Abstract/Details

Study of electrostatic effects on protein folding and binding stabilities


2005 2005

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Abstract (summary)

The electrostatic effects of 113 charge mutations on the folding stabilities of 8 different proteins were studied by carrying out the continuum electrostatic calculations. Instead of the widely used solvent-exclusion (SE) surface, we used the van der Waals (vdW) surface as the boundary between the protein and solvent dielectrics. The calculated effects were directly compared with the experimental results and the calculations using SE surface. In general, vdW surface did better work than SE surface. We conclude that: (1) the popular view that electrostatic interactions are generally destabilizing may have been based on overestimated desolvation cost as a result of using the SE surface as the dielectric boundary; (2) while solvent-exposed charges may not reliably contribute to protein stability, semi-buried salt bridges can provide significant stabilization; (3) the good correlations between the calculated results using van der Waals surface and the measurements (0.98 correlation for 27 mutations on cold shock protein, 0.7 correlation for 52 mutations on staphylococcal nuclease, and 0.8 correlation for 34 mutations on other 5 proteins) suggest electrostatic interaction make significant contributions to protein folding stabilities.

In addition, the electrostatic effects of 80 mutations on the binding stabilities of 6 different complexes were also studied. Three different protocols were used: (a) the dielectric boundary specified as the van der Waals (vdW) surface of the protein along with a protein dielectric constant (ϵ p) of 4; (b) the dielectric boundary specified as solvent exclusion (SE) surface along with ϵp = 4; and (c) “SE + (ϵp = 20)”. The “vdW + (ϵp = 4)” and “SE + (ϵp = 4)” protocol predicted an overall electrostatic destabilization. The “vdW + (ϵp = 4)” protocol was most consistent with experiment. At the very least, this study demonstrates that caution is required in drawing conclusions on electrostatic contributions based on a particular Poisson-Boltzmann calculation protocol.

Indexing (details)


Subject
Biophysics;
Biomedical research;
Molecular biology
Classification
0786: Biophysics
0541: Biomedical research
0307: Molecular biology
Identifier / keyword
Applied sciences; Biological sciences; Electrostatic; Protein folding
Title
Study of electrostatic effects on protein folding and binding stabilities
Author
Dong, Feng
Number of pages
157
Publication year
2005
Degree date
2005
School code
0065
Source
DAI-B 66/03, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
ISBN
9780542032158, 0542032155
Advisor
Zhou, Huan-Xiang; Ferrone, Frank
University/institution
Drexel University
University location
United States -- Pennsylvania
Degree
Ph.D.
Source type
Dissertations & Theses
Language
English
Document type
Dissertation/Thesis
Dissertation/thesis number
3167567
ProQuest document ID
304993850
Copyright
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
http://search.proquest.com/docview/304993850
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