Literature DB >> 17726097

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain.

Thomas F Miller1, Eric Vanden-Eijnden, David Chandler.   

Abstract

With computer simulations of >100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain was obtained by tiling space with (0.2 nm)(3) cubes and projecting the atomistic water molecule positions onto this grid. With the coarse-grained field thus defined, the string method in collective variables was used to compute a minimum free-energy pathway (MFEP) for the collapsing chain. These calculations provide a proof of principle for a coarse-grained description of water solvent. Furthermore, the calculated MFEP characterizes the mechanism for the collapse of the hydrated chain by providing a path of maximum likelihood for dynamical trajectories. The reliability of the calculated MFEP was confirmed with the use of conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, we show that length-scale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.

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Year:  2007        PMID: 17726097      PMCID: PMC1955457          DOI: 10.1073/pnas.0705830104

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  11 in total

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Authors:  D M Huang; D Chandler
Journal:  Proc Natl Acad Sci U S A       Date:  2000-07-18       Impact factor: 11.205

2.  Drying-induced hydrophobic polymer collapse.

Authors:  Pieter Rein ten Wolde; David Chandler
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-30       Impact factor: 11.205

3.  Some factors in the interpretation of protein denaturation.

Authors:  W KAUZMANN
Journal:  Adv Protein Chem       Date:  1959

4.  Dewetting-induced collapse of hydrophobic particles.

Authors:  X Huang; C J Margulis; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-24       Impact factor: 11.205

5.  A computer simulation study of water drying at the interface of protein chains.

Authors:  Qiang Huang; Shangwu Ding; Chih-Yu Hua; Hsiao-Ching Yang; Cheng-Lung Chen
Journal:  J Chem Phys       Date:  2004-07-22       Impact factor: 3.488

6.  Observation of a dewetting transition in the collapse of the melittin tetramer.

Authors:  Pu Liu; Xuhui Huang; Ruhong Zhou; B J Berne
Journal:  Nature       Date:  2005-09-01       Impact factor: 49.962

7.  Finite temperature string method for the study of rare events.

Authors:  Weinan E; Weiqing Ren; Eric Vanden-Eijnden
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

8.  Drying and hydrophobic collapse of paraffin plates.

Authors:  Xuhui Huang; Ruhong Zhou; Bruce J Berne
Journal:  J Phys Chem B       Date:  2005-03-03       Impact factor: 2.991

9.  Simplified and improved string method for computing the minimum energy paths in barrier-crossing events.

Authors:  Weinan E; Weiqing Ren; Eric Vanden-Eijnden
Journal:  J Chem Phys       Date:  2007-04-28       Impact factor: 3.488

10.  Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water.

Authors:  Manoj V Athawale; Gaurav Goel; Tuhin Ghosh; Thomas M Truskett; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

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  45 in total

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Authors:  Jeremy L England; Vijay S Pande
Journal:  Biochem Cell Biol       Date:  2010-04       Impact factor: 3.626

2.  Extended surfaces modulate hydrophobic interactions of neighboring solutes.

Authors:  Amish J Patel; Patrick Varilly; Sumanth N Jamadagni; Hari Acharya; Shekhar Garde; David Chandler
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-10       Impact factor: 11.205

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Authors:  Andrew L Ferguson; Athanassios Z Panagiotopoulos; Pablo G Debenedetti; Ioannis G Kevrekidis
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-19       Impact factor: 11.205

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Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-01       Impact factor: 11.205

7.  On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

Authors:  Jason B Brokaw; Jhih-Wei Chu
Journal:  Biophys J       Date:  2010-11-17       Impact factor: 4.033

8.  Molecular pathways for defect annihilation in directed self-assembly.

Authors:  Su-Mi Hur; Vikram Thapar; Abelardo Ramírez-Hernández; Gurdaman Khaira; Tamar Segal-Peretz; Paulina A Rincon-Delgadillo; Weihua Li; Marcus Müller; Paul F Nealey; Juan J de Pablo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-29       Impact factor: 11.205

9.  Perspective: Computer simulations of long time dynamics.

Authors:  Ron Elber
Journal:  J Chem Phys       Date:  2016-02-14       Impact factor: 3.488

10.  Fluctuations of water near extended hydrophobic and hydrophilic surfaces.

Authors:  Amish J Patel; Patrick Varilly; David Chandler
Journal:  J Phys Chem B       Date:  2010-02-04       Impact factor: 2.991

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