Literature DB >> 17026275

Morphometric approach to the solvation free energy of complex molecules.

Roland Roth1, Yuichi Harano, Masahiro Kinoshita.   

Abstract

We show that the solvation free energy of a complex molecule such as a protein can be calculated using only four geometrical measures of the molecular structure and corresponding thermodynamical coefficients. We compare results from this morphometric approach to those obtained by an elaborate statistical-mechanical theory in liquid state physics for a large variety of different structures of protein G and find excellent agreement. Since the computational time is drastically reduced, the new approach provides a practical and efficient way for calculating the solvation free energy which can be employed when this quantity has to be calculated for a large number of structures, as in a simulation study of protein folding.

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Year:  2006        PMID: 17026275     DOI: 10.1103/PhysRevLett.97.078101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  17 in total

1.  Generalized fundamental measure theory for atomistic modeling of macromolecular crowding.

Authors:  Sanbo Qin; Huan-Xiang Zhou
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-03-26

2.  A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Authors:  Hui Sun; Jiayi Wen; Yanxiang Zhao; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

3.  Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation.

Authors:  Yanxiang Zhao; Yuen-Yick Kwan; Jianwei Che; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2013-07-14       Impact factor: 3.488

4.  Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects.

Authors:  Hiraku Oshima; Tomohiko Hayashi; Masahiro Kinoshita
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

Review 5.  Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

Authors:  Jinzen Ikebe; Koji Umezawa; Junichi Higo
Journal:  Biophys Rev       Date:  2016-01-11

Review 6.  A new theoretical approach to biological self-assembly.

Authors:  Masahiro Kinoshita
Journal:  Biophys Rev       Date:  2013-02-01

7.  Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins.

Authors:  Cayla M Miller; Young C Kim; Jeetain Mittal
Journal:  Biophys J       Date:  2016-07-12       Impact factor: 4.033

Review 8.  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 9.  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

10.  Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.

Authors:  Tomohiko Hayashi; Hiraku Oshima; Tsukasa Mashima; Takashi Nagata; Masato Katahira; Masahiro Kinoshita
Journal:  Nucleic Acids Res       Date:  2014-05-06       Impact factor: 16.971

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