Systematic stepsize variation: Efficient method for searching conformational space of polypeptides

✍ Scribed by Klein, Christian T.; Mayer, Bernd; K�hler, Gottfried; Wolschann, Peter

• Publisher: John Wiley and Sons
• Year: 1998
• Tongue: English
• Weight: 235 KB
• Volume: 19
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(199810)19:13<1470::aid-jcc4>3.0.co;2-n

✦ Synopsis

A new and efficient method for overcoming the multiple minima

Ž

. problem of polypeptides, the systematic stepsize variation SSV method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly Ž chosen dihedral angles are updated starting with a small stepsize i.e., magnitude . of rotation . A new structure is accepted only if it possesses a lower energy than the precedent one. Local minima are passed over by increasing the stepsize systematically. When no new structures are found any longer, the simulation is continued with the starting structure, but other trajectories will be followed due to the random order in updating the torsional angles. First, the method is tested with Met-enkephalin, a peptide with a known global minimum structure; in all runs the latter is found at least once. The global minimum conformations obtained in the simulations show deviations of "0.0004 kcalrmol from the reference structure and, consequently, are perfectly superposable. For Ž . comparison, Metropolis Monte Carlo simulated annealing MMC-SA is performed. To estimate the efficiency of the algorithm depending on the complexity of the optimization problem, homopolymers of Ala and Gly of different lengths are simulated, with both the SSV and the MMC-SA method. The comparative simulations clearly reveal the higher efficiency of SSV compared with MMC-SA.