83 results on '"Tadashi Ando"'
Search Results
2. Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNATyr with an extra guanosine residue at the 5ʹ-terminus
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Ryohei Noguchi, Tadashi Ando, Takahiro Hashimoto, Tatsuya Horikoshi, Sam-Yong Park, Ryodai Kurihara, Takuya Umehara, Kenichi Kamata, Hiromi Mutsuro-Aoki, Yuki Watanabe, Koji Tamura, and Hiroki Noguchi
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biology ,Base pair ,Stereochemistry ,Mutant ,Biophysics ,Guanosine ,Methanocaldococcus jannaschii ,Aminoacylation ,Cell Biology ,Thermus thermophilus ,biology.organism_classification ,environment and public health ,Biochemistry ,enzymes and coenzymes (carbohydrates) ,chemistry.chemical_compound ,chemistry ,parasitic diseases ,Transfer RNA ,Nanoarchaeum equitans ,Molecular Biology - Abstract
tRNATyr of Nanoarchaeum equitans has a remarkable feature with an extra guanosine residue at the 5ʹ-terminus. However, the N. equitans tRNATyr mutant without extra guanosine at the 5ʹ-end was tyrosylated by tyrosyl-tRNA synthase (TyrRS). We solved the crystal structure of N. equitans TyrRS at 2.80 A resolution. By comparing the present solved structure with the complex structures TyrRS with tRNATyr of Thermus thermophilus and Methanocaldococcus jannaschii, an arginine substitution mutant of N. equitans TyrRS at Ile200 (I200R), which is the putative closest candidate to the 5ʹ-phosphate of C1 of N. equitans tRNATyr, was prepared. The I200R mutant tyrosylated not only wild-type tRNATyr but also the tRNA without the G-1 residue. Further tyrosylation analysis revealed that the second base of the anticodon (U35), discriminator base (A73), and C1:G72 base pair are strong recognition sites.
- Published
- 2021
3. Molecular Dynamics Simulation of the Resist Filling Process in UV-nanoimprint Lithography
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Ryosuke Imoto, Tadashi Ando, Hiroki Uchida, Takao Okabe, and Jun Taniguchi
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Molecular dynamics ,Materials science ,Polymers and Plastics ,Resist ,law ,Scientific method ,Organic Chemistry ,Materials Chemistry ,Nanotechnology ,Nanoimprint lithography ,law.invention - Published
- 2021
4. Hi-CO: 3D genome structure analysis with nucleosome resolution
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David G. Priest, Yuichi Taniguchi, Masae Ohno, and Tadashi Ando
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Saccharomyces cerevisiae ,Locus (genetics) ,Computational biology ,Molecular Dynamics Simulation ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Chromosome conformation capture ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Nucleosome ,030304 developmental biology ,Physics ,0303 health sciences ,Base Sequence ,biology ,Resolution (electron density) ,High-Throughput Nucleotide Sequencing ,biology.organism_classification ,Nucleosomes ,chemistry ,biology.protein ,Genome, Fungal ,030217 neurology & neurosurgery ,DNA ,Micrococcal nuclease - Abstract
The nucleosome is the basic organizational unit of the genome. The folding structure of nucleosomes is closely related to genome functions, and has been reported to be in dynamic interplay with binding of various nuclear proteins to genomic loci. Here, we describe our high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) technology to derive 3D nucleosome positions with their orientations at every genomic locus in the nucleus. This technology consists of an experimental procedure for nucleosome proximity analysis and a computational procedure for 3D modeling. The experimental procedure is based on an improved method of high-throughput chromosome conformation capture (Hi-C) analysis. Whereas conventional Hi-C allows spatial proximity analysis among genomic loci with 1-10 kbp resolution, our Hi-CO allows proximity analysis among DNA entry or exit points at every nucleosome locus. This analysis is realized by carrying out ligations among the entry/exit points in every nucleosome in a micrococcal-nuclease-fragmented genome, and by quantifying frequencies of ligation products with next-generation sequencing. Our protocol has enabled this analysis by cleanly excluding unwanted non-ligation products that are abundant owing to the frequent genome fragmentation by micrococcal nuclease. The computational procedure is based on simulated annealing-molecular dynamics, which allows determination of optimized 3D positions and orientations of every nucleosome that satisfies the proximity ligation data sufficiently well. Typically, examination of the Saccharomyces cerevisiae genome with 130 million sequencing reads facilitates analysis of a total of 66,360 nucleosome loci with 6.8 nm resolution. The technique requires 2-3 weeks for sequencing library preparation and 2 weeks for simulation.
- Published
- 2021
5. Mechanism of Chiral-Selective Aminoacylation of an RNA Minihelix Explored by QM/MM Free-Energy Simulations
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Tadashi Ando and Koji Tamura
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homochirality of amino acids ,aminoacylation ,RNA ,QM/MM ,MD ,Space and Planetary Science ,Paleontology ,General Biochemistry, Genetics and Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Abstract
Aminoacylation of a primordial RNA minihelix composed of D-ribose shows L-amino acid preference over D-amino acid without any ribozymes or enzymes. This preference in the amino acylation reaction likely plays an important role in the establishment of homochirality in L-amino acid in modern proteins. However, molecular mechanisms of the chiral selective reaction remain unsolved mainly because of difficulty in direct observation of the reaction at the molecular scale by experiments. For seeking a possible mechanism of the chiral selectivity, quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations of the aminoacylation reactions in a modeled RNA were performed to investigate differences in their free-energy profiles along the reactions for L- and D-alanine and its physicochemical origin. The reaction is initiated by approaching a 3′-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. The QM/MM umbrella sampling MD calculations showed that the height of the free-energy barrier for L-alanine aminoacylation reaction was 17 kcal/mol, which was 9 kcal/mol lower than that for the D-alanine system. At the transition state, the distance between the negatively charged 3′-oxygen and the positively charged amino group of L-alanine was shorter than that of D-alanine, which was caused by the chirality difference of the amino acid. These results indicate that the transition state for L-alanine is more electrostatically stabilized than that for D-alanine, which would be a plausible mechanism previously unexplained for chiral selectivity in the RNA minihelix aminoacylation.
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- 2023
6. Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center
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Mai Kawabata, Kentaro Kawashima, Hiromi Mutsuro-Aoki, Tadashi Ando, Takuya Umehara, and Koji Tamura
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endocrine system diseases ,Space and Planetary Science ,tRNA ,minihelix ,peptide bond formation ,ribosomal symmetrical region ,proto-ribosome ,Paleontology ,General Biochemistry, Genetics and Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Abstract
The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis depended on both the existence of the dimeric P1c2UGGU and the sequence complementarity between the ACCA-3′ sequence of the minihelix. Thus, the tRNA-like structures derived from the PTC could have originated as a scaffold of aminoacyl-minihelices for peptide bond formation through an interaction of the CCA sequence of minihelices. Moreover, with the same origin, some would have evolved to constitute the present PTC of the ribosome, and others to function as present tRNAs.
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- 2022
7. The crystal structure of the tetrameric human vasohibin-1–SVBP complex reveals a variable arm region within the structural core
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Akihito Ikeda, Yasufumi Sato, Yasuhiro Suzuki, Tadashi Ando, Seia Urata, and Tatsuya Nishino
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Models, Molecular ,vasohibin ,Cell Cycle Proteins ,Crystal structure ,Crystallography, X-Ray ,Hydrophobic effect ,Carboxypeptidase activity ,03 medical and health sciences ,0302 clinical medicine ,Protein Domains ,Structural Biology ,Humans ,Molecule ,030304 developmental biology ,MD simulations ,0303 health sciences ,Chemistry ,Hydrogen bond ,protein complex ,microtubule modification ,Substrate (chemistry) ,VASH1–SVBP complex ,small vasohibin-binding protein ,X-ray crystal structure ,Research Papers ,Heterotetramer ,Intramolecular force ,Biophysics ,Protein Multimerization ,Carrier Proteins ,030217 neurology & neurosurgery - Abstract
Vasohibin-1 and small vasohibin-binding protein (SVBP) form an intermolecular heterotetramer in the crystal. The heterotetramer was stabilized by exchange of the conserved N-terminal region., Vasohibins regulate angiogenesis, tumor growth, metastasis and neuronal differentiation. They form a complex with small vasohibin-binding protein (SVBP) and show tubulin tyrosine carboxypeptidase activity. Recent crystal structure determinations of vasohibin–SVBP complexes have provided a molecular basis for complex formation, substrate binding and catalytic activity. However, the regulatory mechanism and dynamics of the complex remain elusive. Here, the crystal structure of the VASH1–SVBP complex and a molecular-dynamics simulation study are reported. The overall structure of the complex was similar to previously reported structures. Importantly, however, the structure revealed a domain-swapped heterotetramer that was formed between twofold symmetry-related molecules. This heterotetramerization was stabilized by the mutual exchange of ten conserved N-terminal residues from the VASH1 structural core, which was intramolecular in other structures. Interestingly, a comparison of this region with previously reported structures revealed that the patterns of hydrogen bonding and hydrophobic interactions vary. In the molecular-dynamics simulations, differences were found between the heterotetramer and heterodimer, where the fluctuation of the N-terminal region in the heterotetramer was suppressed. Thus, heterotetramer formation and flexibility of the N-terminal region may be important for enzyme activity and regulation.
