Pearl-Necklace-Like Local Ordering Drives Polypeptide Collapse
arXiv:1901.03066 · doi:10.1021/acs.macromol.9b00562
Abstract
Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between hydration effects and intra-peptide interactions. Once intra-peptide van der Waal interactions dominate, the chain collapses along a nonequilibrium pathway characterized by formation of pearl-necklace-like local clusters as intermediates that eventually coagulate into a single globule. By describing this coarsening through the contact probability as a function of distance along the chain, we extract a time-dependent length scale that grows in linear fashion. The collapse dynamics is characterized by a dynamical critical exponent that is much smaller than the values of reported for non-biological polymers. This difference in the exponents is explained by the instantaneous formation of intra-chain hydrogen bonds and local ordering that may be correlated with the observed fast folding times in proteins.
14 pages, 4 figures