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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Florián, Jan Goodman, Myron F. Warshel, Arieh |
| Description | Author Affiliation: Florián J ( Department of Chemistry, Loyola University, Chicago, IL 60626, USA. jfloria@luc.edu); |
| Abstract | The use of computers to simulate the functions of complex biological macromolecules is essential to achieve a microscopic description of biological processes and to model and interpret experimental data. Here we apply theoretical computational approaches to investigate the fidelity of T7 DNA polymerase, divided into discrete steps that include contributions from substrate binding, pK(a) shifts, and rate constants for the PO bond-breaking and bond-making processes. We begin by defining the discrimination between right and wrong nucleotides in terms of the free energy landscape for the dNMP incorporation reaction. We then use the linear response approximation and the empirical valence bond methods to obtain converging results for the contribution of the binding and chemical steps to the overall fidelity. These approaches are successful in reproducing general trends in the observed polymerase incorporation fidelity. The calculations demonstrate the potential for further integration of theoretical and experimental studies to analyze high- and low-fidelity DNA polymerases. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 19 |
| Volume Number | 102 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2005-05-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | DNA-Directed DNA Polymerase Chemistry Proteins Base Pairing Binding Sites Catalysis Computational Biology Computer Simulation DNA Hot Temperature Hydrogen-Ion Concentration Hydrolysis Ions Kinetics Ligands Macromolecular Substances Magnesium Models, Molecular Nucleic Acid Conformation Nucleotides Protein Conformation Structure-Activity Relationship Thermodynamics Research Support, N.I.H., Extramural Research Support, U.S. Gov't, P.H.S. Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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