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- 2020
8. Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA
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Tatsuya, Horikoshi, Hiroki, Noguchi, Takuya, Umehara, Hiromi, Mutsuro-Aoki, Ryodai, Kurihara, Ryohei, Noguchi, Takahiro, Hashimoto, Yuki, Watanabe, Tadashi, Ando, Kenichi, Kamata, Sam-Yong, Park, and Koji, Tamura
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Models, Molecular ,RNA, Transfer, Tyr ,Guanosine ,Tyrosine-tRNA Ligase ,Archaeal Proteins ,Nanoarchaeota ,Aminoacylation ,Protein Structural Elements ,Crystallography, X-Ray - Abstract
tRNA
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- 2021
9. Molecular Dynamics Study on Behavior of Resist Molecules in UV-Nanoimprint Lithography Filling Process
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Jun, Iwata and Tadashi, Ando
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General Chemical Engineering ,nanoimprint lithography ,UV-curable resin ,molecular dynamics ,General Materials Science - Abstract
In this study, we performed molecular dynamics (MD) simulations of the filling process of few-nanometer-wide trenches with various resist materials in ultraviolet nanoimprint lithography (UV-NIL) to identify the main molecular features necessary for a successful filling process. The 2- and 3-nm wide trenches were successfully filled with the resist materials that had (experimentally determined) viscosities less than 10 mPa·s. The resist composed of a three-armed bulky and highly viscous molecule could not fill the trenches. The radius of gyration of this molecule was smaller than half of the distance in which the first peak of its radial distribution function occurred. The available shapes of 1,6-hexanediol diacrylate (HDDA) and tri(propylene glycol) diacrylate (TPGDA), which are linear photopolymers, were compared to reveal that TPGDA is more flexible and adopts more conformations than HDDA. The terminal functional groups of TPGDA can be close due to its flexibility, which would increase the probability of intramolecular crosslinking of the molecule. This simulation result could explain the difference in hardness between the UV-cured HDDA and TPGDA based materials observed by experiments. The findings revealed by our MD simulations provide useful information for selecting and designing resists for fine patterning by UV-NIL.
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- 2022
10. Tohoku Region
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Hiroshi Fujii, Shizuka Mori, Yumi Matsumoto, Yuka Sasaki, Chiharu Ito, Shinpei Nakagawa, Tadashi Takahashi, Nobuhiko Matsuyama, Mizuhiko Nishida, Yoshihiro Kaneta, Haruki Fujisawa, Norimasa Tanikawa, null Tadashi Ando, Hiroyuki Shiono, Teruo Shima, Masakazu Aoyama, Mikio Morioka, null Takayuki Ando, Keitaro Tawaraya, Takumi Sato, Fumiaki Takakai, Takashi Sato, Tomoki Takahashi, Masashi Ito, Weiguo Cheng, Miyuki Nakajima, Toyoaki Ito, Hisashi Nasukawa, Toru Uno, Ryousuke Tajima, Tomonori Abe, Takuro Shinano, Takashi Saito, Shokichi Wakabayashi, Shigeto Fujimura, Hisaya Matsunami, Takashi Hirayama, Katashi Kubo, Takeshi Ota, Masanori Saito, Tetsuya Katagiri, and Kazuto Ando
- Published
- 2021
11. A patient with a 6q22.1 deletion and a phenotype of non-progressive early-onset generalized epilepsy with tremor
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Kenichi Nagamatsu, Noriko Miyake, Kazutaka Jin, Naomichi Matsumoto, Mitsugu Uematsu, Naomi Hino-Fukuyo, Tadashi Ando, Hiroyuki Yokoyama, Mitsutoshi Munakata, Futoshi Sekiguchi, Kazuhiro Haginoya, and Shigeo Kure
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Neurophysiology and neuropsychology ,Pediatrics ,medicine.medical_specialty ,Deep brain stimulation ,medicine.medical_treatment ,DBS ,Propranolol ,Myoclonic tremor ,Article ,Behavioral Neuroscience ,Intellectual disability ,medicine ,Seizure control ,Generalized epilepsy ,RC346-429 ,Early onset ,Valproic Acid ,business.industry ,QP351-495 ,medicine.disease ,Phenotype ,nervous system diseases ,Neurology ,NUS1 ,Neurology (clinical) ,Neurology. Diseases of the nervous system ,business ,medicine.drug ,6q22.1 deletion - Abstract
Highlights • Generalized epilepsy with tremor phenotype ss a clinical marker of 6q22.1 microdeletion. • Deep brain stimulation may be applicable choince for intractable myoclonic tremor. • Over activation of basal ganglia may be related to this patient's symptoms., We report a patient with a 6q22.1 deletion, who presented with a rare syndrome of generalized epilepsy, myoclonic tremor, and intellectual disability. There was no clinical progression after follow-up for more than 10 years. Our report presents the genetic basis for a phenotype involving a non-progressive generalized epilepsy with tremor. The efficacy of valproic acid for seizure control and the partial efficacy of deep brain stimulation with propranolol for myoclonic tremor is detailed.
- Published
- 2021
12. ALGORITHMS FOR BROWNIAN DYNAMICS SIMULATION
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Yuji Sugita and Tadashi Ando
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Computer science ,Brownian dynamics ,Statistical physics - Published
- 2020
13. G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases
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Takuya Umehara, Tadashi Ando, Ryodai Kurihara, Koji Tamura, Haruka Takano, Kei Tokunaga, Hiromi Mutsuro-Aoki, Toru Matsuoka, Hiroki Takahashi, Misa Arutaki, Tomomasa Ohno, and Ayako Inami
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Alanine ,endocrine system ,biology ,Aminoacyl tRNA synthetase ,Base pair ,Archaeal Proteins ,Alanine-tRNA Ligase ,RNA ,Aminoacylation ,biology.organism_classification ,Tetraloop ,Amino Acyl-tRNA Synthetases ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Transfer RNA ,Genetics ,Nanoarchaeota ,Nucleic Acid Conformation ,Nanoarchaeum equitans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Abstract
Nanoarchaeum equitans is a species of hyperthermophilic archaea with the smallest genome size. Its alanyl-tRNA synthetase genes are split into AlaRS-α and AlaRS-β, encoding the respective subunits. In the current report, we surveyed N. equitans AlaRS-dependent alanylation of RNA minihelices, composed only of the acceptor stem and the T-arm of tRNAAla. Combination of AlaRS-α and AlaRS-β showed a strong alanylation activity specific to a single G3:U70 base pair, known to mark a specific tRNA for charging with alanine. However, AlaRS-α alone had a weak but appreciable alanylation activity that was independent of the G3:U70 base pair. The shorter 16-mer RNA tetraloop substrate mimicking only the first four base pairs of the acceptor stem of tRNAAla, but with C3:G70 base pair, was also successfully aminoacylated by AlaRS-α. The end of the acceptor stem, including CCA-3' terminus and the discriminator A73, was able to function as a minimal structure for the recognition by the enzyme. Our findings imply that aminoacylation by N. equitans AlaRS-α may represent a vestige of a primitive aminoacylation system, before the appearance of the G3:U70 pair as an identity element for alanine.
