidL.
- Author
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Jialin Yao, Fan Yang, Qi Liu, Dingdong Liu, Xia Zhang, Dawen Niu, Yuquan Wei, Da Jia, Xiaodong Sun, Shen Wang, Cong Ma, Ninghai Gan, Zhao-Qing Luo, and Qingxiang Sun
- Subjects
- *
ENDOPLASMIC reticulum , *VESICLES (Cytology) , *HOST-parasite relationships , *LEGIONELLA pneumophila , *ENDOSOMES , *GOLGI apparatus - Abstract
Retrograde vesicle trafficking pathways are responsible for returning membrane-associated components from endosomes to the Golgi apparatus and the endoplasmic reticulum (ER), and they are critical for maintaining organelle identity, lipid homeostasis, and many other cellular functions. The retrograde transport pathway has emerged as an important target for intravacuolar bacterial pathogens. The opportunistic pathogen Legionella pneumophila exploits both the secretory and recycling branches of the vesicle transport pathway for intracellular bacterial proliferation. Its Dot/ Icm effector RidL inhibits the activity of the retromer by directly engaging retromer components. However, the mechanism underlying such inhibition remains unknown. Here we present the crystal structure of RidL in complex with VPS29, a subunit of the retromer. Our results demonstrate that RidL binds to a highly conserved hydrophobic pocket of VPS29. This interaction is critical for endosomal recruitment of RidL and for its inhibitory effects. RidL inhibits retromer activity by direct competition, in which it occupies the VPS29- binding site of the essential retromer regulator TBC1d5. The mechanism of retromer inhibition by RidL reveals a hotspot on VPS29 critical for recognition by its regulators that is also exploited by pathogens, and provides a structural basis for the development of small molecule inhibitors against the retromer. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
29. Protein kinase WNK3 regulates the neuronal splicing factor Fox-1
- Author
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Yu Chi Juang, Jon Self, Fan Yang, Xiaojun Ding, A-Young Lee, Melanie H. Cobb, Wei Chen, She Chen, and Steve Stippec
- Subjects
RNA Splicing Factors ,Immunoprecipitation ,animal diseases ,RNA-binding protein ,Electrophoretic Mobility Shift Assay ,Biology ,Protein Serine-Threonine Kinases ,Splicing factor ,Mice ,Two-Hybrid System Techniques ,parasitic diseases ,Animals ,Humans ,Protein kinase A ,DNA Primers ,Gene Library ,Multidisciplinary ,Reverse Transcriptase Polymerase Chain Reaction ,RNA ,virus diseases ,food and beverages ,Brain ,RNA-Binding Proteins ,Biological Sciences ,Deuterium ,Cell biology ,HEK293 Cells ,Biochemistry ,RNA splicing ,Phosphorylation ,population characteristics ,Phosphorus Radioisotopes - Abstract
We report an action of the protein kinase WNK3 on the neuronal mRNA splicing factor Fox-1. Fox-1 splices mRNAs encoding proteins important in synaptic transmission and membrane excitation. WNK3, implicated in the control of neuronal excitability through actions on ion transport, binds Fox-1 and inhibits its splicing activity in a kinase activity-dependent manner. Phosphorylation of Fox-1 by WNK3 does not change its RNA binding capacity; instead, WNK3 increases the cytoplasmic localization of Fox-1, thereby suppressing Fox-1–dependent splicing. These findings demonstrate a role of WNK3 in RNA processing. Considering the implication of WNK3 and Fox-1 in disorders of neuronal development such as autism, WNK3 may offer a target for treatment of Fox-1–induced disease.
- Published
- 2012
30. Genetic engineering of human stem cells for enhanced angiogenesis using biodegradable polymeric nanoparticles
- Author
-
Suk Ho Bhang, Robert Langer, Said R. Bogatyrev, Fan Yang, Deepika Singh, Sohyun Park, Byung-Soo Kim, Daniel G. Anderson, Sun Mi Son, Jordan J. Green, Seung Woo Cho, and Ying Mei
- Subjects
Vascular Endothelial Growth Factor A ,Angiogenesis ,Polymers ,Neovascularization, Physiologic ,Biocompatible Materials ,Mice, Inbred Strains ,Biology ,chemistry.chemical_compound ,Mice ,Ischemia ,Animals ,Humans ,Regeneration ,Muscle, Skeletal ,Embryonic Stem Cells ,Stem cell transplantation for articular cartilage repair ,Multidisciplinary ,Regeneration (biology) ,Mesenchymal stem cell ,Gene Transfer Techniques ,Extremities ,Regenerative Medicine Special Feature ,Anatomy ,Embryonic stem cell ,Fibrosis ,Vascular endothelial growth factor ,Vascular endothelial growth factor A ,Disease Models, Animal ,chemistry ,Cancer research ,Nanoparticles ,Stem cell ,Genetic Engineering - Abstract
Stem cells hold great potential as cell-based therapies to promote vascularization and tissue regeneration. However, the use of stem cells alone to promote angiogenesis remains limited because of insufficient expression of angiogenic factors and low cell viability after transplantation. Here, we have developed vascular endothelial growth factor (VEGF) high-expressing, transiently modified stem cells for the purposes of promoting angiogenesis. Nonviral, biodegradable polymeric nanoparticles were developed to deliver hVEGF gene to human mesenchymal stem cells (hMSCs) and human embryonic stem cell-derived cells (hESdCs). Treated stem cells demonstrated markedly enhanced hVEGF production, cell viability, and engraftment into target tissues. S.c. implantation of scaffolds seeded with VEGF-expressing stem cells (hMSCs and hESdCs) led to 2- to 4-fold-higher vessel densities 2 weeks after implantation, compared with control cells or cells transfected with VEGF by using Lipofectamine 2000, a leading commercial reagent. Four weeks after intramuscular injection into mouse ischemic hindlimbs, genetically modified hMSCs substantially enhanced angiogenesis and limb salvage while reducing muscle degeneration and tissue fibrosis. These results indicate that stem cells engineered with biodegradable polymer nanoparticles may be therapeutic tools for vascularizing tissue constructs and treating ischemic disease.
