Journal of Chemical Physics, Vol.114, No.20, 9184-9191, 2001
Ribonucleic acid folder: The earliest moves of a good structure seeker
We identify the earliest folding events of a classical soft-mode ribonucleic acid chain under renaturation conditions. Due to hard-mode elimination, when this problem is cast in terms of intrinsic (dihedral torsional) coordinates, the weight of the differential volume, resulting merely from the transformation from Cartesian onto intrinsic coordinates, is not constant. This inherent geometry resulting from the embedding of the infinite Cartesian space onto the compact torsional manifold has physical consequences, especially in the earliest folding times, when the intramolecular potential has not yet had a chance to outweigh it. Thus, the early folding events are induced by a coupling between the inherent geometry and the hydrodynamic drag, and they predate the occurrence of nonbonded intrachain interactions. Thus, by contrasting the early geometrically determined probability distribution in torsional conformation space with the energetically favorable regions, we elucidate how the interplay between hydrodynamic control and potential energy surface during the early stages of folding (10 ps-1 mus) determines the expediency of the process. In this way we are able to decide in simple cases whether geometry and Watson-Crick complementarities represent reinforcing or conflicting propensities, defining a good seeker or a bad folder.