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Methyl aldohexopyranosides were 13C-labeled at contiguous carbons, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy to examine the degree to which density functional...

Methyl aldohexopyranosides were 13C-labeled at contiguous carbons, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy to examine the degree to which density functional theory (DFT) can calculate one-bond 13C-13C spin-coupling constants (1JCC) in saccharides with sufficient accuracy to permit their use in MA’AT analysis (J. Chem. Inf. Model., 2022, 62, 3135–3141). Experimental 1JCC values in crystalline samples of the doubly 13C-labeled compounds were measured by solid-state 13C NMR and compared to those calculated from four different DFT models: (1) 1JCC values calculated from a single structure identical to that observed in crystalline samples by X-ray crystallography; (2) 1JCC values calculated from the same single structure in (1) but allowing all C–H bonds to optimize during the DFT calculations; and (3 and 4) 1JCC values calculated in rotamers of torsion angle theta 2 (C1–C2–O2–O2H) or omega (C4–C5–C6–O6) from which either specific or generalized parameterized equations were obtained and used to calculate 1JCC values in the specific theta 2 or omega rotamer observed in crystalline samples. Good qualitative agreement was observed between calculated 1JCC values and those measured by solid-state 13C NMR regardless of the DFT model, but in no cases were calculated 1JCC values quantitative, differing on average by 4–5% from experimental values. Calculated 1JCC values were consistently larger than experimental values. These findings, and those reported in recent solution NMR studies (Tetrault et al., J. Phys. Chem. B 2022, in press), indicate that improvements in DFT calculations are needed before calculated 1JCC values can be used as reliable constraints in MA’AT analyses of saccharides in solution.

This study examined the influences of infants’ age for the first use of smart devices and the amount of time to use them on the externalizing problem behavior as well as investigated whether maternal managing behavior (setting rules on accessing smart devices and monitoring their child’s use of smart devices) had moderating effects. The study participants consisted of 521 three to six year old infants (235 boys and 286 girls). The data were analyzed by means of descriptive statistics and a hierarchical regression. The results of this study indicated that the age at first use of smart devices and maternal managing behavior had significant effects on the externalizing problem behavior of infants. The earlier the infants first used smart devices, the higher the level of externalizing problem behavior. Externalizing problem behavior was also found to be higher when the mothers showed no managing behavior. Second, maternal managing behavior moderated the relation between the age at first use of smart devices and the externalizing problem behavior of infants. The effects of the age at first use of smart devices on the externalizing problem behavior of infants were greater when the mothers did not set rules regarding the use of smart devices and did not supervise children when using smart devices.

In response to genotoxic stress, the tumor suppressor protein p73 induces apoptosis and cell cycle arrest. Despite extensive studies on p73-mediated apoptosis, little is known about the cytoplasmic apoptotic function of p73. Here, using H1299 lung cancer cells and diverse biochemical approaches, including colony formation, DNA fragmentation, GST pulldown, and apoptosis assays along with NMR spectroscopy, we show that p73 induces transcription-independent apoptosis via its transactivation domain (TAD) through a mitochondrial pathway and that this apoptosis is mediated by the interaction between p73-TAD and the anti-apoptotic protein B-cell lymphoma-extra large (Bcl-X(L) or BCL2L1). This binding disrupted an interaction between Bcl-X(L) and the pro-apoptotic protein BH3-interacting domain death agonist (Bid). In particular, we found that a 16-mer p73-TAD peptide motif (p73-TAD16) mediates transcription-independent apoptosis, accompanied by cytochrome c release from the mitochondria, by interacting with Bcl-X(L). Interestingly, the structure of the Bcl-X(L)–p73-TAD16 peptide complex revealed a novel mechanism of Bcl-X(L) recognition by p73-TAD. We observed that the α-helical p73-TAD16 peptide binds to a noncanonical site in Bcl-X(L), comprising the BH1, BH2, and BH3 domains in an orientation opposite to those of pro-apoptotic BH3 peptides. Taken together, our results indicate that the cytoplasmic apoptotic function of p73 is mediated through a noncanonical mode of Bcl-X(L) recognition. This finding sheds light on a critical transcription-independent, p73-mediated mechanism for apoptosis induction, which has potential implications for anticancer therapy.