- Published
- 2009
31. Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner.
- Author
-
Nemec, Corey M., Fan Yang, Gilmore, Joshua M., Hintermair, Corinna, Yi-Hsuan Ho, Tseng, Sandra C., Heidemann, Martin, Ying Zhang, Florens, Laurence, Gasch, Audrey P., Eick, Dirk, Washburn, Michael P., Varani, Gabriele, and Ansari, Aseem Z.
- Subjects
- *
RNA polymerase II , *PHOSPHORYLATION kinetics , *GENE expression , *NON-coding DNA , *PROTEIN analysis - Abstract
The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar RNA (snoRNA) genes. Quantitative proteomics reveals an interactome of known readers as well as protein complexes that were not known to rely on Thr4 for association with Pol II. The data indicate a key role for Thr4 in engaging the machinery used for transcription elongation and termination. We focus on Rtt103, a protein that binds phospho-Ser2 and phospho-Thr4 marks and facilitates transcription termination at protein-coding genes. To elucidate how Rtt103 engages two distinct CTD modifications that are differentially enriched at noncoding genes, we relied on NMR analysis of Rtt103 in complex with phospho-Thr4- or phospho-Ser2-bearing CTD peptides. The structural data reveal that Rtt103 interacts with phospho-Thr4 in a manner analogous to its interaction with phospho-Ser2-modified CTD. The same set of hydrogen bonds involving either the oxygen on phospho-Thr4 and the hydroxyl on Ser2, or the phosphate on Ser2 and the Thr4 hydroxyl, can be formed by rotation of an arginine side chain, leaving the intermolecular interface otherwise unperturbed. This economy of design enables Rtt103 to engage Pol II at distinct sets of genes with differentially enriched CTD marks. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
32. Selective in vivo removal of pathogenic anti-MAG autoantibodies, an antigen-specific treatment option for anti-MAG neuropathy.
- Author
-
Herrendorff, Ruben, Hänggi, Pascal, Pfister, Hélène, Fan Yang, Demeestere, Delphine, Hunziker, Fabienne, Frey, Samuel, Ernst, Beat, Schaeren-Wiemers, Nicole, and Steck, Andreas J.
- Subjects
PERIPHERAL neuropathy ,IMMUNOGLOBULINS ,MYELIN proteins ,EPITOPES ,AUTOANTIBODIES - Abstract
Anti-MAG (myelin-associated glycoprotein) neuropathy is a disabling autoimmune peripheral neuropathy caused by monoclonal IgM autoantibodies that recognize the carbohydrate epitope HNK-1 (human natural killer-1). This glycoepitope is highly expressed on adhesion molecules, such as MAG, present in myelinated nerve fibers. Because the pathogenicity and demyelinating properties of anti-MAG autoantibodies are well established, current treatments are aimed at reducing autoantibody levels. However, current therapies are primarily immunosuppressive and lack selectivity and efficacy. We therefore hypothesized that a significant improvement in the disease condition could be achieved by selectively neutralizing the pathogenic anti-MAG antibodies with carbohydrate-based ligands mimicking the natural HNK-1 glycoepitope 1. In an inhibition assay, a mimetic (2, mimHNK-1) of the natural HNK-1 epitope blocked the interaction of MAG with pathogenic IgM antibodies from patient sera but with only micromolar affinity. Therefore, considering the multivalent nature of the MAG-IgM interaction, polylysine polymers of different sizes were substituted with mimetic 2. With the most promising polylysine glycopolymer PL
84 (mimHNK-1)45 the inhibitory effect on patient sera could be improved by a factor of up to 230,000 per epitope, consequently leading to a low-nanomolar inhibitory potency. Because clinical studies indicate a correlation between the reduction of anti-MAG IgM levels and clinical improvement, an immunological surrogate mouse model for anti-MAG neuropathy producing high levels of anti-MAG IgM was developed. The observed efficient removal of these antibodies with the glycopolymer PL84 (mimHNK-1)45 represents an important step toward an antigen-specific therapy for anti-MAG neuropathy. [ABSTRACT FROM AUTHOR]- Published
