Reversible peptide folding: Dependence on molecular force field used
β Scribed by Damm, Wolfgang; van Gunsteren, Wilfred F.
- Book ID
- 101221816
- Publisher
- John Wiley and Sons
- Year
- 2000
- Tongue
- English
- Weight
- 312 KB
- Volume
- 21
- Category
- Article
- ISSN
- 0192-8651
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β¦ Synopsis
Temperature-dependent nuclear magnetic resonance (NMR) and CD spectra of methanol solutions of a Ξ²-heptapeptide have been interpreted in such a way that the secondary structure, a 3 14 -helix, is assumed to be stable in a temperature range of between 298 and 393 K. This is in contrast to the results of a 50-ns molecular dynamics simulation using the GROMOS96 force field, which found a melting temperature of about 340 K. This discrepancy is addressed by further computational studies using the OPLS-AA force field. The conformational energetics of N-formyl-3-aminobutanamide in vacuo are obtained using ab initio and density functional quantum-mechanical calculations at the HF/6-31G * , B3LYP/6-31G * , and B3LYP/6-311+G * levels of theory. The results permit development of torsional parameters for the OPLS-AA force field that reproduce the conformational energetics of the monomer. By varying the development procedure, three parameter sets are obtained that focus on reproducing either low-energy or high-energy conformations. These parameter sets are tested by simulating the reversible folding of the Ξ²-heptapeptide in methanol. The melting temperature of the helix formed (>360 K) is found to be higher than the one obtained from simulations using the GROMOS96 force field (βΌ340 K). Differences in the potential energy functions of the latter two force fields are evaluated and point to the origins of the difference in stability.
π SIMILAR VOLUMES
## Abstract Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model an
The C96 and AMBER95 force fields were compared with small model peptides Ac-(Ala) n -NMe (Ac = CH 3 CO, NMe = NHCH 3 , n = 2 and 3) in vacuo and in TIP3P water by computing the free-energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER