Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques

Biopolymers - Tập 34 Số 3 - Trang 347-355 - 1994
Franca Fraternali1, Wilfred F. van Gunsteren1
1Department of Physical Chemistry, Swiss Federal Institute of Technology Zürich ETH-Zentrum, 8092 Zürich Switzerland

Tóm tắt

AbstractThe free energy difference between two states of a molecular system separated by an energy barrier can generally be computed using the technique of umbrella sampling along a chosen reaction coordinate or pathway. The effect of a particular choice of pathway upon the obtained free energy difference is investigated by molecular dynamics simulation of a model system consisting of a glycine dipeptide in aqueous solution. Two different reaction coordinates connecting the so‐called C5 and C7 conformations, one involving intramolecular hydrogen bonds and the other involving the peptide ϕ, ψ angles, are considered.The Gibbs free energy differences ΔG(C5 – C7) are small in both cases, 1.5 ± 1 kJ mol−1 and 2.2 ± 1 kJ mol −1, respectively. The two different reaction coordinates yield free energy differences that are identical to within their statistical error. It is found that the exchange of solute–solute, solute–water, and water–water hydrogen bonds involves free energy changes of less than kBT, which points at the existence of a multitutde of low free energy pathways connecting the C5 and C7 dipeptide conformations. © 1994 John Wiley & Sons, Inc.

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Tài liệu tham khảo

10.1002/9780470141205.ch1

van Gunsteren W. F.(1991) inAdvances in Biomolecular Simulations American Institute of Physics (A.I.P.) Conference Proceedings Vol. 239 Lavery R. Rivail J.‐L. & Smith J. Eds. New York pp.131–146.

10.1016/0021-9991(77)90121-8

Beveridge D. L., 1989, Ann. Rev. Biophys. Biophys. Chem., 18, 431, 10.1146/annurev.bb.18.060189.002243

10.1063/1.458713

10.1063/1.461335

10.1002/prot.340030408

10.1021/ja00390a043

10.1073/pnas.79.13.4035

10.1021/ja00231a018

Tobias D. J. Sneddon S. F.&Brooks C. L. III (1991) inAdvances in Biomolecular Simulations American Institute of Physics (A.I.P.) Conference Proceedings Vol. 239 Lavery R. Rivail J.‐L. & Smith J. Eds. New York pp.181–199.

10.1016/0022-2836(90)90399-7

Seitfer S., 1966, The Proteins

10.1021/ma00209a027

10.1002/bip.1973.360120716

10.1021/ja00294a005

10.1002/qua.560290542

van Gunsteren W. F.&Berendsen H. J. C.(1987)Groningen Molecular Simulation (GROMOS) library Manual Biomos Nijenborgh 16 Groningen The Netherlands.

10.1007/978-94-015-7658-1_21

10.1016/0021-9991(77)90098-5

10.1063/1.448118

10.1002/bip.360270607

10.1016/0022-2860(75)87006-2

10.1002/bip.360261102

10.1021/ja00016a010

Head‐Gordon T., 1989, Int. J. Quantum. Chem., Quantum Biol. Symp., 16, 311

10.1016/0166-1280(89)85023-7

10.1016/0040-6031(90)80336-W

10.1021/ja00315a051

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Biopolymers

Tập 34 Số 3

347-355

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