- 2017
- Full Text
- View/download PDF
33. Distinct conformations of GPCR-β-arrestin complexes mediate desensitization, signaling, and endocytosis.
- Author
-
Cahill III, Thomas J., Thomsen, Alex R. B., Tarrasch, Jeffrey T., Plouffe, Bianca, Nguyen, Anthony H., Fan Yang, Li-Yin Huang, Kahsai, Alem W., Bassoni, Daniel L., Gavino, Bryant J., Lamerdin, Jane E., Triest, Sarah, Shukla, Arun K., Berger, Benjamin, Little IV, John, Antar, Albert, Blanc, Adi, Chang-Xiu Qu, Xin Chen, and Kawakami, Kouki
- Subjects
ARRESTINS ,G protein coupled receptors ,ENDOCYTOSIS ,PROTEIN conformation ,CELLULAR signal transduction - Abstract
β-Arrestins (βarrs) interact with G protein-coupled receptors (GPCRs) to desensitize G protein signaling, to initiate signaling on their own, and to mediate receptor endocytosis. Prior structural studies have revealed two unique conformations of GPCR–βarr complexes: the "tail" conformation, with βarr primarily coupled to the phosphorylated GPCR C-terminal tail, and the "core" conformation, where, in addition to the phosphorylated C-terminal tail, βarr is further engaged with the receptor transmembrane core. However, the relationship of these distinct conformations to the various functions of βarrs is unknown. Here, we created a mutant form of βarr lacking the "finger-loop" region, which is unable to form the core conformation but retains the ability to form the tail conformation. We find that the tail conformation preserves the ability to mediate receptor internalization and βarr signaling but not desensitization of G protein signaling. Thus, the two GPCR–βarr conformations can carry out distinct functions. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
34. Aerosol indirect effect from turbulence-induced broadening of cloud-droplet size distributions.
- Author
-
Chandrakar, Kamal Kant, Cantrell, Will, Kelken Chang, Ciochetto, David, Shaw, Raymond A., Fan Yang, Niedermeier, Dennis, and Ovchinnikov, Mikhail
- Subjects
AEROSOLS ,CLOUD droplets ,MICROPHYSICS ,SUPERSATURATION ,RAYLEIGH-Benard convection - Abstract
The influence of aerosol concentration on the cloud-droplet size distribution is investigated in a laboratory chamber that enables turbulent cloud formation through moist convection. The experiments allow steady-state microphysics to be achieved, with aerosol input balanced by cloud-droplet growth and fallout. As aerosol concentration is increased, the cloud-droplet mean diameter decreases, as expected, but the width of the size distribution also decreases sharply. The aerosol input allows for cloud generation in the limiting regimes of fast microphysics (T
c t) for high aerosol concentration, and slow microphysics (T c t) for low aerosol concentration; here, T c is the phase-relaxation time and Tt is the turbulence-correlation time. The increase in the width of the droplet size distribution for the low aerosol limit is consistent with larger variability of supersaturation due to the slow microphysical response. A stochastic differential equation for supersaturation predicts that the standard deviation of the squared droplet radius should increase linearly with a system time scale defined as Ts -1 = Tc -1 + Tt -1 , and the measurements are in excellent agreement with this finding. The result underscores the importance of droplet size dispersion for aerosol indirect effects: increasing aerosol concentration changes the albedo and suppresses precipitation formation not only through reduction of the mean droplet diameter but also by narrowing of the droplet size distribution due to reduced supersaturation fluctuations. Supersaturation fluctuations in the low aerosol/slow microphysics limit are likely of leading importance for precipitation formation. [ABSTRACT FROM AUTHOR]- Published
- 2016
- Full Text
- View/download PDF
35. Nanoparticle engineered TRAIL-overexpressing adipose-derived stem cells target and eradicate glioblastoma via intracranial delivery.
- Author
-
Xinyi Jiang, Jianfeng Li, Fan Yang, Sergio Fitch, Wang, Christine, Wilson, Christy, and Grant, Gerald A.
