An evolutionary strategy for all-atom protein folding of the sixty-amino acid bacterial ribosomal protein L20

¹ Forschungszentrum Karlsruhe

^* To whom correspondence should be addressed. E-mail: wenzel{at}int.fzk.de.

Submitted on July 11, 2005
Revised on September 25, 2005
Accepted on 10 January 2006

	Abstract

We have investigated an evolutionary algorithm for de-novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations which converge to near-native conformations of this sixty amino-acid, four-helix protein. We observe a steady increase of "native content" in both simulated ensembles and a large number of near native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy forcefield PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin hopping technique for the trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population with leads to faster overall convergence.

Key Words: biomolecular forcefield, evolutionary algorithm, helical protein, protein folding, protein structure prediction, stochastic optimization