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- 2019
14. Correction to: G:U‑Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl‑tRNA Synthetase: An Insight into the Evolution of Aminoacyl‑tRNA Synthetases
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Misa Arutaki, Tadashi Ando, Ryodai Kurihara, Tomomasa Ohno, Kei Tokunaga, Toru Matsuoka, Hiroki Takahashi, Ayako Inami, Hiromi Aoki, Koji Tamura, Haruka Takano, and Takuya Umehara
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biology ,Aminoacyl tRNA synthetase ,RNA ,Aminoacylation ,Alanyl-tRNA Synthetase ,biology.organism_classification ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Molecular evolution ,Genetics ,Nanoarchaeum equitans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Published
- 2020
15. GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
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Motoshi Kamiya, Koichi Tamura, Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Yasuhiro Matsunaga, Tadashi Ando, and Yuji Sugita
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0301 basic medicine ,Quantitative Biology::Biomolecules ,010304 chemical physics ,Computer science ,String (computer science) ,Graphics processing unit ,General Chemistry ,01 natural sciences ,Power (physics) ,Computational science ,Modeling and simulation ,03 medical and health sciences ,Computational Mathematics ,symbols.namesake ,Molecular dynamics ,Variable (computer science) ,030104 developmental biology ,0103 physical sciences ,symbols ,Umbrella sampling ,Simulation ,Gibbs sampling - Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc.
- Published
- 2017
16. Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation
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Hiromi Hayashi, Sam-Yong Park, Hiromi Doi, Tomoko Shoji, Hiroki Noguchi, Alma Fujisawa, Arnout Voet, Koji Tamura, Rina Hanabusa, Tadashi Ando, Risako Toki, Hideaki Miyake, Hiromi Mutsuro-Aoki, and Takuya Umehara
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0301 basic medicine ,Glycine-tRNA Ligase ,Models, Molecular ,Protein Conformation ,Archaeal Proteins ,Mutant ,Biophysics ,Aminoacylation ,Crystallography, X-Ray ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,RNA, Transfer ,Nanoarchaeum equitans ,Nucleotide ,Amino Acid Sequence ,Guanidine ,Molecular Biology ,Alanine ,chemistry.chemical_classification ,DNA ligase ,biology ,Chemistry ,Cell Biology ,biology.organism_classification ,030104 developmental biology ,030220 oncology & carcinogenesis ,Transfer RNA ,Nanoarchaeota ,Sequence Alignment - Abstract
This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans — a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long β-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNAGly was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNAGly with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNAGly elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNAGly G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS.
- Published
- 2019
17. Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation
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Shunichi Takahashi, Koji Tamura, and Tadashi Ando
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0301 basic medicine ,Static Electricity ,Glycine ,Aminoacylation ,Geometry ,Biology ,Dihedral angle ,Molecular Dynamics Simulation ,01 natural sciences ,Chemical reaction ,Phosphates ,03 medical and health sciences ,chemistry.chemical_compound ,Chemical Biology and Nucleic Acid Chemistry ,0103 physical sciences ,Genetics ,Amino Acids ,Alanine ,010304 chemical physics ,Oligonucleotide ,RNA ,Stereoisomerism ,Oxygen ,030104 developmental biology ,chemistry ,Nucleic Acid Conformation ,Homochirality ,Methyl group - Abstract
The origin of homochirality in L-amino acid in proteins is one of the mysteries of the evolution of life. Experimental studies show that a non-enzymatic aminoacylation reaction of an RNA minihelix has a preference for L-amino acid over D-amino acid. The reaction initiates by approaching of a 3′-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. Here, employing molecular dynamics simulations, we examined the possible mechanisms that determine this chiral selectivity. The simulation system adopted a geometry required for the chemical reaction to occur more frequently with L-alanine than that with D-alanine. For L-alanine, the structure with this geometry was formed by a combination of stable dihedral angles along alanyl phosphate backbone with a canonical RNA structure, where the methyl group of alanine was placed on the opposite side of the approaching 3′-hydroxyl group with respect to the carbonyl plane. For D-alanine, the methyl group and the 3′-hydroxyl group were placed on the same side with respect to the carbonyl plane, which significantly decreased its ability to approach 3′-oxygen close to the carbonyl carbon compared to L-alanine. The mechanism suggested herein can explain experimentally observed chiral preferences.
- Published
- 2018
18. Left–right asymmetry is formed in individual cells by intrinsic cell chirality
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Kiichiro Taniguchi, Tadashi Ando, Shunya Hozumi, Mitsutoshi Nakamura, Kenji Matsuno, Junichi Kikuta, Ryo Hatori, Naotaka Nakazawa, Masaru Ishii, and Takeshi Sasamura
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Embryology ,Mutant ,Genes, Insect ,Biology ,Mechanotransduction, Cellular ,Models, Biological ,Animals, Genetically Modified ,Motor protein ,Myosin Type I ,Myosin ,Animals ,Drosophila Proteins ,Computer Simulation ,Cell Shape ,Actin ,Body Patterning ,Mosaicism ,Cell Polarity ,Hindgut ,Anatomy ,biology.organism_classification ,Embryonic stem cell ,Cell biology ,Drosophila melanogaster ,Mutation ,Chirality (chemistry) ,Digestive System ,Developmental Biology - Abstract
Many animals show left-right (LR) asymmetric morphology. The mechanisms of LR asymmetric development are evolutionarily divergent, and they remain elusive in invertebrates. Various organs in Drosophila melanogaster show stereotypic LR asymmetry, including the embryonic gut. The Drosophila embryonic hindgut twists 90° left-handedly, thereby generating directional LR asymmetry. We recently revealed that the hindgut epithelial cell is chiral in shape and other properties; this is termed planar cell chirality (PCC). We previously showed by computer modeling that PCC is sufficient to induce the hindgut rotation. In addition, both the PCC and the direction of hindgut twisting are reversed in Myosin31DF (Myo31DF) mutants. Myo31DF encodes Drosophila MyosinID, an actin-based motor protein, whose molecular functions in LR asymmetric development are largely unknown. Here, to understand how PCC directs the asymmetric cell-shape, we analyzed PCC in genetic mosaics composed of cells homozygous for mutant Myo31DF, some of which also overexpressed wild-type Myo31DF. Wild-type cell-shape chirality only formed in the Myo31DF-overexpressing cells, suggesting that cell-shape chirality was established in each cell and reflects intrinsic PCC. A computer model recapitulating the development of this genetic mosaic suggested that mechanical interactions between cells are required for the cell-shape behavior seen in vivo. Our mosaic analysis also suggested that during hindgut rotation in vivo, wild-type Myo31DF suppresses the elongation of cell boundaries, supporting the idea that cell-shape chirality is an intrinsic property determined in each cell. However, the amount and distribution of F-actin and Myosin II, which are known to help generate the contraction force on cell boundaries, did not show differences between Myo31DF mutant cells and wild-type cells, suggesting that the static amount and distribution of these proteins are not involved in the suppression of cell-boundary elongation. Taken together, our results suggest that cell-shape chirality is intrinsically formed in each cell, and that mechanical force from intercellular interactions contributes to its formation and/or maintenance.
- Published
- 2014
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19. Ion Selectivity Mechanism of Escherichia Coli OmpF Porin: a Molecular Dynamics Simulation/ free Energy Calculation Study
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Ichiro Yamato, Tadashi Ando, Atsushi Suenaga, and Yasuhiro Matsuura
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Molecular dynamics ,Ion selectivity ,Chemical physics ,Chemistry ,Porin ,medicine ,Conductance ,medicine.disease_cause ,Escherichia coli ,Mechanism (sociology) ,Energy (signal processing) - Published
- 2014
20. Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model
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Michael Feig, Yuji Sugita, Isseki Yu, and Tadashi Ando
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0301 basic medicine ,Cytoplasm ,genetic structures ,Chemistry ,Macromolecular Substances ,Thermodynamics ,Proteins ,Mycoplasma genitalium ,Molecular Dynamics Simulation ,Crowding ,Article ,Surfaces, Coatings and Films ,03 medical and health sciences ,Molecular dynamics ,030104 developmental biology ,Materials Chemistry ,Brownian dynamics ,Protein folding ,Physical and Theoretical Chemistry ,Macromolecular crowding ,Macromolecule - Abstract
The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell. Here, we evaluate the free energy changes upon macromolecular association in a cell-like inhomogeneous crowding system via a theory of hard-sphere fluids and free energy calculations using Brownian dynamics trajectories. The inhomogeneous crowding model based on 41 different types of macromolecules represented by spheres with different radii mimics the physiological concentrations of macromolecules in the cytoplasm of Mycoplasma genitalium. The free energy changes of macromolecular association evaluated by the theory and simulations were in good agreement with each other. The crowder size distribution affects both specific and non-specific molecular associations, suggesting that not only the volume fraction but also the size distribution of macromolecules are important factors for evaluating in vivo crowding effects. This study relates in vitro experiments on macromolecular crowding to in vivo crowding effects by using the theory of hard-sphere fluids with crowder-size heterogeneity.
