Guo Weihua, Lampoudi Sotiria, Shea Joan-Emma
Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, USA.
Proteins. 2004 May 1;55(2):395-406. doi: 10.1002/prot.20053.
The temperature dependence of the free energy landscape of the src-SH3 protein domain is investigated through fully atomic simulations in explicit solvent. Simulations are performed above and below the folding transition temperature, enabling an analysis of both protein folding and unfolding. The transition state for folding and unfolding, identified from the free energy surfaces, is found to be very similar, with structure in the central hydrophobic sheet and little structure throughout the rest of the protein. This is a result of a polarized folding (unfolding) mechanism involving early formation (late loss) of the central hydrophobic sheet at the transition state. Unfolding simulations map qualitatively well onto low-temperature free energy surfaces but appear, however, to miss important features observed in folding simulations. In particular, details of the folding mechanism involving the opening and closing of the hydrophobic core are not captured by unfolding simulations performed under strongly denaturing conditions. In addition, free energy surfaces at high temperatures do not display a desolvation barrier found at lower temperatures, involving the expulsion of water molecules from the hydrophobic core.
通过在显式溶剂中的全原子模拟，研究了src-SH3蛋白结构域自由能景观的温度依赖性。在折叠转变温度之上和之下进行模拟，从而能够对蛋白质折叠和去折叠进行分析。从自由能表面确定的折叠和去折叠的过渡态非常相似，中心疏水片层有结构，而蛋白质其余部分几乎没有结构。这是一种极化折叠（去折叠）机制的结果，该机制涉及在过渡态中心疏水片层的早期形成（后期丧失）。去折叠模拟在定性上与低温自由能表面吻合良好，但似乎遗漏了折叠模拟中观察到的重要特征。特别是，在强变性条件下进行的去折叠模拟没有捕捉到涉及疏水核心打开和关闭的折叠机制细节。此外，高温下的自由能表面没有显示出低温下发现的去溶剂化屏障，该屏障涉及水分子从疏水核心中排出。
