Literature DB >> 28510109

A new theoretical approach to biological self-assembly.

Masahiro Kinoshita1.   

Abstract

Upon biological self-assembly, the number of accessible translational configurations of water in the system increases considerably, leading to a large gain in water entropy. It is important to calculate the solvation entropy of a biomolecule with a prescribed structure by accounting for the change in water-water correlations caused by solute insertion. Modeling water as a dielectric continuum is not capable of capturing the physical essence of the water entropy effect. As a reliable tool, we propose a hybrid of the angle-dependent integral equation theory combined with a multipolar water model and a morphometric approach. Using our methods wherein the water entropy effect is treated as the key factor, we can elucidate a variety of processes such as protein folding, cold, pressure, and heat denaturating of a protein, molecular recognition, ordered association of proteins such as amyloid fibril formation, and functioning of ATP-driven proteins.

Entities:  

Keywords:  ATP-driven protein; Biological self-assembly; Integral equation theory; Molecular recognition; Morphometric approach; Protein denaturation; Protein folding; Solvation entropy

Year:  2013        PMID: 28510109      PMCID: PMC5425704          DOI: 10.1007/s12551-013-0100-8

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  31 in total

1.  Cell biology: join the crowd.

Authors:  R John Ellis; Allen P Minton
Journal:  Nature       Date:  2003-09-04       Impact factor: 49.962

2.  Characterization of experimentally determined native-structure models of a protein using energetic and entropic components of free-energy function.

Authors:  Hirokazu Mishima; Satoshi Yasuda; Takashi Yoshidome; Hiraku Oshima; Yuichi Harano; Mitsunori Ikeguchi; Masahiro Kinoshita
Journal:  J Phys Chem B       Date:  2012-06-29       Impact factor: 2.991

3.  Translational-entropy gain of solvent upon protein folding.

Authors:  Yuichi Harano; Masahiro Kinoshita
Journal:  Biophys J       Date:  2005-07-29       Impact factor: 4.033

4.  Helical tubes in crowded environments.

Authors:  Yehuda Snir; Randall D Kamien
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-05-18

5.  Solvation of proteins: linking thermodynamics to geometry.

Authors:  Hendrik Hansen-Goos; Roland Roth; Klaus Mecke; S Dietrich
Journal:  Phys Rev Lett       Date:  2007-09-17       Impact factor: 9.161

6.  Molecular origin of the hydrophobic effect: analysis using the angle-dependent integral equation theory.

Authors:  Masahiro Kinoshita
Journal:  J Chem Phys       Date:  2008-01-14       Impact factor: 3.488

7.  Pressure effects on structures formed by entropically driven self-assembly: illustration for denaturation of proteins.

Authors:  Takashi Yoshidome; Yuichi Harano; Masahiro Kinoshita
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-01-20

8.  Physical origin of hydrophobicity studied in terms of cold denaturation of proteins: comparison between water and simple fluids.

Authors:  Takashi Yoshidome; Masahiro Kinoshita
Journal:  Phys Chem Chem Phys       Date:  2012-09-26       Impact factor: 3.676

9.  Effects of side-chain packing on the formation of secondary structures in protein folding.

Authors:  Satoshi Yasuda; Takashi Yoshidome; Hiraku Oshima; Ryota Kodama; Yuichi Harano; Masahiro Kinoshita
Journal:  J Chem Phys       Date:  2010-02-14       Impact factor: 3.488

10.  Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes.

Authors:  Hiraku Oshima; Satoshi Yasuda; Takashi Yoshidome; Mitsunori Ikeguchi; Masahiro Kinoshita
Journal:  Phys Chem Chem Phys       Date:  2011-08-15       Impact factor: 3.676

View more
  7 in total

1.  Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent.

Authors:  Fumitaka Kamo; Ryosuke Ishizuka; Nobuyuki Matubayasi
Journal:  Protein Sci       Date:  2015-08-06       Impact factor: 6.725

Review 2.  Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions.

Authors:  Masahiro Kinoshita; Tomohiko Hayashi
Journal:  Biophys Rev       Date:  2020-03-17

Review 3.  Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors.

Authors:  Takeshi Murata; Satoshi Yasuda; Tomohiko Hayashi; Masahiro Kinoshita
Journal:  Biophys Rev       Date:  2020-04-08

4.  Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB.

Authors:  Alessio Atzori; Giuliano Malloci; Jigneshkumar Dahyabhai Prajapati; Andrea Basciu; Andrea Bosin; Ulrich Kleinekathöfer; Jürg Dreier; Attilio V Vargiu; Paolo Ruggerone
Journal:  J Phys Chem B       Date:  2019-05-28       Impact factor: 2.991

5.  Enhanced enzymatic activity exerted by a packed assembly of a single type of enzyme.

Authors:  Huyen Dinh; Eiji Nakata; Kaori Mutsuda-Zapater; Masayuki Saimura; Masahiro Kinoshita; Takashi Morii
Journal:  Chem Sci       Date:  2020-07-27       Impact factor: 9.825

6.  Physicochemical origin of high correlation between thermal stability of a protein and its packing efficiency: a theoretical study for staphylococcal nuclease mutants.

Authors:  Koji Oda; Masahiro Kinoshita
Journal:  Biophys Physicobiol       Date:  2015-07-31

7.  Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures.

Authors:  Takashi Yoshidome; Mitsunori Ikeguchi; Masateru Ohta
Journal:  J Comput Chem       Date:  2020-08-19       Impact factor: 3.376

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.