- Published
- 2016
21. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
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Takaharu Mori, Jaewoon Jung, Michael Feig, Tadashi Ando, Isseki Yu, Ryuhei Harada, and Yuji Sugita
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0301 basic medicine ,Cytoplasm ,Macromolecular Substances ,QH301-705.5 ,Science ,Systems biology ,Mycoplasma genitalium ,Molecular Dynamics Simulation ,Biology ,Bioinformatics ,General Biochemistry, Genetics and Molecular Biology ,native state stability ,03 medical and health sciences ,Spatio-Temporal Analysis ,None ,Biology (General) ,General Immunology and Microbiology ,crowding effects ,General Neuroscience ,diffusion ,Dynamics (mechanics) ,Rigid structure ,General Medicine ,Biophysics and Structural Biology ,Small molecule ,whole-cell modeling ,quinary interactions ,030104 developmental biology ,Structural biology ,metabolite dynamics ,Medicine ,Whole cell ,Biological system ,Computational and Systems Biology ,Research Article ,Macromolecule - Abstract
Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001, eLife digest Much of the work that has been done to understand how cells work has involved studying parts of a cell in isolation. This is particularly true of studies that have examined the arrangement of atoms in large molecules with elaborate structures like proteins or DNA. However, cells are densely packed with many different molecules and there is little proof that proteins keep the same structures inside cells that they have when they are studied alone. To really understand how cells work, new ways to understand how molecules behave inside cells are needed. While this cannot be achieved directly, technology has now reached the stage where we can, to some extent, study living cells by recreating them virtually. Simulated cells can copy the atomic details of all the molecules in a cell and can estimate how different molecules might behave together. Yu et al. have now developed a computer simulation of part of a cell from the bacterium, Mycoplasma genitalium, one of the simplest forms of life on Earth. This model suggested new possible interactions between molecules inside cells that cannot currently be studied in real cells. The model shows that some proteins have a much less rigid structure in cells than they do in isolation, whilst others are able to work together more closely to carry out certain tasks. Finally, the model predicted that small molecules such as food, water and drugs would move more slowly through cells as they become stuck or trapped by larger molecules. These results could be particularly important in helping to improve drug design. Currently the simulations are limited, and can only model parts of simple cells for less than a thousandth of a second. However, in future it should be possible to recreate larger and more complex cells, including human cells, for longer periods of time. These could be used to better study human diseases and help to design new treatments. The ultimate goal is to simulate a whole cell in full detail by combining all the available experimental data. DOI: http://dx.doi.org/10.7554/eLife.19274.002
- Published
- 2016
22. Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs
- Author
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Tadashi Ando, Yamato Yoshida, Yuichi Taniguchi, Masae Ohno, David G. Priest, and Vipin Kumar
- Subjects
0303 health sciences ,Saccharomyces cerevisiae Proteins ,Beta sheet ,Saccharomyces cerevisiae ,Computational biology ,Biology ,Chromatin Assembly and Disassembly ,Chromatin ,Chromosomes ,General Biochemistry, Genetics and Molecular Biology ,Nucleosomes ,Chromosome conformation capture ,Folding (chemistry) ,03 medical and health sciences ,0302 clinical medicine ,Nucleosome ,Protein folding ,Epigenetics ,Transcription Initiation Site ,Structural motif ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Elucidating the global and local rules that govern genome-wide, hierarchical chromatin architecture remains a critical challenge. Current high-throughput chromosome conformation capture (Hi-C) technologies have identified large-scale chromatin structural motifs, such as topologically associating domains and looping. However, structural rules at the smallest or nucleosome scale remain poorly understood. Here, we coupled nucleosome-resolved Hi-C technology with simulated annealing-molecular dynamics (SA-MD) simulation to reveal 3D spatial distributions of nucleosomes and their genome-wide orientation in chromatin. Our method, called Hi-CO, revealed distinct nucleosome folding motifs across the yeast genome. Our results uncovered two types of basic secondary structural motifs in nucleosome folding: α-tetrahedron and β-rhombus analogous to α helix and β sheet motifs in protein folding. Using mutants and cell-cycle-synchronized cells, we further uncovered motifs with specific nucleosome positioning and orientation coupled to epigenetic features at individual loci. By illuminating molecular-level structure-function relationships in eukaryotic chromatin, our findings establish organizational principles of nucleosome folding.
- Published
- 2019
23. On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation
- Author
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Jeffrey Skolnick and Tadashi Ando
- Subjects
Time Factors ,Chemistry ,Lipid Bilayers ,Kinetics ,Intermolecular force ,Membrane ,Biophysics ,Models, Theoretical ,Molecular Dynamics Simulation ,Lipids ,Random coil ,Diffusion ,Motion ,Molecular dynamics ,Chemical physics ,Computational chemistry ,Hydrodynamics ,Brownian dynamics ,Particle ,Lipid bilayer - Abstract
Hydrodynamic interactions (HI) give rise to collective motions between molecules, which are known to be important in the dynamics of random coil polymers and colloids. However, their role in the biological self-assembly of many molecule systems has not been investigated. Here, using Brownian dynamics simulations, we evaluate the importance of HI on the kinetics of self-assembly of lipid membranes. One-thousand coarse-grained lipid molecules in periodic simulation boxes were allowed to assemble into stable bilayers in the presence and absence of intermolecular HI. Hydrodynamic interactions reduce the monomer-monomer association rate by 50%. In contrast, the rate of association of lipid clusters is much faster in the presence of intermolecular HI. In fact, with intermolecular HI, the membrane self-assembly rate is 3–10 times faster than that without intermolecular HI. We introduce an analytical model to describe the size dependence of the diffusive encounter rate of particle clusters, which can qualitatively explain our simulation results for the early stage of the membrane self-assembly process. These results clearly suggest that HI greatly affects the kinetics of self-assembly and that simulations without HI will significantly underestimate the kinetic parameters of such processes.
- Published
- 2013
24. Development of Cell Systems Simulator Using Biochemical Data
- Author
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Seigo Itoh, Tadashi Ando, and Ichiro Yamato
- Subjects
medicine.anatomical_structure ,Chemistry ,Cell ,medicine ,Simulation - Published
- 2013
25. Author response: Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
- Author
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Michael Feig, Ryuhei Harada, Isseki Yu, Takaharu Mori, Jaewoon Jung, Yuji Sugita, and Tadashi Ando
- Subjects
Chemistry ,Cytoplasm ,Dynamics (mechanics) ,Biophysics ,Macromolecule - Published
- 2016
26. Protein Diffusion Around Bacterial Nucleoid
- Author
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Tadashi Ando, Yuji Sugita, Asli Yildirim, and Michael Feig
- Subjects
Genetics ,Caulobacter crescentus ,Anomalous diffusion ,Protein dynamics ,Biophysics ,Chromosome ,Bacterial nucleoid ,Biology ,biology.organism_classification ,Chromosome conformation capture ,bacteria ,Nucleoid ,Macromolecular crowding - Abstract
The effect of macromolecular crowding on protein diffusion has been extensively studied in order to understand the protein dynamics in cellular environments. Previous studies have generally focused on proteins as crowding agents as they are known to occupy 20-30% of the cell volume. The volume fraction of the nucleoid in bacterial cells is also significant, around 10-20%, but the effect of chromosomal DNA as a crowding agent on protein diffusion has drawn relatively limited attention. Using recently build high-resolution models of bacterial nucleoids, Brownian and Stokesian dynamics simulations of coarse-grained model systems containing chromosomal DNA and proteins were carried out to investigate the effect of nucleoid crowding on protein diffusion. The coarse-grained model for the nucleoid is an experimentally-derived 3D model of the Caulobacter crescentus chromosome at base-pair resolution built by combining topological information of chromosomal DNA with distance restraints obtained from high-throughput Chromosome Conformation Capture (HiC) experiments, while proteins in the systems are modeled as hard-spheres. Results show that diffusion of proteins are slower around the nucleoid compared to in protein crowding and that there is size-dependent exclusion of proteins from the chromosome interior. Further analysis was carried to examine the degree of anomalous diffusion at different time and length scales.
