(308g) Thermal and Mechanical, Multistate Folding Mechanisms of Ribonuclease H

Though several models describing the folding of proteins have been proposed, a clear understanding of the process remains elusive. Two of the most prominent theories concerning folding mechanisms are the hierarchical and the molten globule. The hierarchical process suggests that local secondary structures form first followed by formation of tertiary structure. The molten globule approach proposes that folding begins with hydrophobic collapse followed by a rearrangement of side chains where both secondary and tertiary structures form at approximately the same time. One of the difficulties in clarifying this apparent contradiction is that two different classes of experimental techniques exist by which protein folding mechanisms are ascertained. The first class, of which circular dichroism is an example, probes thermally-induced folding. The second class, which includes atomic force microscopy and optical-tweezers, measures mechanically-induced folding. In this work, we investigate if proteins fold/unfold via the same mechanisms both thermally and mechanically. We do so using a combined replica exchange and umbrella sampling approach to study Ribonuclease H, a protein that has been shown to fold through a three-state mechanism experimentally. A detailed, molecular-level description of the states involved in the folding processes shows that RNaseH follows a hierarchical process mechanically but a molten globule mechanism thermally (See Figure 1). Comparison to previous work suggests a universal folding behavior for proteins with a core helical bundle and gives answers to traditional criticisms about the hierarchical theory. Taken as a whole, the results offer improved understanding of 1) two-state vs. multistate folders, 2) mechanical vs. thermal denaturation, and 3) hierarchical vs. molten globule models.