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Fast In Silico Protein Folding by Introduction of Alternating Hydrogen Bond Potentials

Technical University of Delft, 2628 BL Delft, The Netherlands

Correspondence: Address reprint requests to M. G. Wolf, Technical University of Delft, Julianalaan 136, 2628 BL Delft, The Netherlands. E-mail: m.g.wolf{at}tudelft.nl.

We accelerate protein folding in all-atom molecular dynamics simulations by introducing alternating hydrogen bond potentials as a supplement to the force field. The alternating hydrogen bond potentials result in accelerated hydrogen bond reordering, which leads to rapid formation of secondary structure elements. The method does not require knowledge of the native state but generates the potentials based on the development of the tertiary structure in the simulation. In protein folding, the formation of secondary structure elements, especially -helix and β-sheet, is very important, and we show that our method can fold both efficiently and with great speed.