Literature DB >> 18691127

Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions.

Danilo Roccatano1.   

Abstract

Pure organic solvents or mixtures with water are very common environments for studying protein and peptide in solution. These milieu conditions are used either for improving the catalytic performance of enzymes or for studying the effect of solvent on the protein stability and hence gaining insight into the protein folding mechanism. The atomic details of these processes are mainly addressed using computer simulation approaches. In particular, Molecular Dynamics simulation represents the most powerful and versatile tool to investigate the details of solvation processes at atomic level. In the last few years, the number of publications peptide and protein simulations in non-natural environments has proliferated. These studies are providing important contributions to shed light on the nature of non-aqueous solvent effects. In this review, the achievements and the future prospects in this field of computational biochemistry are reviewed by summarizing the most important theoretical results published in the last 10 years.

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Year:  2008        PMID: 18691127     DOI: 10.2174/138920308785132686

Source DB:  PubMed          Journal:  Curr Protein Pept Sci        ISSN: 1389-2037            Impact factor:   3.272


  8 in total

1.  Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study.

Authors:  Harpreet Kaur; Yellamraju U Sasidhar
Journal:  J Mol Model       Date:  2015-03-17       Impact factor: 1.810

2.  Quantitative characterization of local protein solvation to predict solvent effects on protein structure.

Authors:  Vincent Vagenende; Bernhardt L Trout
Journal:  Biophys J       Date:  2012-09-19       Impact factor: 4.033

3.  Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

Authors:  Michael T Zimmermann; Sumudu P Leelananda; Pawel Gniewek; Yaping Feng; Robert L Jernigan; Andrzej Kloczkowski
Journal:  J Struct Funct Genomics       Date:  2011-06-15

4.  Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.

Authors:  Pawel Gniewek; Sumudu P Leelananda; Andrzej Kolinski; Robert L Jernigan; Andrzej Kloczkowski
Journal:  Proteins       Date:  2011-04-19

5.  Circular dichroism and UV resonance raman study of the impact of alcohols on the Gibbs free energy landscape of an alpha-helical peptide.

Authors:  Kan Xiong; Sanford A Asher
Journal:  Biochemistry       Date:  2010-04-20       Impact factor: 3.162

6.  The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study.

Authors:  Carlo Meneghini; Loris Leboffe; Monica Bionducci; Gabriella Fanali; Massimiliano Meli; Giorgio Colombo; Mauro Fasano; Paolo Ascenzi; Settimio Mobilio
Journal:  PLoS One       Date:  2014-08-25       Impact factor: 3.240

7.  In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function.

Authors:  Rajni Verma; Katie Mitchell-Koch
Journal:  Catalysts       Date:  2017-07-14       Impact factor: 4.146

8.  Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

Authors:  Vincent Vagenende; Alvin X Han; Han B Pek; Bernard L W Loo
Journal:  PLoS Comput Biol       Date:  2013-05-16       Impact factor: 4.475

  8 in total

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