Literature DB >> 19402609

Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects.

Nidhi Singh1, Arieh Warshel.   

Abstract

The evaluation of the solvation entropies is a major conceptual and practical challenge. On the one hand, it is interesting to quantify the factors that are responsible for the solvation entropies in solutions, whereas on the other, it is essential to be able to assess the contributions of the solvation entropies to the binding free energies and related properties. In fact, the solvation entropies are neglected in almost all of the studies of the binding entropies. The main problem is that widely used approaches, such as the quasiharmonic (QH) approximation, do not provide reliable results particularly in cases of shallow potential and multidimensional surfaces while brute force evaluations of the entropic effects by simulating temperature dependence of the free energy converges very slowly. This paper addresses the above issue by starting with an analysis of the factors that are responsible for the negative solvation entropy of ions, showing that it is not due to the change in the solvent vibration modes or to the solvent force constant but to the changes in the solvent configurational space upon change in the solute charges. We begin by clarifying that when one deals with aqueous solutions, it is easy to evaluate the corresponding entropic effect by the Langevin dipole (LD) treatment. However, in this work we are interested in developing a general microscopic tool that can be used to study similar effects in the proteins. To this end, we explore the ability of our restraint release (RR) approach to evaluate the solvation entropy. We start this analysis by reviewing the foundation of this approach and in particular, the requirements of minimizing the enthalpy contribution to the RR free energy. We then establish that our approach is not a specialized harmonic treatment but a rather powerful general approach. Moving to the main topic of this work, we demonstrate that the RR approach provides quantitative results for the solvation entropies of monovalent and divalent ions and effectively captures the physics of these entropic effects. The success of the current approach indicates that it should be applicable to the studies of the solvation entropies in the proteins and also, in examining hydrophobic effects. Thus, we believe that the RR approach provides a powerful tool for evaluating the corresponding contributions to the binding entropies and, eventually, to the binding free energies. This holds promise for extending the information theory modeling to proteins and protein-ligand complexes in aqueous solutions and consequently, facilitating computer-aided drug design.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 19402609      PMCID: PMC2738853          DOI: 10.1021/jp811063v

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  34 in total

1.  The consequences of translational and rotational entropy lost by small molecules on binding to proteins.

Authors:  Christopher W Murray; Marcel L Verdonk
Journal:  J Comput Aided Mol Des       Date:  2002-10       Impact factor: 3.686

2.  Evaluating the Accuracy of the Quasiharmonic Approximation.

Authors:  Chia-En Chang; Wei Chen; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2005-09       Impact factor: 6.006

3.  Calculations of solute and solvent entropies from molecular dynamics simulations.

Authors:  Jens Carlsson; Johan Aqvist
Journal:  Phys Chem Chem Phys       Date:  2006-09-08       Impact factor: 3.676

4.  Evaluation of configurational entropy methods from peptide folding-unfolding simulation.

Authors:  Da-Wei Li; Mina Khanlarzadeh; Jinbu Wang; Shuanghong Huo; Rafael Brüschweiler
Journal:  J Phys Chem B       Date:  2007-11-20       Impact factor: 2.991

5.  Cold adaptation of enzyme reaction rates.

Authors:  Sinisa Bjelic; Bjørn O Brandsdal; Johan Aqvist
Journal:  Biochemistry       Date:  2008-08-30       Impact factor: 3.162

6.  Loss of translational entropy in binding, folding, and catalysis.

Authors:  L M Amzel
Journal:  Proteins       Date:  1997-06

7.  Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration.

Authors:  P L Privalov; G I Makhatadze
Journal:  J Mol Biol       Date:  1993-07-20       Impact factor: 5.469

8.  Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.

Authors:  Y Y Sham; Z T Chu; H Tao; A Warshel
Journal:  Proteins       Date:  2000-06-01

9.  Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods.

Authors:  Vladimir Hnizdo; Jun Tan; Benjamin J Killian; Michael K Gilson
Journal:  J Comput Chem       Date:  2008-07-30       Impact factor: 3.376

10.  Entropy and free energy of a mobile protein loop in explicit water.

Authors:  Srinath Cheluvaraja; Mihail Mihailescu; Hagai Meirovitch
Journal:  J Phys Chem B       Date:  2008-07-10       Impact factor: 2.991

View more
  8 in total

1.  Exploring the Drug Resistance of HCV Protease.

Authors:  Garima Jindal; Dibyendu Mondal; Arieh Warshel
Journal:  J Phys Chem B       Date:  2017-07-05       Impact factor: 2.991

2.  Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions.

Authors:  Subhendu Roy; Patrick Schopf; Arieh Warshel
Journal:  J Phys Chem B       Date:  2017-07-05       Impact factor: 2.991

3.  Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B.

Authors:  Patrick Schopf; Arieh Warshel
Journal:  Proteins       Date:  2014-01-25

4.  Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions.

Authors:  Nidhi Singh; Arieh Warshel
Journal:  Proteins       Date:  2010-05-15

Review 5.  Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues.

Authors:  Shina Caroline Lynn Kamerlin; Janez Mavri; A Warshel
Journal:  FEBS Lett       Date:  2010-04-29       Impact factor: 4.124

6.  A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes.

Authors:  Nidhi Singh; Arieh Warshel
Journal:  Proteins       Date:  2010-05-15

7.  Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization.

Authors:  Jeronimo Lameira; Ram Prasad Bora; Zhen T Chu; Arieh Warshel
Journal:  Proteins       Date:  2015-01-07

Review 8.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01
  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.