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| Content Provider | PubMed Central |
|---|---|
| Author | Straub, J. E. Thirumalai, D. |
| Abstract | We present two methods to probe the energy landscape and motions of proteins in the context of molecular dynamics simulations of the helix-forming S-peptide of RNase A and the RNase A-3'-UMP enzyme-product complex. The first method uses the generalized ergodic measure to compute the rate of conformational space sampling. Using the dynamics of nonbonded forces as a means of probing the time scale for ergodicity to be obtained, we argue that even in a relatively short time (< 10 psec) several different conformational substrates are sampled. At longer times, barriers on the order of a few kcal/mol (1 cal = 4.184 J) are involved in the large-scale motion of proteins. We also present an approximate method for evaluating the distribution of barrier heights g(EB) using the instantaneous normal-mode spectra of a protein. For the S-peptide, we show that g(EB) is adequately represented by a Poisson distribution. By comparing with previous work on other systems, we suggest that the statistical characteristics of the energy landscape may be a "universal" feature of all proteins. |
| Starting Page | 809 |
| File Format | |
| ISSN | 10916490 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 3 |
| Volume Number | 90 |
| Language | English |
| Publisher Date | 1993-02-01 |
| Access Restriction | Open |
| Subject Keyword | Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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