NMR studies of two 13C-labeled disaccharides and a tetrasaccharide were undertaken that comprise the backbone of a novel thermal hysteresis glycolipid containing a linear glycan sequence of alternating [βXyl p-(1→4)-βMan p-(1→4)] n dimers. Experimental trans-glycoside NMR J-couplings, parameterized equations obtained from density functional theory (DFT) calculations, and an in-house circular statistics package ( MA'AT) were used to derive conformational models of linkage torsion angles ϕ and ψ in solution, which were compared to those obtained from molecular dynamics simulations. Modeling using different probability distribution functions showed that MA'AT models of ϕ in βMan(1→4)βXyl and βXyl(1→4)βMan linkages are very similar in the disaccharide building blocks, whereas MA'AT models of ψ differ. This pattern is conserved in the tetrasaccharide, showing that linkage context does not influence linkage geometry in this linear system. Good agreement was observed between the MA'AT and MD models of ψ with respect to mean values and circular standard deviations. Significant differences were observed for ϕ, indicating that revision of the force-field employed by GLYCAM is probably needed. Incorporation of the experimental models of ϕ and ψ into the backbone of an octasaccharide fragment leads to a helical amphipathic topography that may affect the thermal hysteresis properties of the glycolipid.

Volatile organic compounds including acetaldehyde, methanol, and higher alcohols such as 1-propanol and 3-methyl-1-butanol in 75 domestic and imported alcoholic beverages consumed in Korea were investigated and evaluated using a gas chromatograph equipped with a mass spectrometer. The acetaldehyde contents in the studied samples ranged from 0.02 to 11.73 mg/L, and were highest in refined rice wines and fruit wines. Only the wine and fruit wine samples contained methanol, at concentrations in the range of 1.42–23.81 mg/L. The 1-propanol content was highest in whisky, while the 3-methyl-1-butanol content ranged from 4.45 to 280 mg/L in all samples other than Korean distilled liquor.

NMR spin–spin coupling constants (scalar couplings, J-couplings) are highly abundant in saccharides, with multiple values often reporting on the same structural domain (redundancy). While conventional analyses of J-couplings typically involve studies of these parameters in relation to individual structural elements, future treatments are more likely to involve simultaneous analyses of large numbers of redundant (and in some cases correlated) J-couplings sensitive to multiple structural domains, providing a more complete appraisal of local molecular structure in solution. These analyses require quantitative relationships between J-couplings and saccharide structure. This chapter provides a detailed look at structural information encoded in one-bond (1J), two-bond (2J), three-bond (3J), four-bond (4J), and dual pathway (2+3J, 3+3J) scalar couplings involving hydrogen and carbon as coupled nuclei in saccharides. Experimental and computational data are integrated to illustrate correlations between saccharide structure, J-coupling magnitude and J-coupling sign. Topics ranging from selective isotopic labeling to enable J-coupling measurements, experimental methods to determine J-coupling magnitudes and signs, and the effects of specific types of molecular motions on the behaviors of saccharide J-couplings are treated. While work published over the past fifteen years comprise the main discussion, new data are included to augment or refine prior findings, notably on long-range 4JHH values in aldopyranosyl rings and across O-glycosidic linkages, and J-couplings pertinent to conformational analyses of glycosidic linkages.

Molecular interactions between the tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins play an important role in the transcription-independent apoptosis of p53. The p53 transactivation domain (p53TAD) contains two conserved ΦXXΦΦ motifs (Φ indicates a bulky hydrophobic residue and X is any other residue) referred to as p53TAD1 (residues 15–29) and p53TAD2 (residues 39–57). We previously showed that p53TAD1 can act as a binding motif for anti-apoptotic Bcl-2 family proteins. In this study, we have identified p53TAD2 as a binding motif for anti-apoptotic Bcl-2 family proteins by using NMR spectroscopy, and we calculated the structures of Bcl-XL/Bcl-2 in complex with the p53TAD2 peptide. NMR chemical shift perturbation data showed that p53TAD2 peptide binds to diverse members of the anti-apoptotic Bcl-2 family independently of p53TAD1, and the binding between p53TAD2 and p53TAD1 to Bcl-XL is competitive. Refined structural models of the Bcl-XL·p53TAD2 and Bcl-2·p53TAD2 complexes showed that the binding sites occupied by p53TAD2 in Bcl-XL and Bcl-2 overlap well with those occupied by pro-apoptotic BH3 peptides. Taken together with the mutagenesis, isothermal titration calorimetry, and paramagnetic relaxation enhancement data, our structural comparisons provided the structural basis of p53TAD2-mediated interaction with the anti-apoptotic proteins, revealing that Bcl-XL/Bcl-2, MDM2, and cAMP-response element-binding protein-binding protein/p300 share highly similar modes of binding to the dual p53TAD motifs, p53TAD1 and p53TAD2. In conclusion, our results suggest that the dual-site interaction of p53TAD is a highly conserved mechanism underlying target protein binding in the transcription-dependent and transcription-independent apoptotic pathways of p53. Background: Interactions between p53 and Bcl-2 family proteins serve a critical role in transcription-independent p53 apoptosis. Results: We studied the interactions of p53TAD2 with anti-apoptotic Bcl-2 family proteins at the atomic level by NMR, mutagenesis, and structure calculation. Conclusion: Bcl-XL/Bcl-2, MDM2, and CBP/p300 share similar modes of binding to the dual p53TAD motifs. Significance: Dual-site interaction of p53TAD is a highly conserved mechanism in the transcription-dependent and transcription-independent p53 apoptotic pathways.