- Published
- 2017
27. Alanine-based peptides containing polar residues presumably favour α-helical structure entropically
- Author
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Ichiro Yamato, Wankee Kim, and Tadashi Ando
- Subjects
Alanine ,Arginine ,Chemistry ,General Chemical Engineering ,Enthalpy ,Solvation ,General Chemistry ,Dihedral angle ,Condensed Matter Physics ,Residue (chemistry) ,Crystallography ,Modeling and Simulation ,Brownian dynamics ,General Materials Science ,Umbrella sampling ,Information Systems - Abstract
To evaluate the enthalpic and entropic contributions of polar residues in alanine-based peptides to α-helical propensities of peptides, we applied a Brownian dynamics simulation, together with the umbrella sampling, to two alanine-based 21-residue peptides: one composed of alanine only (AAA), the other composed of 18 alanines and 3 arginines (ARA). Higher α-helical propensity of ARA than that of AAA was obtained. However, they showed similar conformational stability in enthalpy, considering the contribution of the solvation energy and the potential energy. As an evaluation of entropic effects, the fluctuation of a dihedral angle, ψ, was investigated. Arginine residue showed smaller fluctuation than alanine in elongated states. Higher α-helical propensity might originate from entropic effects. Furthermore, arginine seems to affect the α-helical propensity of alanines interacting with arginine.
- Published
- 2011
28. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
- Author
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Jeffrey Skolnick and Tadashi Ando
- Subjects
Models, Molecular ,Cytoplasm ,Multidisciplinary ,Macromolecular Substances ,Chemistry ,Green Fluorescent Proteins ,Intermolecular force ,Dynamics (mechanics) ,Radius ,Biological Sciences ,Thermal diffusivity ,Models, Biological ,Fick's laws of diffusion ,Biophysical Phenomena ,Recombinant Proteins ,Diffusion ,Motion ,Crystallography ,Chemical physics ,Multiprotein Complexes ,Escherichia coli ,Brownian dynamics ,Diffusion (business) ,Macromolecule - Abstract
To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules in vivo from that at infinite dilution. In an Escherichia coli cytoplasm model comprised of 15 different macromolecule types at physiological concentrations, BD simulations of molecular-shaped and equivalent sphere representations were performed with a soft repulsive potential. At cellular concentrations, the calculated diffusion constant of GFP is much larger than experiment, with no significant shape dependence. Next, using the equivalent sphere system, hydrodynamic interactions (HI) were considered. Without adjustable parameters, the in vivo experimental GFP diffusion constant was reproduced. Finally, the effects of nonspecific attractive interactions were examined. The reduction in diffusivity is very sensitive to macromolecular radius with the motion of the largest macromolecules dramatically slowed down; this is not seen if HI dominate. In addition, long-lived clusters involving the largest macromolecules form if attractions dominate, whereas HI give rise to significant, size independent intermolecular dynamic correlations. These qualitative differences provide a testable means of differentiating the importance of HI vs. nonspecific attractive interactions on macromolecular motion in cells.
- Published
- 2010
29. Dynamics and Interactions of Proteins and Metabolites in Cellular Crowding Environments: All-Atom Molecular Dynamics Study of Proteins and Metabolites in Cellular Crowding Environments: All-atom Molecular Dynamics Study
- Author
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Takaharu Mori, Tadashi Ando, Michael Feig, Jaewoon Jung, Ryuhei Harada, Yuji Sugita, and Isseki Yu
- Subjects
Molecular dynamics ,Chemistry ,Chemical physics ,Dynamics (mechanics) ,Biophysics ,Atom (order theory) ,Crowding - Published
- 2018
30. Relationship between mineral composition or soil texture and available silicon in alluvial paddy soils on the Shounai Plain, Japan
- Author
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Ken-ichi Kakuda, Hiroshi Fujii, Yuka Sasaki, Ho Ando, Tadashi Ando, and Shuhei Makabe
- Subjects
Materials science ,Soil texture ,Soil water ,Particle-size distribution ,Soil Science ,Mineralogy ,Soil classification ,Weathering ,Alluvium ,Plant Science ,Silt ,Clay minerals ,complex mixtures - Abstract
To evaluate the relationship between the amount of available Silicon (Si) in paddy soils and their mineral properties on the Shounai Plain in Japan, which is formed from several parent materials, we evaluated the amount of available Si, the particle size distribution, the oxide composition of crystalline minerals and the amount of oxalate-extractable Si (Sio), iron (Feo) and aluminum (Alo) in the soil. The amount of available Si in the soil and the oxide content of the crystalline minerals differed among four soil groups that were distinguished by their clay mineral composition. There was no difference in the particle size distribution among the soil groups. The amount of available Si was positively related to the SiO2/Al2O3 ratio of clay, the CaO concentration of silt and fine sand, and the amounts of Sio, Feo and Alo in the soil. The amount of available Si in the soils was negative correlated with the Na2O and K2O concentrations of silt, the K2O concentration of fine sand, and the coarse sand c...
- Published
- 2009
31. [Untitled]
- Author
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TADASHI ANDO
- Subjects
Management of Technology and Innovation - Published
- 2009
32. Development of an Implicit Membrane Model for Brownian Dynamics Simulation
- Author
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Takahiro Ito, Wankee Kim, Tadashi Ando, and Ichiro Yamato
- Subjects
Physics ,Membrane ,Mathematical analysis ,Brownian dynamics ,Development (differential geometry) - Abstract
ブラウン動力学(Brownian Dynamics;BD)法は溶媒を明示的に扱わないため計算を高速化することができる。従来のBD法は水環境でのタンパク質シミュレーションを対象にしていたため、膜タンパク質には適用できなかった。本研究では膜環境をも非明示的に再現することによってBD法を膜タンパク質のシミュレーションに適用できるように拡張した。αヘリックス構造のポリアラニンペプチドやパピロマーウイルス由来のE5タンパク質、蜂毒のメリチンをモデルとしてシミュレーションした結果、疎水性であるポリアラニンとE5膜タンパク質は膜中で安定に存在した。また、両親媒性であるメリチンペプチドは膜表面に安定に結合していた。これらの結果から、本膜モデルを用いたBD法は膜タンパク質のシミュレーションに有効であると考えられる。
- Published
- 2007
33. DNA double-strand breaks alter the spatial arrangement of homologous loci in plant cells
- Author
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Tadashi Ando, Takeshi Hirakawa, Sachihiro Matsunaga, and Yohei Katagiri
- Subjects
DNA Repair ,DNA, Plant ,DNA damage ,DNA repair ,Arabidopsis ,Time-Lapse Imaging ,Article ,chemistry.chemical_compound ,Plant Cells ,Homologous chromosome ,Arabidopsis thaliana ,DNA Breaks, Double-Stranded ,Homologous Recombination ,Genetics ,Multidisciplinary ,biology ,Arabidopsis Proteins ,fungi ,DNA Helicases ,biology.organism_classification ,Chromatin ,chemistry ,Microscopy, Fluorescence ,Gamma Rays ,Genetic Loci ,Comet Assay ,Homologous recombination ,Monte Carlo Method ,DNA - Abstract
Chromatin dynamics and arrangement are involved in many biological processes in nuclei of eukaryotes including plants. Plants have to respond rapidly to various environmental stimuli to achieve growth and development because they cannot move. It is assumed that the alteration of chromatin dynamics and arrangement support the response to these stimuli; however, there is little information in plants. In this study, we investigated the chromatin dynamics and arrangement with DNA damage in Arabidopsis thaliana by live-cell imaging with the lacO/LacI-EGFP system and simulation analysis. It was revealed that homologous loci kept a constant distance in nuclei of A. thaliana roots in general growth. We also found that DNA double-strand breaks (DSBs) induce the approach of the homologous loci with γ-irradiation. Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. These results suggest that homologous loci approach each other to repair DSBs and AtRAD54 mediates these phenomena.
