Fischer, Andre and Seitz, Tobias and Lochner, Adriane and Sterner, Reinhard and Merkl, Rainer and Bocola, Marco (2011) A Fast and Precise Approach for Computational Saturation Mutagenesis and its Experimental Validation by Using an Artificial (beta alpha)(8)-Barrel Protein. CHEMBIOCHEM, 12 (10). pp. 1544-1550. ISSN 1439-4227,
Full text not available from this repository. (Request a copy)Abstract
We present a computational saturation mutagenesis protocol (CoSM) that predicts the impact on stability of all possible amino acid substitutions for a given site at an internal protein interface. CoSM is an efficient algorithm that uses a combination of rotamer libraries, side-chain flips, energy minimization, and molecular dynamics equilibration. Because CoSM considers full side-chain and backbone flexibility in the local environment of the mutated position, amino acids larger than the wild-type residue are also modeled in a proper manner. To assess the performance of CoSM, the effect of point mutations on the stability of an artificial (beta alpha)(8)-barrel protein that has been designed from identical (beta alpha)(4)-half barrels, was studied. In this protein, position 234(N) is a previously identified stability hot-spot that is located at the interface of the two half barrels. By using CoSM, changes in protein stability were predicted for all possible single point mutations replacing wild-type Val234(N). In parallel, the stabilities of 14 representative mutants covering all amino acid classes were experimentally determined. A linear correlation of computationally and experimentally determined energy values yielded an R-2 value of 0.90, which is statistically significant. This degree of coherence is stronger than the ones we obtained for established computational methods of mutational analysis.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | SYNTHASE ALPHA-SUBUNIT; STRUCTURE PREDICTION; TRYPTOPHAN SYNTHASE; FORCE-FIELD; STABILITY; EVOLUTION; ENZYME; DISSECTION; MUTATIONS; MODELS; beta-alpha-barrels; molecular dynamics; molecular modeling; mutagenesis; protein engineering |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Reinhard Sterner Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Rainer Merkl |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 05 Jun 2020 08:51 |
| Last Modified: | 05 Jun 2020 08:51 |
| URI: | https://pred.uni-regensburg.de/id/eprint/20554 |
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