Background Korea has experienced diverse kind of disasters these days. Among them the 2015 middle eastern respiratory syndrome (MERS) outbreak imposed great psychological stress on almost all Korean citizens. Following the MERS outbreak, government is reviewing overall infectious disease management system and prioritizing the establishment of mental health service systems for infectious disease. This study makes suggestions for implementing disaster-related mental health service systems by analyzing the example of Gyeonggi Province, which proactively intervened with residents’ psychological problems caused by the large-scale outbreak of an infectious disease. Case description Mental health service system for MERS victims had the following two parts: a mental health service for people who had been placed in quarantine and a service provided to families of patients who had died or recovered patients. The government of Gyeonggi province, public health centers, regional and local Community Mental Health Centers and the National Center for Crisis Mental Health Management participated in this service system. Among 1221 Gyeonggi people placed in quarantine and who experienced psychological and emotional difficulties, 350 required continuing services; 124 of this group received continuing services. That is, 35 % of people who required psychological intervention received contact from service providers and received the required services. Conclusions This study reflects a proactive monitoring system for thousands of people placed under quarantine for the first time in Korea. It is significant that the service utilization rate by a proactive manner, that is the professionals administering it actively approached and contacted people with problems rather than passively providing information was much higher than other general mental health situation in Korea. The core value of public mental health services is adequate public accessibility; it is therefore essential for governments to strengthen their professional competence and establish effective systems. These criteria should also be applied to psychological problems caused by disastrous infectious disease outbreaks.

Recently, concerns about the volatile hazardous compounds including acetaldehyde, methanol, and fusel oils in alcoholic beverages, which cause hangover such as headache and dizziness after consumption, have been raised. The volatile hazardous compounds might also lead to an increased incidence of liver diseases and even cancers with a high consumption of alcoholic beverages. Acetaldehyde is a volatile compound naturally found in alcoholic beverages and used as flavor in many foods. However this is also regarded as possibly being carcinogenic to humans. Furthermore, acetaldehyde with alcoholic consumption is recently classified as Group 1, carcinogenic to humans. On the other hand, methanol is generated from demethoxylation of pectin by pectinolytic enzyme during alcoholic fermentation. Higher alcohols occur naturally in alcoholic beverages as by-products of alcoholic fermentation and are generally regarded as important flavor compounds. In the current study, we reviewed on the health concern, maximum levels, analytical methods, and current levels of hazardous volatile compounds in alcoholic beverages.

Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)–cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27′s regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs.

The Common Reflection Surface (CRS) stack is a promising alternative stacking technique for reflection data. This technique is an automatic multi-parameter stack that does not require the explicit knowledge of a stacking velocity model. Furthermore, it significantly improves the signal-to-noise ratio as it considers more traces during the zero-offset stacking than the conventional CMP stack. Especially, for low-fold data in heterogeneous settings, the CRS stack is able to further enhance reflections. Recently, the CRS stack was applied to reflection data from sedimentary basins for oil and gas exploration purposes. It was not yet applied to crustal and deeper reflection data. We used the CRS stack for deep reflection data from the North German Basin. The data were acquired in the late 1970's and early 1980's with recording times down to 15 s TWT and mean CMP-folds of about 20. We reprocessed the data focusing on lower crustal and deeper structures. Compared to the conventional CMP processing of the 1980's, the reprocessed sections show an improved image quality at all time levels, i.e. from the sedimentary cover down to the crust and upper mantle. Especially, the reflections from the salt structures and Moho events are enhanced. Further, a constrained CRS stack was applied to the data using a stacking velocity model from conventional velocity analysis. The latter further improved the coherency and visibility of the reflections, especially in the area of the salt plugs and in the upper crust where multiples were suppressed. The data examples demonstrate that the CRS stack is a suitable tool for improving the quality of seismic images, especially for deep reflection data from low low-fold data acquisitions.