- Published
- 2015
34. Modes I and II interlaminar fracture toughness and fatigue delamination of CF/epoxy laminates with self-same epoxy interleaf
- Author
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Shojiro Ochiai, Yoshihiro Endo, Mototsugu Tanaka, Tadashi Ando, Taiji Adachi, and Masaki Hojo
- Subjects
Toughness ,Materials science ,Mechanical Engineering ,mode II ,Delamination ,Fracture mechanics ,self-same epoxy interleaf ,Epoxy ,Paris' law ,polymer-matrix composites ,delamination ,Industrial and Manufacturing Engineering ,fatigue crack growth ,Fracture toughness ,Mechanics of Materials ,Modeling and Simulation ,visual_art ,mode I ,Fracture (geology) ,visual_art.visual_art_medium ,General Materials Science ,Composite material ,Double cantilever beam - Abstract
Interlaminar fracture toughness and delamination fatigue crack growth behavior were investigated for carbon fiber (CF)/epoxy laminates with the self-same epoxy interleaf. The matrix epoxy with a thickness of 50 μm was chosen as the interleaf material in order to clarify the effect of resin-rich layer thickness on the delamination fatigue crack growth behavior. Tests under mode I loading were carried out using double cantilever beam specimens. For tests under mode II loading, three-point end notched flexure specimens were used for interlaminar fracture toughness tests, while four-point end notched flexure specimens were used for delamination fatigue tests. The mode I properties (interlaminar fracture toughness and delamination fatigue threshold) of these epoxy-interleaved CFRP laminates were almost identical to those of the laminates without interleaf (base CFRP laminates). The effect of epoxy interleaf was completely different under mode II loading. The mode II interlaminar fracture toughness for the epoxy-interleaved laminates was 1.6 (initial value) and 3.4 (propagation value) times higher than that for the base CFRP laminates. The mode II delamination fatigue threshold of the epoxy-interleaved laminates was 2–2.3 times higher than those of the base CFRP laminates. While the toughness of the interleaf is the key factor under mode I, the thickness of interlayer is the key factor under mode II. The difference in the effect of the self-same epoxy interlayer on the interlaminar fracture properties under modes I and II loadings was discussed on the bases of the fractographic observations and mechanism considerations.
- Published
- 2006
35. Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models
- Author
-
Jeffrey Skolnick and Tadashi Ando
- Subjects
Biophysical Simulations ,Mass diffusivity ,Biophysics ,Plasma protein binding ,Biology ,Molecular Dynamics Simulation ,DNA-binding protein ,Structural genomics ,Cellular and Molecular Neuroscience ,chemistry.chemical_compound ,Molecular dynamics ,Genetics ,lcsh:QH301-705.5 ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Ecology ,Biology and Life Sciences ,Computational Biology ,Proteins ,DNA ,genomic DNA ,lcsh:Biology (General) ,Computational Theory and Mathematics ,chemistry ,Biochemistry ,Modeling and Simulation ,Brownian dynamics ,Algorithms ,Research Article ,Protein Binding - Abstract
DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome., Author Summary DNA binding proteins efficiently search for their cognitive sites on long genomic DNA in cells to control biological activities. Recent experimental studies have revealed that the proteins use not only three-dimensional diffusion, but also one-dimensional diffusion (sliding) on DNA for this search process. For a better understanding of this biological process, we need to elucidate the mechanism of sliding. We report here molecular simulations using newly developed coarse-grained protein and DNA models for elucidating the nature of the sliding motions. Our simulation results show that: 1) hydrodynamic interactions between protein and DNA reduce sliding rate by 30%, 2) structural fluctuations of DNA give rise to steric collisions between proteins and DNA, which facilitate sliding motions, and 3) proteins with low binding affinities to DNA can hop along the DNA, resulting in a significant increase in sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome.
- Published
- 2014
36. Free energy landscapes of two model peptides: α-helical and β-hairpin peptides explored with Brownian dynamics simulation
- Author
-
Tadashi Ando and Ichiro Yamato
- Subjects
chemistry.chemical_classification ,General Chemical Engineering ,Peptide ,General Chemistry ,Condensed Matter Physics ,Folding (chemistry) ,symbols.namesake ,chemistry ,Computational chemistry ,Chemical physics ,Modeling and Simulation ,symbols ,Brownian dynamics ,Cluster (physics) ,General Materials Science ,Protein folding ,van der Waals force ,Root-mean-square deviation ,Energy (signal processing) ,Information Systems - Abstract
We applied an atomistic Brownian dynamics (BD) simulation with multiple time step method for the folding simulation of a 13-mer α-helical peptide and a 12-mer β-hairpin peptide, giving successful folding simulations. In this model, the driving energy contribution towards folding came from both electrostatic and van der Waals interactions for the α-helical peptide and from van der Waals interactions for the β-hairpin peptide. Although, many non-native structures having the same or lower energy than that of native structure were observed, the folded states formed the most populated cluster when the structures obtained by the BD simulations were subjected to the cluster analysis based on distance-based root mean square deviation of side-chains between different structures. This result indicates that we can predict the native structures from conformations sampled by BD simulation.
- Published
- 2005
37. FCANAL: Structure based protein function prediction method. Application to enzymes and binding proteins
- Author
-
Ayumi Suzuki, Tadashi Ando, Satoru Miyazaki, and Ichiro Yamato
- Subjects
Computational biology ,computer.file_format ,Biology ,Protein structure prediction ,Protein Data Bank ,Biochemistry ,DNA-binding protein ,Structural genomics ,Protein structure ,Protein function prediction ,Threading (protein sequence) ,Statistical potential ,computer - Abstract
Structural genomics projects are beginning to produce protein structures with unknown functions, thereby creating a need for high-throughput methods to predict functions. Although sequence-based function prediction methods have been used extensively, structure-based prediction is believed to provide higher specificity and sensitivity because functions are closely related to the three-dimensional structures of functional sites, which are more strongly conserved during evolution than sequence. We have developed FCANAL, a method to predict functions using a score matrix obtained from the distances between Cα atoms and frequencies of appearance [1]. The previous report used key residues predicted from sequence comparisons (motifs). In this report, we have expanded the method to include enzymes and binding proteins with key residues predicted on the basis of three-dimensional structures. Using FCANAL, we constructed score matrices for 31 enzymes. When we applied them to all of the structure entries deposited in the Protein Data Bank, FCANAL could detect functional sites with high accuracy. This suggests that FCANAL will help identify the functions of newly determined structures and pinpoint their functionally important regions.
