Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model.
Using a recently developed statistical mechanics methodology, the solution structures and populations of the cyclic pentapeptide cyclo(D-Pro(1)-Ala(2)-Ala(3)-Ala(4)-Ala(5)) in DMSO are obtained ab initio, i.e., without using experimental restraints. An important ingredient of this methodology is a novel optimization of implicit solvation parameters, which in our previous publication [Baysal, C.; Meirovitch, H. J Am Chem Soc 1998, 120, 800-812] has been applied to a cyclic hexapeptide in DMSO. The molecule has been described by the simplified energy function E(tot) = E(GRO) + summation operator(k) sigma(k)A(k), where E(GRO) is the GROMOS force-field energy, sigma(k) and A(k) are the atomic solvation parameter (ASP) and the solvent accessible surface area of atom k. This methodology, which relies on an extensive conformational search, Monte Carlo simulations, and free energy calculations, is applied here with E(tot) based on the ASPs derived in our previous work, and for comparison also with E(GRO) alone. For both models, entropy effects are found to be significant. For E(tot), the theoretical values of proton-proton distances and (3)J coupling constants agree very well with the NMR results [Mierke, D. F.; Kurz, M.; Kessler, H. J Am Chem Soc 1994, 116, 1042-1049], while the results for E(GRO) are significantly worse. This suggests that our ASPs might be transferrable to other cyclic peptides in DMSO as well, making our methodology a reliable tool for an ab initio structure prediction; obviously, if necessary, parts of this methodology can also be incorporated in a best-fit analysis where experimental restraints are used.
Baysal
C
C
Supercomputer Computations Research Institute, Florida State University, Tallahassee, Florida 32306, USA.
Meirovitch
H
H
D004121:Dimethyl Sulfoxide; D006860:Hydrogen Bonding; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D012996:Solutions; D012997:Solvents; D013816:Thermodynamics
D010456:Peptides, Cyclic; D012996:Solutions; D012997:Solvents; C407429:cyclo(prolyl-alanyl-alanyl-alanyl-alanyl); D004121:Dimethyl Sulfoxide