In order to design and develop the various silhouette of pants pattern for standardized pants patterns, this study is to classify the pants style by the silhouette and to characterize each pants pattern which are classified. Recent 37 ready-made pants patterns of various style were collected in order to analyze their silhouette from April to July 2007. Measurement of each region of the pants pattern were compared and analysed. After analyse the standard deviation, coefficient of variance, minimum, maximum, range about the measurement of each region of the pants pattern, major pattern design factors were extracted. Five major factors are the angle of center front line and center back line, the crotch extension, the position of center back line against center front line, the curvature of center back line, and amount of waist dart. As a result, pants style were grouped as the culottes, formal, basic and tight style after considering the extracted design factors, and analysing correlation, degree of dispersion of the measurement by part. As the silhouette of pants classification from culotte to tight, the fits are closer to the figure, crotch depth increases, crotch extensions are shorter, and angle of the center back increases. The shape of the connected front and back center lines is U-shape for culotte and is closer to V-shape as the silhouette becomes tight.

Reprocessing of seismic data of a salt stock family from the North German Basin provided new insights into the structural evolution of this area. The Common Reflection Surface (CRS) stack technique was applied to reprocess the reflection data acquired by the hydrocarbon industry in the 1980s. Due to the low fold of these data and the complex geology in the study area severe imaging challenges were encountered when the data were initially processed using conventional CMP stack. The CRS stack technique is particularly suited for low fold data in complex areas since it builds physically correct super gathers even if dipping structures are present. This leads to a considerably improved signal-to-noise ratio in the CRS stack compared to CMP stack sections. Moreover, the CRS stack parameters obtained during the stack form the foundation for a robust reflection tomography used for velocity model building. These models allowed the application of pre-stack and post-stack depth migration. The obtained depth images provided structural details not seen before, motivating an alternative view on the structural setting of the area. The image of the Jurassic salt plug indicates tectonics similar to observations in the Allertal region, where reverse faulting plays a major role in the evolution of the salt structures. As a consequence, shortening of the Mesozoic strata was included into the revised interpretation of the Glueckstadt Graben area. The new depth images also allowed an updated look on the petroleum system of this graben, which indicates new possible exploration targets.

Probably the most unusual class of proteins in nature is the intrinsically unstructured proteins (IUPs), because they are not structured yet play essential roles in protein-protein signaling. Many IUPs can bind different proteins, and in many cases, adopt different bound conformations. The p21 protein is a small IUP (164 residues) that is ubiquitous in cellular signaling, for example, cell cycle control, apoptosis, transcription, differentiation, and so forth; it binds to approximately 25 targets. How does this small, unstructured protein recognize each of these targets with high affinity? Here, we characterize residual structural elements of the C-terminal segment of p21 encompassing residues 145-164 using a combination of NMR measurements and molecular dynamics simulations. The N-terminal half of the peptide has a significant helical propensity which is recognized by calmodulin while the C-terminal half of the peptide prefers extended conformations that facilitate binding to the proliferating cell nuclear antigen (PCNA). Our results suggest that the final bound conformations of p21 (145-164) pre-exist in the free peptide even without its binding partners. While the conformational flexibility of the p21 peptide is essential for adapting to diverse binding environments, the intrinsic structural preferences of the free peptide enable promiscuous yet high affinity binding to a diverse array of molecular targets.

The influence of deep crustal processes on basin formation and evolution and its relation to current morphology is not well understood yet. A key feature to unravel these issues is a detailed seismic image of the crust. A part of the data recorded by the hydrocarbon industry in the late 1970s and 1980s in the North German Basin were released to the public recently. The seismic reflection data were recorded down to 15 s two-way travel time. The mean Common Midpoint fold of about 20 is relatively low compared to contemporary seismic acquisitions. The processing of the 1980s focussed on the sedimentary structures to explore the hydrocarbon potential of this area. We applied the Common Reflection Surface stack technique to the data sets, which is well suited for low-fold data. The reprocessing was focussed on the imaging of the subsedimentary crustal range. The reprocessed images show enhanced reflections, especially in the mid and lower crustal part. Also, the image of the salt structures in the graben area was improved. Furthermore, the reprocessed images indicate an almost flat Moho topography in the area of the Gluckstadt Graben and an additional lower crustal structure, which can be correlated with a high-density body found in recent gravity modeling studies.