- Published
- 2005
38. The role of σ-receptors in levodopa-induced dyskinesia in patients with advanced Parkinson disease: a positron emission tomography study
- Author
-
Takeshi Nakajima, Masatoshi Itoh, Keiichiro Yamaguchi, Teiji Tominaga, Taro Nimura, Tadashi Ando, and Reizo Shirane
- Subjects
Male ,Dyskinesia, Drug-Induced ,medicine.medical_specialty ,Levodopa ,Deep brain stimulation ,medicine.medical_treatment ,Electric Stimulation Therapy ,Neurological disorder ,Globus Pallidus ,Severity of Illness Index ,Gastroenterology ,Antiparkinson Agents ,Central nervous system disease ,Degenerative disease ,Cerebellum ,Internal medicine ,medicine ,Humans ,Receptors, sigma ,Antipsychotic ,Aged ,Levodopa-induced dyskinesia ,business.industry ,Parkinson Disease ,Middle Aged ,medicine.disease ,Surgery ,Dyskinesia ,Female ,medicine.symptom ,business ,Tomography, Emission-Computed ,medicine.drug - Abstract
Object. Levodopa-induced dyskinesia (LID) in patients with Parkinson disease (PD) mimics acute dystonic reactions induced by antipsychotic agents, possibly mediated by σ-receptors; however, there are few reports in which the relationship between σ-receptors and LID in advanced PD is investigated. The binding potential of cerebellar σ-receptors before and after a pallidal surgery for dyskinesia in patients with advanced PD is assessed. Methods. Six patients with advanced PD (male/female ratio 3:3, age 56.7 ± 9.8 years) underwent stereotactic pallidal surgery (two posteroventral pallidotomy procedures and four deep brain stimulation of the globus pallidus internus, including one bilateral case). Clinical features of patients with PD were assessed using Hoehn and Yahr (H & Y) stages, the Unified Parkinson's Disease Rating Scale (UPDRS), and the Schwab and England Activities of Daily Life Scale (S & E). The LID was evaluated by LID severity score. The binding potential of cerebellar σ-receptors was determined before and after the surgery by 11C-nemonapride positron emission tomoraphy, a specific radioligand for σ-receptors in the cerebellum. All clinical scores, especially the LID severity score, were dramatically improved after the surgery (p < 0.05). Preoperatively, contralateral cerebellar binding potential was significantly elevated (p < 0.01), and it was reduced after the surgery, but it was still higher than that of healthy volunteers (p < 0.05). The ipsilateral cerebellar binding potential remained unchanged after the surgery. The level of binding potential did not correlate with H & Y stage, UPDRS, or S & E score, but a strong positive correlation was seen between the binding potential and the preoperative LID severity score when the patients were receiving medication (r = 0.893, p < 0.05). Conclusions. Cerebellar σ-receptors may potentially involve the genesis of LID in advanced PD.
- Published
- 2004
39. A New Implicit Solvent Model for Brownian Dynamics Simulation: Solvent-Accessible Surface Area Dependent Effective Charge Model
- Author
-
Tadashi Ando, Toshiyuki Meguro, and Ichiro Yamato
- Subjects
Root mean square ,Solvent ,Quantitative Biology::Biomolecules ,Molecular dynamics ,Classical mechanics ,Chemistry ,Solvent models ,Brownian dynamics ,Thermodynamics ,Force field (chemistry) ,Effective nuclear charge ,Accessible surface area - Abstract
A new simple implicit solvent model, effective charge (EC) model, was introduced into the Brownian dynamics algorithm based on AMBER united-atom force field. In the EC model, an atomic charge was decreased as a function of solvent-accessible surface area of the atom. We carried out the Brownian dynamics simulations of a 28-mer ββα fold peptide using four implicit solvent models: a generalized Born/solvent-accessible surface area (GB/SA) model, a solvent-accessible surface area (SA) based solvent model, a SA in combination with distance-dependent dielectric (DD/SA) and the EC combined with DD/SA (DD/SA/EC) model; and the calculated results on structure and dynamics of the peptide were compared with those of molecular dynamics simulation using explicit solvent model. Several artifacts were observed in the simulation using the GB/SA model. On the other hand, simulation using the DD/SA and DD/SA/EC implicit solvent models were free from such artifacts. Especially BD with the DD/SA/EC model gave the most stable trajectory as judged by root mean square deviations from the initial structure without large computational cost.
- Published
- 2004
40. Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules
- Author
-
Tadashi Ando, Toshiyuki Meguro, and Ichiro Yamato
- Subjects
Physics ,chemistry.chemical_classification ,Quantitative Biology::Biomolecules ,Scale (ratio) ,General Chemical Engineering ,Computation ,Biomolecule ,Dynamics (mechanics) ,General Chemistry ,Folding (DSP implementation) ,Condensed Matter Physics ,Molecular dynamics ,chemistry ,Modeling and Simulation ,Brownian dynamics ,Multiple time ,General Materials Science ,Statistical physics ,Information Systems - Abstract
We report a multiple time step algorithm applied to an atomistic Brownian dynamics simulation for simulating the long time scale dynamics of biomolecules. The algorithm was based on the original multiple time step method; a short time step was used to keep faster motions in local equilibrium. When applied to a 28-mer # # ! folded peptide, the simulation gave stable trajectories and the computation time was reduced by a factor of 160 compared to a conventional molecular dynamics simulation using explicit water molecules. We applied it for the folding simulation of a 13-mer ! -helical peptide, giving a successful folding simulation. These results indicate that the Brownian dynamics with the multiple time step algorithm is useful for studies of biomolecular motions by long time simulation.
- Published
- 2003
41. Decadal Variability of Subsurface Temperature in the Central North Pacific
- Author
-
Satoshi Sugimoto, Tadashi Ando, and Takashi Yoshida
- Subjects
Ekman layer ,Temperature gradient ,Heat flux ,Climatology ,Wind stress curl ,Heat transfer ,Temperature front ,Subtropics ,Oceanography ,Subarctic climate ,Geology - Abstract
Decadal variability of subsurface temperature in the North Pacific has been investigated. Two dominant regions were found; the central subarctic region (CSa) and the north-eastern subtropical region (NESt). In CSa, cooling (warming) of wintertime subsurface temperature corresponds to the large (small) temperature gradient and southward (northward) shift of subsurface temperature front, associated with the increase (decrease) of positive wind stress curl and the southward (northward) shift of curl τ zero line with 2 years delay. It is suggested that the relocation of subtropical-subarctic boundary plays an important role. In NESt, importance of heat flux through the sea surface and heat divergence in the Ekman layer is also discussed.
- Published
- 2003
42. Development of Multifunctional Object-Oriented Program Library for Molecular Simulation and Structure Analysis
- Author
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Ichiro Yamato, Toshiyuki Meguro, and Tadashi Ando
- Subjects
Set (abstract data type) ,Object-oriented programming ,Class (computer programming) ,Theoretical computer science ,Development (topology) ,Computer science ,Fortran ,Subroutine ,Genetic algorithm ,Monte Carlo method ,computer ,computer.programming_language - Abstract
We developed the object-oriented class library "YLO" to study molecular structures. YLO is written in C++ and composed of a set of classes, which are a kind of program units, resembling subroutines in Fortran. Each class performs a certain job independently in a whole program. YLO deals with non-organic, organic molecules and biological macromolecules. The coordinate file of a molecule is read / written in PDB format. Using the YLO library, one can make various types of application programs efficiently, such as Monte Carlo simulator, Genetic Algorithm optimizer and so on.
- Published
- 2003
43. Resonance of elliptical muffler chamber having a nonuniformly perforated pipe
- Author
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Tatsuyu Ikeda, Tadashi Ando, and Tsuyoshi Nishimura
- Subjects
Muffler ,Engineering ,business.industry ,Acoustics ,Resonance ,Structural engineering ,Sound power ,law.invention ,Flow noise ,law ,Electrical and Electronic Engineering ,business ,Body orifice ,Noise (radio) - Abstract
Perforated pipe is an essential component in contemporary automotive mufflers, since such a pipe reduces the acoustic power of the flow noise, which is significantly influenced by its velocity. Nonuniformly perforated pipes, the orifices of which are arranged in a belt configuration, are widely used in muffler systems. The resonance of such perforated pipe when located inside the elliptic cavity is investigated experimentally in this paper. The results obtained are also compared with the predictions of our method of theoretical analysis for a uniformly perforated pipe in order to clarify the resonance mechanism. It was found that the difference between the measured and theoretical values is less than 5 Hz for a short pipe. © 2002 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 85(7): 22–28, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjc.1104
- Published
- 2002
44. Development of an Atomistic Brownian Dynamics Algorithm with Implicit Solvent Model for Long Time Simulation
- Author
-
Toshiyuki Meguro, Ichiro Yamato, and Tadashi Ando
- Subjects
Solvent ,Quantitative Biology::Biomolecules ,Molecular dynamics ,Chemistry ,Protein dynamics ,Computation ,Brownian dynamics ,A protein ,Statistical physics ,Force field (chemistry) - Abstract
We report the implementation of an atomistic Brownian dynamics simulation of proteins. A protein was described by united-atom model with AMBER91 force field. The solvent was treated by distance-dependent dielectric/surface area model. The computation time of the Brownian dynamics and the calculated results on structure and dynamics of 28-mer ββα fold peptide with the implicit solvent model were compared with those of molecular dynamics simulation with explicit solvent. The Brownian dynamics simulation was 53 times faster than molecular dynamics simulation with explicit solvent. The simulation was stable and the artifacts often observed in simulations at vacuum condition were reduced. The results indicate that the Brownian dynamics with the implicit solvent model can be widely used in studies of protein dynamics by long time simulation in future.
