Literature DB >> 1317584

Solvent dielectric effects on protein dynamics.

R Affleck1, C A Haynes, D S Clark.   

Abstract

Electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations were used to investigate the dynamics of alpha-chymotrypsin in solvents ranging in dielectric constant from 72 to 1.9. EPR measurements showed that motions in the vicinity of two spin-labeled amino acids (Met-192 and Ser-195) decreased dramatically with decreasing solvent dielectric constant, a trend consistent with changes in the electrostatic force between charged residues of the protein. EPR results and MD simulations revealed a very similar functional dependence between rates of motion in the protein and the dielectric constant of the bulk solvent; however, predicted motions of protein atoms were markedly faster than measured motions of the spin labels. MD calculations for dielectric constants of 5 and 72 showed the greatest differences near the outer surface of the protein. In general, at the lower dielectric constant many atoms of the protein move more slowly, and many of the slowest residues are near the exterior. These results suggest that altered dynamics may contribute to the unusual properties--e.g., modified stereoselectivities--of enzymes in nearly dry organic solvents.

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Year:  1992        PMID: 1317584      PMCID: PMC49250          DOI: 10.1073/pnas.89.11.5167

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


  17 in total

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Authors:  A Zaks; A M Klibanov
Journal:  J Biol Chem       Date:  1988-03-05       Impact factor: 5.157

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Authors:  S Bone
Journal:  Biochim Biophys Acta       Date:  1987-11-05

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Authors:  J E Bailey; D S Clark
Journal:  Methods Enzymol       Date:  1987       Impact factor: 1.600

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Authors:  S S Wong; K Quiggle; C Triplett; L J Berliner
Journal:  J Biol Chem       Date:  1974-03-25       Impact factor: 5.157

5.  Spin-labeled sulfonyl fluorides as active site probes of protease structure. I. Comparison of the active site environments in alpha-chymotrypsin and trypsin.

Authors:  L J Berliner; S S Wong
Journal:  J Biol Chem       Date:  1974-03-25       Impact factor: 5.157

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Authors:  D J Kosman; L H Piette
Journal:  Arch Biochem Biophys       Date:  1972-04       Impact factor: 4.013

Review 7.  Mapping protein dynamics by X-ray diffraction.

Authors:  D Ringe; G A Petsko
Journal:  Prog Biophys Mol Biol       Date:  1985       Impact factor: 3.667

8.  Protein structure determination in solution by nuclear magnetic resonance spectroscopy.

Authors:  K Wüthrich
Journal:  Science       Date:  1989-01-06       Impact factor: 47.728

Review 9.  Calculations of electrostatic interactions in biological systems and in solutions.

Authors:  A Warshel; S T Russell
Journal:  Q Rev Biophys       Date:  1984-08       Impact factor: 5.318

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Authors:  H Tsukada; D M Blow
Journal:  J Mol Biol       Date:  1985-08-20       Impact factor: 5.469

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  17 in total

Review 1.  Characteristics of nearly dry enzymes in organic solvents: implications for biocatalysis in the absence of water.

Authors:  Douglas S Clark
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2004-08-29       Impact factor: 6.237

Review 2.  What can we learn by studying enzymes in non-aqueous media?

Authors:  Peter J Halling
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2004-08-29       Impact factor: 6.237

3.  Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.

Authors:  Juan Zeng; Yongxiu Li; John Z H Zhang; Ye Mei
Journal:  J Mol Model       Date:  2016-07-08       Impact factor: 1.810

4.  Conformational sampling of peptides in cellular environments.

Authors:  Seiichiro Tanizaki; Jacob Clifford; Brian D Connelly; Michael Feig
Journal:  Biophys J       Date:  2007-09-28       Impact factor: 4.033

5.  Predicting enzyme behavior in nonconventional media: correlating nitrilase function with solvent properties.

Authors:  Praveen Kaul; U C Banerjee
Journal:  J Ind Microbiol Biotechnol       Date:  2008-03-04       Impact factor: 3.346

6.  Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions.

Authors:  Ross K Eppler; Elton P Hudson; Shannon D Chase; Jonathan S Dordick; Jeffrey A Reimer; Douglas S Clark
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-07       Impact factor: 11.205

7.  To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent.

Authors:  Jayangika N Dahanayake; Devaki N Gautam; Rajni Verma; Katie R Mitchell-Koch
Journal:  Mol Simul       Date:  2016-03-22       Impact factor: 2.178

8.  Biocatalytic synthesis of acrylates in supercritical fluids: tuning enzyme activity by changing pressure.

Authors:  S V Kamat; B Iwaskewycz; E J Beckman; A J Russell
Journal:  Proc Natl Acad Sci U S A       Date:  1993-04-01       Impact factor: 11.205

9.  Water dynamics and salt-activation of enzymes in organic media: mechanistic implications revealed by NMR spectroscopy.

Authors:  Ross K Eppler; Russell S Komor; Joyce Huynh; Jonathan S Dordick; Jeffrey A Reimer; Douglas S Clark
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-03       Impact factor: 11.205

10.  Hydrogen/deuterium exchange study of subtilisin Carlsberg during prolonged exposure to organic solvents.

Authors:  Ezio Fasoli; Amaris Ferrer; Gabriel L Barletta
Journal:  Biotechnol Bioeng       Date:  2009-03-01       Impact factor: 4.530

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