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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Vorobjev, Yury N. Vila, Jorge A. Scheraga, Harold A. |
| Description | Author Affiliation: Vorobjev YN ( Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia.) |
| Abstract | A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford-Schellman integral if the proteins contain more than approximately 20-25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pK a's of the ionizable groups of these proteins within an average absolute value of 0.4 p K units and a maximum error of 1.2 p K units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford-Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics, as a function of pH. |
| ISSN | 15206106 |
| e-ISSN | 15205207 |
| Journal | The Journal of Physical Chemistry B |
| Issue Number | 35 |
| Volume Number | 112 |
| Language | English |
| Publisher | American Chemical Society (United States) |
| Publisher Date | 2008-09-04 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Proteins Chemistry Solvents Algorithms Animals Electric Conductivity Hydrogen-Ion Concentration Models, Molecular Muramidase Protein Conformation Ribonuclease, Pancreatic Sensitivity And Specificity Static Electricity Thermodynamics Time Factors Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Physical chemistry |
| Content Type | Text |
| Resource Type | Article |
| Subject | Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry |
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