Literature DB >> 11807950

Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin.

Heiko Schäfer1, Lorna J Smith, Alan E Mark, Wilfred F van Gunsteren.   

Abstract

We present entropy estimates based on molecular dynamics simulations of models of the molten globule state of the protein alpha-lactalbumin at low pH. The entropy calculations use the covariance matrix of atom-positional fluctuations and yield the complete configurational entropy. The configurational entropy of the entire protein and of each of its side chains is calculated. Exposed side chains show a larger entropy compared to buried side chains. A comparison to data from rotamer counting is made and significant differences are found. Copyright 2001 Wiley-Liss, Inc.

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Year:  2002        PMID： 11807950     DOI： 10.1002/prot.1166

Source DB:  PubMed          Journal:  Proteins        ISSN： 0887-3585


  17 in total

1.  Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA.

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2.  Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences.

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Journal:  Biophys J       Date:  2005-02-24       Impact factor: 4.033

3.  HIV-1 GP120 V3 conformational and informational entropies.

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4.  Prediction of side-chain conformations on protein surfaces.

Authors:  Zhexin Xiang; Peter J Steinbach; Matthew P Jacobson; Richard A Friesner; Barry Honig
Journal:  Proteins       Date:  2007-03-01

5.  Ligand configurational entropy and protein binding.

Authors:  Chia-en A Chang; Wei Chen; Michael K Gilson
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-22       Impact factor: 11.205

6.  Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study.

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Journal:  J Am Chem Soc       Date:  2006-10-04       Impact factor: 15.419

7.  Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-beta-glucanase by molecular dynamics simulations.

Authors:  Raimundo Gargallo; Juan Cedano; Angel Mozo-Villarias; Enrique Querol; Baldomero Oliva
Journal:  J Mol Model       Date:  2006-03-09       Impact factor: 1.810

8.  Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation.

Authors:  Shang-Te D Hsu; Christine Peter; Wilfred F van Gunsteren; Alexandre M J J Bonvin
Journal:  Biophys J       Date:  2004-10-15       Impact factor: 4.033

9.  Influence of NH-Sgamma bonding interactions on the structure and dynamics of metallothioneins.

Authors:  Núria Romero-Isart; Baldo Oliva; Milan Vasák
Journal:  J Mol Model       Date:  2009-07-16       Impact factor: 1.810

10.  Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3.

Authors:  Carl Diehl; Samuel Genheden; Kristofer Modig; Ulf Ryde; Mikael Akke
Journal:  J Biomol NMR       Date:  2009-07-30       Impact factor: 2.835
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