- Subjects
NANOPARTICLES ,GLIOBLASTOMA multiforme ,FAT cells ,TUMORS ,BRAIN tumor treatment - Abstract
Glioblastoma multiforme (GBM) is one of the most intractable of human cancers, principally because of the highly infiltrative nature of these neoplasms. Tracking and eradicating infiltrating GBM cells and tumor microsatellites is of utmost importance for the treatment of this devastating disease, yet effective strategies remain elusive. Here we report polymeric nanoparticle-engineered human adipose-derived stem cells (hADSCs) overexpressing tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) as drug-delivery vehicles for targeting and eradicating GBM cells in vivo. Our results showed that polymeric nanoparticle-mediated transfection led to robust up-regulation of TRAIL in hADSCs, and that TRAIL-expressing hADSCs induced tumor-specific apoptosis. When transplanted in a mouse intracranial xenograft model of patient-derived glioblastoma cells, hADSCs exhibited long-range directional migration and infiltration toward GBM tumor. Importantly, TRAIL-overexpressing hADSCs inhibited GBM growth, extended survival, and reduced the occurrence of microsatellites. Repetitive injection of TRAIL-overexpressing hADSCs significantly prolonged animal survival compared with single injection of these cells. Taken together, our data suggest that nanoparticle-engineered TRAIL-expressing hADSCs exhibit the therapeutically relevant behavior of "seek-and-destroy" tumortropic migration and could be a promising therapeutic approach to improve the treatment outcomes of patients with malignant brain tumors. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
36. Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor
- Author
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Fan Yang, Alexander Wlodawer, Jacek Lubkowski, George Merkel, Nouri Neamati, Terrence R. Burke, He Zhao, Yves Pommier, Anna Marie Skalka, and Jerry Alexandratos
- Subjects
Models, Molecular ,Stereochemistry ,Molecular Sequence Data ,Crystallography, X-Ray ,Avian sarcoma virus ,Divalent ,Metal ,Naphthalenesulfonates ,Hydrolase ,Molecule ,HIV Integrase Inhibitors ,Binding site ,chemistry.chemical_classification ,Manganese ,Multidisciplinary ,Binding Sites ,biology ,Integrases ,Active site ,Hydrogen-Ion Concentration ,Biological Sciences ,Integrase ,Protein Structure, Tertiary ,chemistry ,Biochemistry ,Avian Sarcoma Viruses ,visual_art ,visual_art.visual_art_medium ,biology.protein - Abstract
The x-ray structures of an inhibitor complex of the catalytic core domain of avian sarcoma virus integrase (ASV IN) were solved at 1.9- to 2.0-Å resolution at two pH values, with and without Mn 2+ cations. This inhibitor (Y-3), originally identified in a screen for inhibitors of the catalytic activity of HIV type 1 integrase (HIV-1 IN), was found in the present study to be active against ASV IN as well as HIV-1 IN. The Y-3 molecule is located in close proximity to the enzyme active site, interacts with the flexible loop, alters loop conformation, and affects the conformations of active site residues. As crystallized, a Y-3 molecule stacks against its symmetry-related mate. Preincubation of IN with metal cations does not prevent inhibition, and Y-3 binding does not prevent binding of divalent cations to IN. Three compounds chemically related to Y-3 also were investigated, but no binding was observed in the crystals. Our results identify the structural elements of the inhibitor that likely determine its binding properties.
- Published
- 1998
37. Improved i.p. drug delivery with bioadhesive nanoparticles.
- Author
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Yang Deng, Fan Yang, Cocco, Emiliano, Eric Song, Junwei Zhang, Jiajia Cui, Mohideen, Muneeb, Bellone, Stefania, Santin, Alessandro D., and Saltzman, W. Mark
- Subjects
- *
CANCER chemotherapy , *CARCINOMA , *OVARIAN epithelial cancer , *BIODEGRADABLE nanoparticles , *XENOGRAFTS - Abstract
The i.p. administration of chemotherapy in ovarian and uterine serous carcinoma patients by biodegradable nanoparticles may represent a highly effective way to suppress peritoneal carcinomatosis. However, the efficacy of nanoparticles loaded with chemotherapeutic agents is currently hampered by their fast clearance by lymphatic drainage. Here, we show that a unique formulation of bioadhesive nanoparticles (BNPs) can interact with mesothelial cells in the abdominal cavity and significantly extend the retention of the nanoparticles in the peritoneal space. BNPs loaded with a potent chemotherapeutic agent [epothilone B (EB)] showed significantly lower systemic toxicity and higher therapeutic efficacy against i.p. chemotherapy-resistant uterine serous carcinomaderived xenografts compared with free EB and non-BNPs loaded with EB. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
38. Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8.
