A physical basis for protein secondary structure

A physical theory of protein secondary structure is proposed and tested by performing exceedingly simple Monte Carlo simulations. In essence, secondary structure propensities are predominantly a consequence of two competing local effects, one favoring hydrogen bond formation in helices and turns, the other opposing the attendant reduction in sidechain conformational entropy on helix and turn formation. These sequence specific biases are densely dispersed throughout the unfolded polypeptide chain, where they serve to preorganize the folding process and largely, but imperfectly, anticipate the native secondary structure.

本研究提出了一种蛋白质二级结构的物理理论，并通过极为简易的蒙特卡洛（Monte Carlo）模拟对该理论进行了验证。本质而言，蛋白质二级结构倾向主要源于两种相互拮抗的局部效应：其一倾向于在螺旋与转角中形成氢键，其二则抵消螺旋与转角形成时伴随的侧链构象熵损失。这些序列特异性偏倚密集分布于未折叠的多肽链中，它们不仅预组织了折叠过程，还能在很大程度上（但并非完全）预判天然状态下的蛋白质二级结构。