Majumder Suman, Hansmann Ulrich H E, Janke Wolfhard
Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States.
Macromolecules. 2019 Aug 13;52(15):5491-5498. doi: 10.1021/acs.macromol.9b00562. Epub 2019 Jul 15.
The 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 intrapeptide interactions. Once intrapeptide 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 a linear fashion. The collapse dynamics is characterized by a dynamical critical exponent ≈ 0.5 that is much smaller than the values of = 1-2 reported for nonbiological polymers. This difference in the exponents is explained by the instantaneous formation of intrachain hydrogen bonds and local ordering that may be correlated with the observed fast folding times of proteins.
多肽主链的塌缩是蛋白质折叠的一个重要组成部分。我们以聚甘氨酸为探针，探索了蛋白质在水中塌缩的非平衡途径。我们发现，塌缩取决于水合作用和肽内相互作用之间的竞争。一旦肽内范德华相互作用占主导，链就会沿着一条非平衡途径塌缩，其特征是形成珍珠项链状的局部簇作为中间体，最终凝聚成一个单一的球状体。通过将这种粗化描述为沿链距离的函数的接触概率，我们提取了一个随时间线性增长的长度尺度。塌缩动力学的特征是动力学临界指数约为0.5，远小于非生物聚合物报道的1-2的值。指数上的这种差异可以通过链内氢键的瞬时形成和局部有序来解释，这可能与观察到的蛋白质快速折叠时间相关。