- Published
- 2002
45. Resonance of elliptical perforated tube muffler
- Author
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Tsuyoshi Usagawa, Tatsuyu Ikeda, Tsuyoshi Nishimura, Tadashi Ando, and Masanao Ebata
- Subjects
Muffler ,Materials science ,business.industry ,Acoustics ,Resonance ,Structural engineering ,Wave equation ,law.invention ,Noise ,law ,Tube (fluid conveyance) ,Electrical and Electronic Engineering ,Sound pressure ,business - Abstract
Perforated pipes are frequently used to attenuate exhaust noise in contemporary automotive mufflers. Resonances at a particular frequency, however, may exceed the overall acoustic reduction effect of the muffler when the shape and fixing position are inappropriate. The theoretical calculations of the sound pressure inside the elliptical perforated tube muffler are carried out by solving the wave equation. The resonance mechanism of the perforated tube muffler is analyzed. The results of the analyses have been confirmed by experiments. © 2000 Scripta Technica, Electron Comm Jpn Pt 3, 83(8): 51-60, 2000
- Published
- 2000
46. IMPORTANCE OF EXCLUDED VOLUME AND HYDRODYNAMIC INTERACTIONS ON MACROMOLECULAR DIFFUSIONIN VIVO
- Author
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Jeffrey Skolnick and Tadashi Ando
- Subjects
In vivo ,Chemistry ,Diffusion ,Intermolecular force ,Kinetics ,Excluded volume ,Brownian dynamics ,Biophysics ,Nanotechnology ,Fick's laws of diffusion ,Article ,Macromolecule - Abstract
The interiors of all living cells are highly crowded with macromolecules, which results in a considerable difference between the thermodynamics and kinetics of biological reactions in vivo from that in vitro. To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules in vivo from that at infinite dilution. In an E. coli cytoplasm modelcomprised of 15 different macromolecule types at physiological concentrations, where macromolecules were represented by spheres with their Stokes radii, BD simulations were performed with and without hydrodynamic interactions (HI). Without HI, the calculated diffusion constant of green fluorescent protein (GFP) is much larger than experiment. On the other hand, when HI were considered, the in vivo experimental GFP diffusion constant is almost reproduced without adjustable parameters. In addition, HI give rise to significant, size independent intermolecular dynamic correlations. These results suggest that HI play an important role on macromolecular dynamics in vivo.
- Published
- 2013
47. CHIROPTICAL PROPERTIES OF FIVE-COORDINATE COMPLEXES OF NICKEL(II) AND COBALT(II) CONTAINING AN OPTICALLY ACTIVE LIGAND WITH NITROGEN AND PHOSPHORUS DONOR ATOMS
- Author
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Tadashi Ando, Shunji Utsuno, and Motoko Ishida
- Subjects
Circular dichroism ,Denticity ,Ligand ,Inorganic chemistry ,chemistry.chemical_element ,Nickel ,Crystallography ,chemistry ,Asymmetric carbon ,Tripodal ligand ,Materials Chemistry ,Amine gas treating ,Physical and Theoretical Chemistry ,Cobalt - Abstract
A new tripodal ligand with an asymmetric carbon atom, Ph2PCH2CH(Me)N(CH2CH2PPh2)2 (S-mnp3) was prepared using L-alanine as an optically active starting material; a series of its complexes, [M(X)(S-mnp3)]BPh4(M = Ni(II) and Co(II); X = NCS−, Cl−, Br− and I−) was prepared. Electronic spectra of these complexes indicated that their coordination geometries are essentially the same as those of corresponding complexes containing the tripodal ligand tris (diphenylphosphinoethyl) amine. Thus, all the present nickel complexes in solution exhibit electronic spectra typical of trigonal-bipyramidal complexes of diamagnetic configuration. CD spectra of these nickel complexes have been discussed on the basis of the selection rules for magnetic dipole transitions under C 3v symmetry. Cobalt(II) complexes are either high-spin or low-spin, depending on the nature of the unidentate ligand. The high-spin cobalt(II) complexes did not show CD spectra typical of trigonal-bipyramidal geometry.
- Published
- 1996
48. Chirality in planar cell shape contributes to left-right asymmetric epithelial morphogenesis
- Author
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Ryo Hatori, Naotaka Nakazawa, Kiichiro Taniguchi, Takashi Okumura, Reo Maeda, Shunya Hozumi, Tadashi Ando, Mitsutoshi Nakamura, Hiroo Fujiwara, and Kenji Matsuno
- Subjects
Rotation ,Cell ,Morphogenesis ,Models, Biological ,Myosin Type I ,Drosophilidae ,Myosin ,medicine ,Animals ,Drosophila Proteins ,Computer Simulation ,Cell Shape ,Body Patterning ,Multidisciplinary ,Polarity (international relations) ,biology ,Cadherin ,Cell Polarity ,Epithelial Cells ,Anatomy ,Adherens Junctions ,biology.organism_classification ,Cadherins ,Epithelium ,Intestines ,medicine.anatomical_structure ,Biophysics ,Drosophila ,Chirality (chemistry) - Abstract
Some organs in animals display left-right (LR) asymmetry. To better understand LR asymmetric morphogenesis in Drosophila, we studied LR directional rotation of the hindgut epithelial tube. Hindgut epithelial cells adopt a LR asymmetric (chiral) cell shape within their plane, and we refer to this cell behavior as planar cell-shape chirality (PCC). Drosophila E-cadherin (DE-Cad) is distributed to cell boundaries with LR asymmetry, which is responsible for the PCC formation. Myosin ID switches the LR polarity found in PCC and in DE-Cad distribution, which coincides with the direction of rotation. An in silico simulation showed that PCC is sufficient to induce the directional rotation of this tissue. Thus, the intrinsic chirality of epithelial cells in vivo is an underlying mechanism for LR asymmetric tissue morphogenesis.
- Published
- 2011
49. Role of Asp187 and Gln190 in the Na+/proline symporter (PutP) of Escherichia coli
- Author
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Anowarul Amin, Tadashi Ando, Ichiro Yamato, and Shinya Saijo
- Subjects
Models, Molecular ,Mutation ,Aspartic Acid ,Symporters ,Chemistry ,Escherichia coli Proteins ,Mutant ,Glutamic Acid ,General Medicine ,medicine.disease_cause ,Biochemistry ,Amino Acid Transport Systems, Neutral ,Proline transport ,Symporter ,medicine ,Escherichia coli ,Homology modeling ,Proline ,Binding site ,Molecular Biology - Abstract
Asp187 and Gln190 were predicted as conserved and closely located at the Na(+) binding site in a topology and homology model structure of Na(+)/proline symporter (PutP) of Escherichia coli. The replacement of Asp187 with Ala or Leu did not affect proline transport activity; whereas, change to Gln abolished the active transport. The binding affinity for Na(+) or proline of these mutants was similar to that of wild-type (WT) PutP. This result indicates Asp187 to be responsible for active transport of proline without affecting the binding. Replacement of Gln190 with Ala, Asn, Asp, Leu and Glu had no effect on transport or binding, suggesting that it may not have a role in the transport. However, in the negative D187Q mutant, a second mutation, of Gln190 to Glu or Leu, restored 46 or 7% of the transport activity of WT, respectively, while mutation to Ala, Asn or Asp had no effect. Thus, side chain at position 190 has a crucial role in suppressing the functional defect of the D187Q mutant. We conclude that Asp187 is responsible for transport activity instead of coupling-ion binding by constituting the translocation pathway of the ion and Gln190 provides a suppressing mutation site to regain PutP functional activity.
- Published
- 2011
50. BROWNIAN DYNAMICS SIMULATION OF MACROMOLECULE DIFFUSION IN A PROTOCELL
- Author
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Tadashi Ando and Jeffrey Skolnick
- Subjects
Chemistry ,Diffusion ,Kinetics ,Excluded volume ,Brownian dynamics ,Biophysics ,Article ,Diffusion Anisotropy ,Brownian motion ,Stokes radius ,Macromolecule - Abstract
The interiors of all living cells are highly crowded with macromolecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4–5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.
- Published
- 2011
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