- Author
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Pröpster, Johannes M., Fan Yang, Rabbani, Said, Ernst, Beat, Allain, Frédéric H.-T., and Schubert, Mario
- Subjects
- *
LECTINS , *GLYCANS , *SULFATION , *SIALIC acids , *NUCLEAR magnetic resonance spectroscopy , *IMMUNOREGULATION , *INFLAMMATION , *EPITOPES - Abstract
Siglec-8 is a human immune-inhibitory receptor that, when engaged by specific self-glycans, triggers eosinophil apoptosis and inhibits mast cell degranulation, providing an endogenous mechanism to down-regulate immune responses of these central inflammatory effector cells. Here we used solution NMR spectroscopy to dissect the fine specificity of Siglec-8 toward different sialylated and sulfated carbohydrate ligands and determined the structure of the Siglec-8 lectin domain in complex with its prime glycan target 6'-sulfo sialyl Lewisx. A canonical motif for sialic acid recognition, extended by a secondary motif formed by unique loop regions, recognizing 6-O-sulfated galactose dictates tight specificity distinct from other Siglec family members and any other endogenous glycan recognition receptors. Structure-guided mutagenesis revealed key contacts of both interfaces to be equally essential for binding. Our work provides critical structural and mechanistic insights into how Siglec-8 selectively recognizes its glycan target, rationalizes the functional impact of site-specific glycan sulfation in modulating this lectin-glycan interaction, and will enable the rational design of Siglec-8-targeted agonists to treat eosinophil- andmast cell-related allergic and inflammatory diseases, such as asthma. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
39. Rational design and validation of a vanilloid-sensitive TRPV2 ion channel.
- Author
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Fan Yang, Vu, Simon, Yarov-Yarovoy, Vladimir, and Jie Zheng
- Subjects
- *
ION channels , *CAPSAICIN , *RESINIFERATOXIN , *LIGAND binding (Biochemistry) , *TRP channels - Abstract
Vanilloids activation of TRPV1 represents an excellent model system of ligand-gated ion channels. Recent studies using cryo-electron microcopy (cryo-EM), computational analysis, and functional quantification revealed the location of capsaicin-binding site and critical residues mediating ligand-binding and channel activation. Based on these new findings, here we have successfully introduced high-affinity binding of capsaicin and resiniferatoxin to the vanilloid-insensitive TRPV2 channel, using a rationally designed minimal set of four point mutations (F467S–S498F–L505T–Q525E, termed TRPV2_Quad). We found that binding of resiniferatoxin activates TRPV2_Quad but the ligand-induced open state is relatively unstable, whereas binding of capsaicin to TRPV2_Quad antagonizes resiniferatoxin-induced activation likely through competition for the same binding sites. Using Rosettabased molecular docking, we observed a common structural mechanism underlying vanilloids activation of TRPV1 and TRPV2_Quad, where the ligand serves as molecular “glue” that bridges the S4–S5 linker to the S1–S4 domain to open these channels. Our analysis revealed that capsaicin failed to activate TRPV2_Quad likely due to structural constraints preventing such bridge formation. These results not only validate our current working model for capsaicin activation of TRPV1 but also should help guide the design of drug candidate compounds for this important pain sensor. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
40. Yeast hormone response element assays detect and characterize GRIP1 coactivator-dependent activation of transcription by thyroid and retinoid nuclear receptors
- Author
-
Yong-Fan Yang, Tauseef R. Butt, Paul G. Walfish, Heng Hong, Michael R. Stallcup, and Thillainathan Yoganathan
- Subjects
Transcriptional Activation ,Multidisciplinary ,Thyroid hormone receptor ,Receptors, Thyroid Hormone ,Retinoid X receptor alpha ,Receptors, Retinoic Acid ,Receptors, Cytoplasmic and Nuclear ,Saccharomyces cerevisiae ,Biology ,Retinoid X receptor ,Biological Sciences ,Retinoid X receptor gamma ,Molecular biology ,Mice ,Nuclear Receptor Coactivator 2 ,Nuclear receptor ,Nuclear receptor coactivator 3 ,Nuclear receptor coactivator 2 ,Animals ,Biological Assay ,Retinoid X receptor beta ,Transcription Factors - Abstract
The mouse glucocorticoid receptor-interacting protein (GRIP1) is a member of the ERAP160 family of nuclear receptor (NR) coactivators (including SRC-1 and TIF2) which function as bridging proteins between ligand-activated NRs bound to cognate hormone-response elements (HREs) and the transcription initiation apparatus (TIA). Although these coactivators bind to several NRs, studies overexpressing these coactivators with these NRs in mammalian cells have not uniformly observed a corresponding enhancement of ligand-dependent transactivation. Here, we show that GRIP1 interacts in vitro in a ligand-dependent manner with thyroid receptor, retinoic acid receptor, and retinoid X receptor. Additionally, in yeast ( Saccharomyces cerevisiae ) GRIP1 coactivator protein markedly increased the ability of these full-length class II NRs to transactivate β-galactosidase reporter genes containing cognate HREs. The magnitude of GRIP1 enhancement of liganded NR homodimer was dependent upon NR subtype and HRE configuration. For most HRE configurations, thyroid receptor and retinoic acid receptor homodimers were essentially unresponsive or very weakly active in the absence of GRIP1, but GRIP1 dramatically restored the ligand-dependent function of these NRs. Although GRIP1 exerted no significant effect on NR homodimers in the absence of their cognate ligands, it increased the transactivation of unliganded NR heterodimers. Whether GRIP1 increased ligand-dependent transactivation of a heterodimer to levels greater than that of the cognate homodimer was determined by HRE configuration and copy number. Compared with the limitations of yeast two-hybrid and mammalian coexpression systems, the yeast HRE-assay systems described in this report facilitated both the detection of putative mammalian NR coactivator function and the elucidation of their mechanisms of transactivational enhancement.