Recently, Basic patterns with excellent body fitness and automation availability are required to be developed in order to automate the patterns of women`s clothes. In this study, this reference points, reference lines and segments were fixed onto 3D scan data for the lower body the women in their twenties, they were directly spread out to be 2D flat pattern to facilitate development into the design of slacks adhered closely to the human body such as special and highly-functional clothes, and then slacks 2D pattern was developed for the purpose of seeking scientific approach to the development into basic form slacks and 3d emotional pattern. For conversion of 3D pattern into 2D flat pattern, reference points and segments were created by using Rapid Form of 3D shape analysis software, and triangle mesh of the body surface of the created shape was developed with Auto CAD 2005. The correspondence between slacks and human body was examined by the fixation of major reference lines. Specially, the wearing characteristics of slacks were considered by the fixation of side lines in consideration of posture. As a result of using the way of development to constantly maintain the length while 3D triangle mesh is converted into 2D flat mesh, the shape was shown to be excellently reproduced, and the area of flat pattern was increased compared to the shape of parting plane. Also, the sunk-in curve like the brief line of front crotch length needed a cutting line when it was closely adhered, when mesh was overlapped, and the pattern area was smaller compared to the actual shape.

We synthesized 2'-deoxy-2'-[18F]fluorouridine (7) as a radiotracer for positron emission tomography from a new nosylate precursor (6). This new precursor was synthesized from uridine in four steps. The overall synthetic yield was 9.4% and we have high stability of >98% purity up to 6 months at 4°C. The optimal manual [18F]fluorination conditions were 30 mg of the precursor 6 in 500 µl of acetonitrile at 145°C for 15 min with 370 MBq of [18F]fluoride. The [18F]fluorination yield was 76.5±2.7% (n = 3). After hydrolysis of protecting groups with 1 N HCl and purification by HPLC, the overall radiochemical yield and purity were 26.5±1.4% and 98.2±2.5%, respectively. The preparation time was 70.0±10.5 min (n = 3 for each result). We also developed an automated method with a radiochemical yield and purity of 24.0±2.8 and 98.0±1.5% (n = 10) using a GE TracerLab MX chemistry module. This new nosylate precursor for 2'-deoxy-2'-[18F]fluorouridine synthesis showed higher radiochemical yields and reproducibility than previous methods. Copyright © 2006 John Wiley & Sons, Ltd.

p73 is a structural and functional homologue of the p53 tumor suppressor protein. Like p53, p73 induces apoptosis and cell cycle arrest and transactivates p53-responsive genes, conferring its tumor suppressive activity. In addition, p73 has unique roles in neuronal development and differentiation. The importance of p73-induced apoptosis lies in its capability to substitute the pro-apoptotic activity of p53 in various human cancer cells in which p53 is mutated or inactive. Despite the great importance of p73-induced apoptosis in cancer therapy, little is known about the molecular basis of p73-induced apoptosis. In this review, we discuss the p73 structures reported to date, detailed structural comparisons between p73 and p53, and current understanding of the transcription-dependent and -independent mechanisms of p73-induced apoptosis. [BMB Reports 2015; 48(2): 81-90]

Y.H. thanks Dr. Zhengding Su and Mr. Cheon-Gil Park for their help in experiments.; International audience; The Cip/Kip family of cyclin-dependent kinase (Cdk) inhibitors includes p21(Cip1) p27(Kip1) and d57(Kip2). Their kinase inhibitory activities are mediated by a homologous N-terminal kinaseinhibitory domain. The Cdk inhibitory activity and stability of p27 have been shown to be regulated by a two-step phosphorylation mechanism involving a tyrosine residue within the kinase inhibitory domain and a threonine residue within the flexible C-terminus. We show that these residues are conserved in p21 and p57, suggesting that a similar phosphorylation cascade regulates these Cdk inhibitors. However, the presence of a cyclin binding motif within its C-terminus alters the regulatory interplay between p21 and Cdk2/cyclin A, as well as its responses to tyrosine phosphorylation and altered p21:Cdk2/cyclin A stoichiometry. We also show that the Cip/Kip proteins can be phosphorylated in vitro by representatives of many non-receptor tyrosine kinase (NRTK) sub-families, suggesting that NRTKs may generally regulate the activity and stability of these Cdk inhibitors. Our results further suggest that the Cip/Kip proteins integrate signals from various NRTK pathways and cell cycle regulation

Cyclic AMP receptor protein (CRP) plays a key role in the regulation of more than 150 genes. CRP is allosterically activated by cyclic AMP and binds to specific DNA sites. A structural understanding of this allosteric conformational change, which is essential for its function, is still lacking because the structure of apo-CRP has not been solved. Therefore, we performed various NMR experiments to obtain apo-CRP structural data. The secondary structure of apo-CRP was determined by analyses of the NOE connectivities, the amide proton exchange rates, and the (1)H-(15)N steady-state NOE values. A combination of the CSI-method and TALOS prediction was also used to supplement the determination of the secondary structure of apo-CRP. This secondary structure of apo-CRP was compared with the known structure of cyclic AMP-bound CRP. The results suggest that the allosteric conformational change of CRP caused by cyclic AMP binding involves subunit realignment and domain rearrangement, resulting in the exposure of helix F onto the surface of the protein. Additionally, the results of the one-dimensional [(13)C]carbonyl NMR experiments show that the conformational change of CRP caused by the binding of cyclic GMP, an analogue of cyclic AMP, is different from that caused by cyclic AMP binding.

