A5009544201- Protein Structure and Dynamics
- Enzyme Structure and Function
- Spectroscopy and Quantum Chemical Studies
- DNA and Nucleic Acid Chemistry
- Bacteriophages and microbial interactions
- Advanced NMR Techniques and Applications
- RNA and protein synthesis mechanisms
- Chemical Synthesis and Analysis
- Photosynthetic Processes and Mechanisms
- Advanced Chemical Physics Studies
- Microtubule and mitosis dynamics
- Genomics and Phylogenetic Studies
- Lipid Membrane Structure and Behavior
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
- Advanced Physical and Chemical Molecular Interactions
- Inflammatory mediators and NSAID effects
- Click Chemistry and Applications
- Theoretical and Computational Physics
- Fluorine in Organic Chemistry
- NMR spectroscopy and applications
- Advanced X-ray Imaging Techniques
- Electron Spin Resonance Studies
- Model Reduction and Neural Networks
- Advanced Electron Microscopy Techniques and Applications
University of Tsukuba
2021-2022
Kitasato University
2013-2020
Osaka University
2006-2011
Protein Research Foundation
2010-2011
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state predictive methodology. Here we describe a community-wide assessment methods to predict effects mutations on protein-protein interactions. Twenty-two groups predicted comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful...
To uncover the adaptation mechanisms of photosystems for halotolerance, changes in stoichiometry and activity response to salinities were examined a halotolerant cyanobacterium, Aphanothece halophytica. Photosynthetic O2 evolution was high even at salinities. increased with increasing external concentration NaCl, reached maximum 1.5 M then decreased. Similar salt dependence observed photosystem II activity. On other hand, I concomitantly increase salinity. Photoacoustic measurements...
Precise and rapid calculation of long-range interactions is crucial importance for molecular dynamics (MD) Monte Carlo simulations. Instead the Ewald method or its high speed variant, PME, we applied our novel method, called force-switching Wolf to computation free energy landscapes a short peptide in explicit water. co-workers showed that electrostatic under periodic boundary condition can be well reproduced even by truncating contribution from distant charges, when charge neutrality taken...
Calmodulin (CaM) is a Ca2+-binding messenger protein having four motifs named 'EF-hand'; the EF-hand undergo conformation change induced by Ca2+-binding. In order to study how induces of and which residues are involved in reaction, two 1μ second long MD simulations were independently performed from apo- holo-CaM their structures interactions compared. The weakens helix-helix interaction all EF-hand, however, adopted close-like form. correlation coefficients obtained MDs show comprising being...
In the absence of experimentally determined three dimensional (3D) structures proteins, prediction protein using computational methods is a standard alternative approach in bioinformatics. When predicted models to compute native structure an unknown target protein, estimating actual quality important for selecting best or near-best model. Moreover, estimates differences between and are obviously useful end users who can then decide on utility their specific problems. This article describes...
We propose a novel application of the Wang–Landau method (WLM) for multicanonical molecular dynamics (McMD) simulations. Originally, WLM was developed Monte Carlo (MC) Fundamentally, remarkably reduces simulation efforts because it estimates optimal energy function automatically. When is applied to McMD, not only but also gradient must be estimated adequately. However, rugged at early stage, applications MD simulations are difficult and require smoothing procedure: such as cubic-spline...
Various factors, such as helical propensity and hydrogen bonds, control protein structures. A frequently used model protein, myoglobin (Mb), can perform 3D domain swapping, in which the loop at hinge region is converted to a structure dimer. We have previously succeeded obtaining monomer-dimer equilibrium native state by introducing high α-helical residue, Ala, region. In this study, we focused on another factor that governs structure, bonding. X-ray crystal structures thermodynamic studies...
We propose a multiscale simulation method combining the efficiency of coarse-grained model (CGM) and accuracy an all-atom (AAM) for free-energy landscape calculation protein systems. A protein’s conformation space is quickly searched first using CGM. Then obtained information incorporated into AAM simulations. The subsequently from This was tested on chignolin folding. results demonstrated that computational time reduced by as much 90%.
Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates various biochemical processes. CaM acts via structural changes and complex forming with its target enzymes. has two globular domains (N-lobe C-lobe) connected by long linker region. Upon calcium binding, the N-lobe C-lobe undergo local conformational changes, after that, entire wraps enzyme through large change. However, regulation mechanism, such as allosteric interactions regulating still unclear. In order to...
Abstract Calcineurin (CaN) is a eukaryotic serine/threonine protein phosphatase activated by both Ca 2+ and calmodulin (CaM), including intrinsically disordered region (IDR). The undergoes folding into an α‐helix form in the presence ‐loaded CaM. To sample ordered structure of IDR conventional all atom model (AAM) molecular dynamics (MD) simulation, CaM must be simultaneously treated. However, it time‐consuming task because coupled binding should include repeated dissociation. Then, this...
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It is widely accepted that the folding process of a protein in large part determined by topology native structure. A class coarse-grained model called Go-like takes only native-state into account has successfully described many proteins. In this letter, we show with reduced number amino acids exhibits similar free-energy landscape for Ribonuclease H to one obtained model. Coarser-grained shows qualitatively same variation due energy balance between domains.
Thc stmctural stability of a protein is deteemined by the free energy difiteTeice bctwecn nativc and dcnatui'cd states.The in aqueous solution dcscribed intrumelecu]ur energy, confomiutienal entrupy,
A 3-dimensional domain swapping (3D-DS) phenomenon is a promising way to make stable multimer because interactions in the about same as that of monomer; it would be useful artificially design functional protein's multimer. In this study, molecular dynamics (MD) simulation cytochrome c(cyt c) known form 3D-DS dimer (PDB ID: 3NBS) was performed study factors enhance structure sampling. Our results show difficulty sampling and necessity method such generalized ensemble method. The also...
Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates variety of biochemical processes. CaM acts through its conformational changes and complex formation with target enzymes. consists two globular domains (N-lobe C-lobe) linked by an extended linker region. Upon calcium binding, the N-lobe C-lobe undergo local changes, followed major change entire to wrap enzyme. However, regulation mechanisms, such as allosteric interactions, regulate large structural are still...