- Published
- 1997
41. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection.
- Author
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Wenhui Hu, Ratal Kaminski, Fan Yang, Yonggang Zhang, Laura Cosentino, Fang Li, Biao Luo, Alvarez-Carbonell, David, Garcia-Mesa, Yoelvis, Karn, Jonathan, Xianming Mo, and Khalili, Kamel
- Subjects
HIV infections ,REVERSE transcriptase ,ANTIRETROVIRAL agents ,GENETIC toxicology ,T cells - Abstract
AIDS remains incurable due to the permanent integration of HIV-1 into the host genome, imparting risk of viral reactivation even after antiretroviral therapy. New strategies are needed to ablate the viral genome from latently infected cells, because current methods are too inefficient and prone to adverse off-target effects. To eliminate the integrated HIV-1 genome, we used the Cas9/guide RNA (gRNA) system, in single and multiplex configurations. We identified highly specific targets within the HIV-1 LTR U3 region that were efficiently edited by Cas9/gRNA, inactivating viral gene expression and replication in latently infected microglial, promon-ocytic, and T cells. Cas9/gRNAs caused neither genotoxicity nor off-target editing to the host cells, and completely excised a 9,709-bp fragment of integrated proviral DNA that spanned from its 5' to 3' LTRs. Furthermore, the presence of multiplex gRNAs within Cas9-expressing cells prevented HIV-1 infection. Our results suggest that Cas9/gRNA can be engineered to provide a specific, efficacious prophylactic and therapeutic approach against AIDS. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
42. BIK1 interacts with PEPRs to mediate ethylene-induced immunity.
- Author
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Zixu Liu, Ying Wu, Fan Yang, Yiyue Zhang, She Chen, Qi Xie, Xingjun Tian, and Jian-Min Zhou
- Subjects
BOTRYTIS ,PHYTOPATHOGENIC microorganisms ,ETHYLENE ,IMMUNE response ,GENE expression in plants ,PHOSPHORYLATION - Abstract
Plants have evolved intricate immune mechanisms to combat pathogen infection. Upon perception of pathogen-derived signals, plants accumulate defense hormones such as ethylene (ET), jasmonate, salicylate, and damage-associated molecular patterns to amplify immune responses. In particular, the Arabidopsis peptide Pep1 and its family members are thought to be damage-associated molecular patterns that trigger immunity through Pep1 receptor kinases PEPR1 and PEPR2. Here we show that PEPR1 specifically interacts with receptor-like cytoplasmic kinases botrytis-induced kinase 1 (BIK1) and PBS1-Iike 1 (PBL1) to mediate Pep1-induced defenses. In vitro and in vivo studies suggested that PEPR1, and likely PEPR2, directly phosphorylates BIK1 in response to Pep1 treatment. Surprisingly, the peprl/pepr2 double-mutant seedlings displayed reduced in sensitivity to ET, as indicated by the elongated hypocotyls. ET-induced expression of defense genes and resistance to Botrytis cinerea were compromised in pepr1/pepr2 and biki mutants, reenforcing an important role of PEPRs and BIK1 in ETmediated defense signaling. Pep treatment partially mimicked ETinduced seedling growth inhibition in a PEPRand BIK1-dependent manner. Furthermore, both El and Pepi treatments induced BIK1 phosphorylation in a PEPR-dependent manner. However, the Pepiinduced BIK1 phosphorylation, seedling growth inhibition, and defense gene expression were independent of canonical ET signaling components. Together our results illustrate a mechanism by which ET and PEPR signaling pathways act in concert to amplify immune responses. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
43. Protein kinase WNK3 regulates the neuronal splicing factor Fox-1.
- Author
-
A-Young cLee, Wei Chen, Stippec, Steve, Self, Jon, Fan Yang, Xiaojun Ding, She Chen, Yu-Chi Juang, and Cobb, Melanie H.
- Subjects
PROTEIN kinases ,GENETIC engineering ,MESSENGER RNA ,CYTOPLASM ,GENETIC code ,LYSINE ,PHOSPHORYLATION ,NEURAL transmission - Abstract
We report an action of the protein kinase WNK3 on the neuronal mRNA splicing factor Fox-1. Fox-1 splices mRNAs encoding proteins important in synaptic transmission and membrane excitation. WNK3, implicated in the control of neuronal excitability through actions on ion transport, binds Fox-1 and inhibits its splicing activity in a kinase activity-dependent manner. Phosphorylation of Fox-1 by WNK3 does not change its RNA binding capacity; instead, WNK3 increases the cytoplasmic localization of Fox-1, thereby suppressing Fox-1-dependent splicing. These findings demonstrate a role of WNK3 in RNA processing. Considering the implication of WNK3 and Fox-1 in disorders of neuronal development such as autism, WNK3 may offer a target for treatment of Fox-1-induced disease. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