International audience; Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.

The classic structure-function paradigm has been challenged by a recently identified class of proteins: intrinsically disordered proteins (IDPs). Despite their lack of stable secondary or tertiary structure, IDPs are prevalent in all forms of life and perform myriad cellular functions, including signaling and regulation. Importantly, disruption of IDP homeostasis is associated with numerous human diseases, including cancer and neurodegeneration. Despite wide recognition of IDPs, the molecular mechanisms underlying their functions are not fully understood. Here we review the structural features and disorder-function relationships for p21 and p27, two cyclin-dependent kinase (Cdk) regulators involved in controlling cell division and fate. Studies of p21 bound to Cdk2/cyclin A revealed that a helix stretching mechanism mediates binding promiscuity. Further, investigations of Tyr88-phosphorylated p27 identified a signaling conduit that controls cell division and is disrupted in certain cancers. These mechanisms rely upon a balance between nascent structure in the free state, induced folding upon binding, and persistent flexibility within functional complexes. Although these disorder-function relationships are likely to be recapitulated in other IDPs, it is also likely that the vocabulary of their mechanisms is much more extensive than is currently understood. Further study of the physical properties of IDPs and elucidation of their links with function are needed to fully understand the mechanistic language of IDPs.

This paper presents new insights into the South American subduction zone from reprocessed seismic images. We applied a 3D Kirchhoff prestack depth migration scheme to data sets containing different narrow frequency ranges in order to extract additional details from seismic reflection images. This approach accounts for the effects of scattering on the seismic image, especially for structures below a heterogeneous overburden. The reflection image in such environments will differ significantly when focusing on different frequency ranges due to the frequency dependence of scattering that is likely to be present. The narrow frequency range images uncover reflectors in one frequency range that are masked in another range. Furthermore, the images enable for instance the characterization of the medium in terms of scatterer concentration and thus improve the structural interpretation. The analysis of these images might help to distinguish between small-scale structures in the high-frequency band and large-scale structures in the low-frequency band. We call this imaging approach Reflection Image Spectroscopy (RIS). We applied the RIS approach to the ANCORP'96 data set, an onshore deep seismic reflection profile across the South American Central Andes. The narrow frequency range images revealed additional details that we interpret as features directly linked to fluid migration processes in the subduction zone. Furthermore, structural details of the oceanic crust and the overlying mantle and crust are revealed. From the narrow-frequency range images we interpret that the top of the so called Nazca reflector at 70 km depth marks the upper limit of the hydrated mantle wedge, whereas the bottom of the reflector represents the top of the subducted oceanic crust. The compilation of our results with local earthquake data confirms this interpretation. Similar features observed in another deep seismic profile (PRECORP'95) support this interpretation, too. Furthermore, the RIS images show a highly reflective heterogeneous zone between the Nazca reflector at 70 km depth and a prominent mid-crustal Bright Spot (Quebrada Blanca Bright Spot) at about 30 km depth. We associate this zone with a complex network of ascending fluids or partial melts, initiated by ascending fluids released from the subducted oceanic plate. This observation links the Quebrada Bright Spot directly to the dehydrating oceanic plate.

The leucine zipper (LZ) domain of the HY5 transcription factor from Arabidopsis thaliana has unique primary structural properties, including major occupation by the Leu residues as well as two buried polar residues in the a positions and a localized distribution of charged and polar residues in the first three heptad repeats. In this study, we solved the crystal structure of the HY5 LZ domain and show that the peculiarities in the primary sequence yield unusual structural characteristics. For example, the HY5 LZ domain exhibits a bipartite charge distribution characterized by a highly negative electrostatic surface potential in its N-terminal half and a nearly neutral potential in its C-terminal half. The LZ N-terminal region also contains two consecutive putative trigger sites for dimerization of the coiled coils. In addition, two buried asparagines at a positions 19 and 33 in the HY5 LZ domain display distinct modes of polar interaction. Whereas Asn(19) shows a conformational flip-flop, Asn(33) is engaged in a permanent hydrogen bond network. CD spectropolarimetry and analytical ultracentrifugation experiments performed with versions of the HY5 LZ domain containing mutations in the a positions yielded further evidence that position a amino acid residues are crucial for achieving an oligomeric state and maintaining stability. However, a low correlation between position a amino acid preference, core packing geometry, and rotamer conformations suggests that the oligomeric state of the LZ domain is not governed entirely by known structural properties. Taken together, our results suggest structural factors conferring conformational integrity of the HY5 LZ homodimer that are more complicated than proposed previously.

