Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space.
A new minimization procedure for the global optimization in cartesian coordinate space of the conformational energy of a polypeptide chain is presented. The Metropolis Monte Carlo minimization is thereby supplemented by a thermalization process, which is initiated whenever a structure becomes trapped in an area containing closely located local minima in the conformational space. The method has been applied to the endogenous opioid pentapeptide methionine enkephalin. Five among 13 different starting conformations led to the same apparent global minimum of an in-house developed energy function, a type II' reverse turn, the central residues of which are Gly-3-Phe-4. A comparison between the ECEPP/2 global minimum conformation of methionine enkephalin and the apparent one achieved by the present method shows that minimum-energy conformations having a certain similarity can be generated by relatively different force fields.
Caflisch
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A
Institute of Biomedical Engineering and Medical Informatics, Swiss Federal Institute of Technology, Zürich.
Niederer
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P
Anliker
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M
D000595:Amino Acid Sequence; D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011487:Protein Conformation; D013816:Thermodynamics
D004744:Enkephalin, Methionine