44. Thermosensitive TRP channel pore turret is part of the temperature activation pathway.
- Author
-
Fan Yang, Yuanyuan Cui, KeWei Wang, and Jie Zheng
- Subjects
- *
WARM-blooded animals , *THERMODYNAMICS , *CONFORMATIONAL analysis , *TEMPERATURE , *PROTEINS - Abstract
Temperature sensing is crucial for homeotherms, including human beings, to maintain a stable body core temperature and respond to the ambient environment. A group of exquisitely temperature-sensitive transient receptor potential channels, termed thermoTRPs, serve as cellular temperature sensors. How thermoTRPs convert thermal energy (heat) into protein conformational changes leading to channel opening remains unknown. Here we demonstrate that the pathway for temperature-dependent activation is distinct from those for ligand- and voltage-dependent activation and involves the pore turret. We found that mutant channels with an artificial pore turret sequence lose temperature sensitivity but maintain normal ligand responses. Using site-directed fluorescence recordings we observed that temperature change induces a significant rearrangement of TRPV1 pore turret that is coupled to channel opening. This movement is specifically associated to temperature-dependent activation and is not observed during ligand- and voltage-dependent channel activation. These observations suggest that the turret is part of the temperature-sensing apparatus in thermoTRP channels, and its conformational change may give rise to the large entropy that defines high temperature sensitivity. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
45. Genetic engineering of human stem cells for enhanced angiogenesis using biodegradable polymeric nanoparticles.
- Author
-
Fan Yang, Seung-Woo Cho, Sun Mi Son, Bogatyrev, Said R., Singh, Deepika, Green, Jordan J., Ying Mei, Sohyun Park, Suk Ho Bhang, Byung-Soo Kim, Langer, Robert, and Anderson, Daniel G.
- Subjects
- *
POLYMERS , *ISCHEMIA , *GENETIC engineering , *STEM cells , *NEOVASCULARIZATION , *NANOPARTICLES - Abstract
Stem cells hold great potential as cell-based therapies to promote vascularization and tissue regeneration. However, the use of stem cells alone to promote angiogenesis remains limited because of insufficient expression of angiogenic factors and low cell viability after transplantation. Here, we have developed vascular endothelial growth factor (VEGF) high-expressing, transiently modified stem cells for the purposes of promoting angiogenesis. Nonviral, biodegradable polymeric nanoparticles were developed to deliver hVEGF gene to human mesenchymal stem cells (hMSCs) and human embryonic stem cell-derived cells (hESdCs). Treated stem cells demonstrated markedly enhanced hVEGF production, cell viability, and engraftment into target tissues. S.c. implantation of scaffolds seeded with VEGF-expressing stem cells (hMSCs and hESdCs) led to 2- to 4-fold-higher vessel densities 2 weeks after implantation, compared with control cells or cells transfected with VEGF by using Lipofectamine 2000, a leading commercial reagent. Four weeks after intramuscular injection into mouse ischemic hindlimbs, genetically modified hMSCs substantially enhanced angiogenesis and limb salvage while reducing muscle degeneration and tissue fibrosis. These results indicate that stem cells engineered with biodegradable polymer nanoparticles may be therapeutic tools for vascularizing tissue constructs and treating ischemic disease. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
46. Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501.
- Author
-
Yongliang Yan, Jian Yang, Yuetan Dou, Ming Chen, Shuzhen Ping, Junping Peng, Wei Lu, Wei Zhang, Ziying Yao, Hongquan Li, Wei Liu, Sheng He, Lizhao Geng, Xiaobing Zhang, Fan Yang, Haiying Yu, Yuhua Zhan, Danhua Li, Zhanglin Lin, and Yiping Wang
- Subjects
NITROGEN fixation ,RHIZOSPHERE ,PSEUDOMONAS ,BIOGEOCHEMICAL cycles ,PLANT roots - Abstract
The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give Al 501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
47. E1A and a nuclear receptor corepressor splice variant (N-CoRI) are thyroid hormone receptor coactivators that bind in the corepressor mode.
- Author
-
Xianwang Meng, Webb, Paul, Yong-Fan Yang, Shuen, Michael, Yousef, Ahmed F., Baxter, John D., Mymryk, Joe S., and Walfish, Paul G.