The Arabidopsis HY5 protein is a basic leucine zipper (bZIP) transcription factor that promotes photomorphogenesis. HY5 binds directly to the promoters of light responsible element containing the G-box and thus regulates their transcriptional activity. The level and activity of HY5 are negatively regulated, in a light-dependent manner, by interaction with the COP1 protein, which targets HY5 for proteasome-mediated degradation in the nucleus. Despite its essential roles in plant development, no structural information exists for HY5. In this article, we report the first structural and biophysical characterization of HY5. Using limited proteolysis in combination with mass spectrometry, circular dichroism, and nuclear magnetic resonance spectroscopy, we have deduced that the N-terminal 77 amino acids of HY5 form a premolten globular structure, while amino acids 78-110, which constitute the basic region (BR) of the protein, exist in a molten globule state. Our studies also revealed that the overall structural features of full-length HY5 are dominated largely by the disordered N-terminal domain, despite the existence of a bZIP domain at its C-terminus. We propose that HY5 is a member of the intrinsically unstructured protein (IUP) family, and that HY5 functions as an unstructured protein and benefits from being the same, in vivo.

Modern seismic imaging methods were used to study the subduction processes of the South American convergent margin. The data came from reflection and from wide-angle/refraction experiments acquired within the framework of the Collaborative Research Center SFB 267 'Deformation Processes in the Andes'. Two areas of differing character and subduction type were investigated: an erosive margin to the north (19-26° S) and an accretionary margin to the south (36-40° S). Results from different seismic models yield three main transects that give an overall impression about the internal structure below the Chilean margin. At the erosive margin, we find that the upper part of the subducting oceanic lithosphere is characterized by a horst-and-graben structure that coincides with the coupling zone between the plates. Strong coupling between oceanic crust and fore-arc in the case of a horst-continent collision is also indicated by plate-parallel faults beneath the lower continental slope, which we interpret as the upper parts of the subduction channel. In this context, the subduction channel represents the downgoing Nazca Plate as well as those portions of the continental crust which moved landward. Low seismic velocities below the coastline also represent parts of the subduction channel and of the hydrofractured base of the upper crust near the plate interface. Between 45 and 60 km depth, a double reflection zone marks the upper and lower boundary of the subducted oceanic crust. Off southern Chile, the ocean bottom is characterized by relatively smooth morphology. In contrast, in the south, the trench is filled with sediments and contains an axial channel (Figs. 7.16 to 7.18) extending in N-S direction along the trench axis within the investigation area. The periodicity of the reflected seismic signal within these sediments correlates with the main glacial cycle during the Quaternary. The recent accretionary wedge is built up from strongly heterogeneous unconsolidated sediments. Frontal accretion takes place within the southern working area except for the region around the Arauco Peninsula, which shows uplift due to basal accretion and antiformal stacking. Below the Coastal Cordillera, the heterogeneity of the modern accretionary wedge and the antiformal stack structure of the Permo-Triassic accretionary wedge complicate imaging at depths greater than about 30 km. Thus, we obtain an image of the top of the subduction channel as a thin reflector segment only to about 25 km depth.

[1] A 400-km-long seismic reflection profile (Andean Continental Research Project 1996 (ANCORP'96)) and integrated geophysical experiments (wide-angle seismology, passive seismology, gravity, and magnetotelluric depth sounding) across the central Andes (21°S) observed subduction of the Nazca plate under the South American continent. An east dipping reflector (Nazca Reflector) is linked to the down going oceanic crust and shows increasing downdip intensity before gradual breakdown below 80 km. We interpret parts of the Nazca Reflector as a fluid trap located at the front of recent hydration and shearing of the mantle, the fluids being supplied by dehydration of the oceanic plate. Patches of bright (Quebrada Blanca Bright Spot) to more diffuse reflectivity underlie the plateau domain at 15–30 km depth. This reflectivity is associated with a low-velocity zone, P to S wave conversions, the upper limits of high conductivity and high Vp/Vs ratios, and to the occurrence of Neogene volcanic rocks at surface. We interpret this feature as evidence of widespread partial melting of the plateau crust causing decoupling of the upper and lower crust during Neogene shortening and plateau growth. The imaging properties of the continental Moho beneath the Andes indicate a broad transitional character of the crust-mantle boundary owing to active processes like hydration of mantle rocks (in the cooler parts of the plate margin system), magmatic underplating and intraplating under and into the lowermost crust, mechanical instability at Moho, etc. Hence all first-order features appear to be related to fluid-assisted processes in a subduction setting.

