Literature DB >> 8506263

Can the stability of protein mutants be predicted by free energy calculations?

Y Y Shi1, A E Mark, C X Wang, F Huang, H J Berendsen, W F van Gunsteren.   

Abstract

The use of free energy simulation techniques in the study of protein stability is critically evaluated. Results from two simulations of the thermostability mutation Asn218 to Ser218 in Subtilisin are presented. It is shown that components of the free energy change can be highly sensitive to the computational details of the simulation leading to the conclusion that free energy calculations cannot currently be used to reliably predict protein stability. The different factors that undermine the reliability are discussed.

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Year:  1993        PMID： 8506263     DOI： 10.1093/protein/6.3.289

Source DB:  PubMed          Journal:  Protein Eng        ISSN： 0269-2139


  12 in total

1.  Computational studies on mutant protein stability: The correlation between surface thermal expansion and protein stability.

Authors:  R Palma; P M Curmi
Journal:  Protein Sci       Date:  1999-04       Impact factor: 6.725

2.  Dependence of protein stability on the structure of the denatured state: free energy calculations of I56V mutation in human lysozyme.

Authors:  Y Sugita; A Kitao
Journal:  Biophys J       Date:  1998-11       Impact factor: 4.033

3.  Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study.

Authors:  B Roux; M Nina; R Pomès; J C Smith
Journal:  Biophys J       Date:  1996-08       Impact factor: 4.033

4.  Understanding the thermodynamic stability of an RNA hairpin and its mutant.

Authors:  S B Singh; P A Kollman
Journal:  Biophys J       Date:  1996-04       Impact factor: 4.033

5.  Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations.

Authors:  T M Frimurer; G H Peters; M D Sørensen; J J Led; O H Olsen
Journal:  Protein Sci       Date:  1999-01       Impact factor: 6.725

Review 6.  Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases.

Authors:  G Vriend; V Eijsink
Journal:  J Comput Aided Mol Des       Date:  1993-08       Impact factor: 3.686

7.  A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design.

Authors:  A Wallqvist; R L Jernigan; D G Covell
Journal:  Protein Sci       Date:  1995-09       Impact factor: 6.725

8.  Electrostatic potentials and electrostatic interaction energies of rat cytochrome b5 and a simulated anion-exchange adsorbent surface.

Authors:  D J Roush; D S Gill; R C Willson
Journal:  Biophys J       Date:  1994-05       Impact factor: 4.033

9.  SDM--a server for predicting effects of mutations on protein stability and malfunction.

Authors:  Catherine L Worth; Robert Preissner; Tom L Blundell
Journal:  Nucleic Acids Res       Date:  2011-05-18       Impact factor: 16.971

10.  Free energy calculations on the stability of the 14-3-3ζ protein.

Authors:  Zuzana Jandova; Zuzana Trosanova; Veronika Weisova; Chris Oostenbrink; Jozef Hritz
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-12-05       Impact factor: 3.036
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