- Subjects
NUCLEAR receptors (Biochemistry) ,CELL receptors ,THYROID hormones ,GENES ,TRANSCRIPTION factors ,SACCHAROMYCES cerevisiae ,SACCHAROMYCES - Abstract
Unliganded thyroid hormone (TH) receptors (TRs) and other nuclear receptors (NR5) repress transcription of hormone-activated genes by recruiting corepressors (CoRs), such as NR CoR (N-C0R) and SMRT. Unliganded TRs also activate transcription of TH-repressed genes. Some evidence suggests that these effects also involve TR/CoR contacts; however, the precise reasons that CoRs activate transcription in these contexts are obscure. Unraveling these mechanisms is complicated by the fact that it is difficult to decipher direct vs. indirect effects of TR-coregulator contacts in mammalian cells. In this study, we used yeast, Saccharomyces cerevisiae, which lack endogenous NRs and NR coregulators, to determine how unliganded TRs can activate transcription. We previously showed that adenovirus 5 early-region 1A coactivates unliganded TRs in yeast, and that these effects are blocked by TH. We show here that human adenovirus type 5 early region 1A (E1A) contains a short peptide (LDQLIEEVL amino acids 20-28) that resembles CoR-NR interaction motifs (CoRNR boxes), and that this motif is required for TR binding and coactivation. Although fulllength N-CoR does not coactivate TR in yeast a naturally occurring N-CoR variant (N-CoR
1 ) and an artificial N-CoR truncation (N-CoRc) that retain CoRNR boxes but lack N-terminal repressor domains behave as potent and direct TH-repressed coactivators for unliganded TRs. We conclude that E1A and N-CoR1 are naturally occurring TR coactivators that bind in the typical CoR mode and suggest that similar factors could mediate transcriptional activation by unliganded TRs in mammals. [ABSTRACT FROM AUTHOR]- Published
- 2005
- Full Text
- View/download PDF
48. Rapid biogenesis and sensitization of secretory lysosomes in NK cells mediated by target-cell recognition.
- Author
-
Liu, Dongfang, Liang Xu, Fan Yang, Dongdong Li, Feili Gong, and Tao Xu
- Subjects
ORGANELLE formation ,KILLER cells ,PROTEIN kinases ,LYSOSOMES ,XENOGRAFTS ,EXOCYTOSIS ,CELL physiology - Abstract
Natural killer (NK) cells play important roles in defense against tumor, viral infection, and cell-mediated xenograft rejection through secretion of secretory lysosomes. In this study, we used high time-resolution membrane capacitance measurement and fluorescence-imaging techniques to study the biogenesis and exocytosis of secretory lysosomes in a human NK cell line. We demonstrated a high-affinity Ca
2+ -dependent exocytosis of secretory lysosomes, which is sensitized further after target-cell stimulation. Our data also suggest an unusual rapid and dramatic de novo formation of secretory lysosomes after target-cell recognition. The rapid biogenesis of secretory lysosomes was blocked by specific protein kinase C inhibitor but not by brefeldin A. We propose that target-cell recognition triggers rapid biogenesis and sensitization of secretory lysosomes in NK cells through activation of PKC. [ABSTRACT FROM AUTHOR]- Published
- 2005
- Full Text
- View/download PDF
49. Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase.
- Author
-
Beuning, Penny J. and Fan Yang
- Subjects
- *
OLIGONUCLEOTIDES - Abstract
Presents a study which look at the charging in vitro of oligonucleotide and full-length tRNA substrates that contain mismatches at the position of the G.U pair. Detailed information on the methodology used to conduct the study; Results of the study; Discussion surrounding the results of the study.
- Published
- 1997
- Full Text
- View/download PDF
50. Cyclic stretch promotes vascular homing of endothelial progenitor cells via Acsl1 regulation of mitochondrial fatty acid oxidation.
- Author
-
Han Y, Yan J, Li ZY, Fan YJ, Jiang ZL, Shyy JY, and Chien S
- Subjects
- Rats, Animals, Mechanotransduction, Cellular, Cell Differentiation, Mitochondria metabolism, Fatty Acids metabolism, Endothelial Progenitor Cells
- Abstract
Endothelial progenitor cells (EPCs) play an important role in vascular repair and re-endothelialization after vessel injury. EPCs in blood vessels are subjected to cyclic stretch (CS) due to the pulsatile pressure, but the role of CS in metabolic reprogramming of EPC, particularly its vascular homing and repair, is largely unknown. In the current study, physiological CS applied to EPCs at a magnitude of 10% and a frequency of 1 Hz significantly promoted their vascular adhesion and endothelial differentiation. CS enhanced mitochondrial elongation and oxidative phosphorylation (OXPHOS), as well as adenosine triphosphate production. Metabolomic study and Ultra-high performance liquid chromatography-mass spectrometry assay revealed that CS significantly decreased the content of long-chain fatty acids (LCFAs) and markedly induced long-chain fatty acyl-CoA synthetase 1 (Acsl1), which in turn facilitated the catabolism of LCFAs in mitochondria via fatty acid β-oxidation and OXPHOS. In a rat carotid artery injury model, transplantation of EPCs overexpressing Acsl1 enhanced the adhesion and re-endothelialization of EPCs in vivo. MRI and vascular morphology staining showed that Acsl1 overexpression in EPCs improved vascular repair and inhibited vascular stenosis. This study reveals a mechanotransduction mechanism by which physiological CS enhances endothelial repair via EPC patency.
- Published
- 2023
- Full Text
- View/download PDF
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