[1] This paper presents the results of Kirchhoff prestack depth migration applied to two onshore deep seismic reflection data sets (ANCORP'96 and PRECORP'95). The prestack depth migration method was implemented in 3D (ANCORP) and in 2D (PRECORP), respectively, from topography. Selective stacking of the migrated depth slices yielded a 3D depth volume (ANCORP) and a 2D depth section (PRECORP), respectively. An additional “offline stacking” provided a final 370 km long 2D depth section (ANCORP). In this paper a 180 km long depth section will be presented. At the beginning of the ANCORP section a double reflection zone is observed, which is associated with the upper and lower boundary of the oceanic crust. Except for some areas a nearly complete image of the Nazca reflector at depths between 60–90 km has been obtained. Moreover, one Bright Spot in each section has been detected: the Quebrada Blanca Bright Spot (QBBS, ANCORP) and the Calama Bright Spot (CBS, PRECORP). The reprocessing yielded two new aspects regarding these structures: Besides the west dip of the QBBS, which was already known from standard poststack processing results, a 3D analysis of the ANCORP data set shows an additional north-dipping trend of the QBBS. Furthermore, the CBS is discovered for the first time.

Cellular materials pass into and out of the nucleus of a eukaryotic cell through pores in the nuclear membrane. Each nuclear pore is a complex of ∼400 modular polypeptide chains [nucleoporins (Nups)] that form a cylindrical structure ( 1 ). The pore functions as a semipermeable filter that allows free diffusion of ions, small molecules, and macromolecules

The conformational preferences of AnxI(N26), a peptide corresponding to residues 2-26 of human annexin I, were investigated using CD and NMR spectroscopy. CD results showed that AnxI(N26) adopts a mainly alpha-helical conformation in membrane-mimetic environments, TFE/water and SDS micelles, while a predominantly random structure with slight helical propensity in aqueous buffer. The helical region of AnxI(N26) showed a nearly identical conformation between in TFE/water and in SDS micelles, except for the orientation of the Trp-12 side-chain, which was quite different between the two. The N-terminal region of the AnxI(N26) helix showed a typical amphipathic nature, which could be stabilized by the neighboring hydrophobic cluster. The helical stability of the peptide in SDS micelles was increased by addition of calcium ions. These results suggest that the N-terminal tail domain of human annexin I interacts with biological membranes in a partially calcium-dependent manner.

Despite the numerous metabolic studies on obesity, gender bias in obesity has rarely been investigated. Here, we report the metabolomic analysis of obesity by using leptin-deficient ob/ob mice based on the gender. Metabolomic analyses of urine and serum from ob/ob mice compared with those from C57BL/6J lean mice, based on the (1)H NMR spectroscopy in combination with multivariate statistical analysis, revealed clear metabolic differences between obese and lean mice. We also identified 48 urine and 22 serum metabolites that were statistically significantly altered in obese mice compared to lean controls. These metabolites are involved in amino acid metabolism (leucine, alanine, ariginine, lysine, and methionine), tricarbocylic acid cycle and glucose metabolism (pyruvate, citrate, glycolate, acetoacetate, and acetone), lipid metabolism (cholesterol and carnitine), creatine metabolism (creatine and creatinine), and gut-microbiome-derived metabolism (choline, TMAO, hippurate, p-cresol, isobutyrate, 2-hydroxyisobutyrate, methylamine, and trigonelline). Notably, our metabolomic studies showed distinct gender variations. The obese male mice metabolism was specifically associated with insulin signaling, whereas the obese female mice metabolism was associated with lipid metabolism. Taken together, our study identifies the biomarker signature for obesity in ob/ob mice and provides biochemical insights into the metabolic alteration in obesity based on gender.

The delta(5)-3-ketosteroid isomerase from Pseudomonas putida biotype B has been crystallized. The crystals belong to the space group P2(1)2(1)2(1) with unit cell dimensions of a = 36.48 angstrom, b = 74.30 angstrom, c = 96.02 angstrom, and contain one homodimer per asymmetric unit. Native diffraction data to 2.19 Angstrom resolution have been obtained from one crystal at room temperature indicating that the crystals are quite suitable for structure determination by multiple isomorphous replacement.

This paper describes an extension to true amplitude prestack Kirchho migration which takes into account scattering losses due to the propagation through a statistically heterogeneous overburden. An additional weighting factor is introduced which is a function of the length of the travel path between source and receiver and the statistical parameters of the overburden (standard deviation and correlation length of the velocity heterogeneities). The practical aspects of the implementation are described and the method is tested on a synthetic data set. This example shows that it is important, simple and eAEcient to account for scattering losses during migration.