A5088515417- Protein Structure and Dynamics
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- Cellular Mechanics and Interactions
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Biotin and Related Studies
- Cellular transport and secretion
- Force Microscopy Techniques and Applications
- RNA Research and Splicing
- Metabolomics and Mass Spectrometry Studies
- Computational Drug Discovery Methods
- Cardiomyopathy and Myosin Studies
- Glycosylation and Glycoproteins Research
- Signaling Pathways in Disease
- ATP Synthase and ATPases Research
- Hemoglobin structure and function
- Proteins in Food Systems
- Gene expression and cancer classification
- Cytomegalovirus and herpesvirus research
- Crystallization and Solubility Studies
- Protein purification and stability
Nagoya University
2014-2024
Tokyo Medical and Dental University
2024
Kyushu University
2018
Maebashi Institute of Technology
2011-2013
Japan Science and Technology Agency
2006-2011
Tokyo Institute of Technology
2006-2008
Computing Center
2007
Kyoto University
2002-2004
Yokohama City University
2004
IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature, http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/) is a collection of intrinsically disordered (IDPs) that cannot adopt stable globular structures under physiological conditions. Since its previous publication in 2012, the number entries has almost tripled (120 to 340). In addition increase quantity, quality been significantly improved. The new incorporates interactions IDPs their binding partners more...
IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators regions, interaction regions to other molecules, post-translational modification sites, references structural domain assignments. In particular, explicitly describes protean segments that can be transformed from state an...
The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and filamentous F-form, which drive organelle transport cell motility. This mechanical work is driven by ATPase activity at catalytic site in F-form. For deeper understanding of cellular functions, reaction mechanism must be elucidated. Here, we show that a single molecule trapped F-form fragmin domain-1 binding present their crystal structures ATP analog-, ADP-Pi-, ADP-bound forms, 1.15-Å...
The actin capping protein (CP) tightly binds to the barbed end of filaments, thus playing a key role in actin-based lamellipodial dynamics. V-1 and CARMIL proteins directly bind CP inhibit filament activity CP. completely inhibits from interacting with end, whereas act on end-bound facilitate its dissociation (called uncapping activity). Previous studies have revealed striking functional differences between two regulators. However, molecular mechanisms describing how these remains poorly...
Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information understanding the related protein functions. We gathered 839 pairs of ligand-free ligand-bound states from monomeric or homo-dimeric proteins, constructed Structural Change DataBase (PSCDB). In database, we focused on whether...
Protein-protein interactions are fundamental for all biological phenomena, and protein-protein interaction networks provide a global view of the interactions. The hub proteins, with many partners, play vital roles in networks. We investigated subcellular localizations proteins human network, found that ones localized multiple compartments, especially nucleus/cytoplasm (NCP), cytoplasm/cell membrane (CMP), nucleus/cytoplasm/cell (NCMP), tend to be hubs. Examinations keywords suggested among...
AlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against DB and discovered an uncharacterized P-loop NTPase family. The the family was surprisingly novel, showing atypical topology for NTPases, noticeable twofold symmetry, two pairs independent putative active sites. Our findings show that structural is powerful approach to identifying undiscovered families.
Transferases and hydrolases catalyze different chemical reactions express dynamic responses upon ligand binding. To insulate the molecule from surrounding water, transferases bury it inside protein by closing cleft, while undergo a small conformational change leave exposed to solvent. Despite these distinct ligand-binding modes, some are homologous. clarify how such catalytic modes possible with same scaffold, we examined solvent accessibility of molecules for 15 SCOP superfamilies, each...
In Pickering–Ramsden emulsions, the packing structure of colloidal particles at liquid–liquid (or liquid–gas) interface significantly affects and behavior emulsion. Here, using a series platelike with regular polygonal shapes Janus amphiphilicity, we created emulsion droplets stabilized by close-packed interface. The systematic variation particle morphology shows that geometrical features polygons in (curved) planar dominate over self-assembled structures. structures are tessellations...
Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely be hidden behind complicated motions with a wide range spatial and temporal scales. A straightforward intuitive analysis protein observed in MD simulation trajectories is therefore growing significance the large increase both time system size. In this study, we propose novel description based on hierarchical clustering fluctuations inter-atomic...
The actin capping protein (CP) binds to filaments block further elongation. activity is inhibited by proteins V-1 and CARMIL interacting with CP via steric allosteric mechanisms, respectively. crystal structures of free CP, CP/V-1, CP/CARMIL complexes suggest that the binding alters flexibility rather than overall structure this an inhibition mechanism. Here, we performed molecular dynamics (MD) simulations in form, complex or V-1. resulting trajectories were analyzed exhaustively using...
Structural symmetry in homooligomeric proteins has intrigued many researchers over the past several decades. However, implication of protein is still not well understood. In this study, we performed molecular dynamics (MD) simulations two forms trp RNA binding attenuation (TRAP), wild-type 11-mer and an engineered 12-mer, having different levels circular symmetry. The results showed that inter-subunit fluctuations TRAP were significantly smaller than 12-mer while internal larger 12-mer....
Large conformational changes of multidomain proteins are difficult to simulate using all-atom molecular dynamics (MD) due the slow time scale. We show that a simple modification structure-based coarse-grained (CG) model enables stable and efficient MD simulation those proteins. "Motion Tree", tree diagram describes between two structures in protein, provides information on rigid structural units (domains) magnitudes domain motions. In our new CG model, which we call DoME (domain motion...
Phosphorylation is a major post-translational modification that plays central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites phosphoproteins has been reported but the specificity phosphorylation not fully resolved. In this report, kinase-substrate pairs identified Kinase-Interacting Substrate Screening (KISS) method were used to...
Most proteins from higher organisms are known to be multi-domain and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those human for instance, we developed a special protein-structure-prediction pipeline accumulated the products in Structure Atlas Human Genome (SAHG) database at http://bird.cbrc.jp/sahg . With pipeline, were examined by local alignment methods (BLAST, PSI-BLAST Smith–Waterman profile–profile alignment), global–local...
The actin capping protein (CP) tightly binds to the barbed end of filaments block further elongation. β-tentacle in CP is an important region that ensures stable interaction with filaments. CARMIL inhibits via C-terminal portion containing CP-binding motif, located intrinsically disordered region. We have proposed allosteric inhibition model which suppresses by population shift mechanism. Here, we solved a crystal structure complex CARMIL-derived peptide, CA32. new clearly represents...
We investigated fragmental sequences that were inserted into proteins during long molecular evolution and relevant to the association of homo-oligomers. Seventeen insertions in 12 SCOP (structure classification proteins) families examined classified large small insertions. The are composed interface-like residues effectively increase interface area. In contrast, not commonly found at interfaces have a area: their roles oligomerization process unclear. located middle protein therefore must...
Abstract Motivation: Protein–protein interactions play vital functional roles in various biological phenomena. Physical contacts between proteins have been revealed using experimental approaches that solved the structures of protein complexes at atomic resolution. To examine huge number available Protein Data Bank, an efficient automated method compares is required. Results: We developed Structural Comparison Complexes (SCPC), a novel to structurally compare complexes. SCPC spatial...
Capping protein (CP) binds to the barbed end of an actin-filament and inhibits its elongation. CARMIL CP dissociates it from actin-filament. The binding peptide alters flexibility CP, which is considered facilitate dissociation. Twinfilin also through C-terminal tail. complex structures CP/twinfilin-tail (TW-tail) indicate that sites TW-tail overlap. However, does not dissociation end. We extensively investigated flexibilities in CP/TW-tail or CP/CARMIL complexes using elastic network model...
ABSTRACT Sarco(endo)plasmic reticulum Ca 2+ ‐ATPase transports two per ATP‐hydrolyzed across biological membranes against a large concentration gradient by undergoing conformational changes. Structural studies with X‐ray crystallography revealed functional roles of coupled motions between the cytoplasmic domains and transmembrane helices in individual reaction steps. Here, we employed “Motion Tree (MT),” tree diagram that describes change structures, applied it to representative structures....