MOLECULAR DYNAMICS SIMULATIONS OF PROTEIN UNFOLDING

拟议研究的直接目标是执行现实的 与蛋白质折叠相关的分子模拟研究。 虽然很多 已知的天然折叠构象的结构细节， 对于蛋白质，人们对实际的折叠过程知之甚少。这 过程对许多生物过程有重要意义：蛋白质 降解、蛋白质移位、衰老和人类疾病，包括 癌症和淀粉样疾病。结构的确定 折叠过程中中间状态的特征对于 了解这些过程的机制。然而，合作社 折叠的性质通常只导致少量的部分 在平衡时折叠的中间体。此外，即使相对 分离出稳定的中间体，它们难以表征 由于增加了运动和缺乏固定结构， 整个分子。 鉴于蛋白质折叠对人类具有如此广泛的重要性， 健康和实验方法只能提供有限的数量， 关于结构转变和相互作用的信息 在蛋白质折叠过程中，计算机模拟方法为 阐明了该过程的分子细节。我们的做法是 进行分子动力学模拟，其中蛋白质是“变性”， 溶液通过这种方法，蛋白质展开时发生的事件 并且该过程中的任何中间体都可以在原子水平上表征， 水平实验方法不太可能永远能够 提供关于这些中间体和折叠的结构信息 其处理细节与天然蛋白质的处理细节相当。 因此，这是一个实验需要理论的领域。但是 模拟必须始终与实验进行比较，以确保它们是 相关的因此，α-裂解蛋白酶和胰凝乳蛋白酶抑制剂 2，和细胞色素b5的研究，作为实验研究， 这些蛋白质的折叠行为正在被积极地研究， 与这些实验者的合作已经开始。的结果 所有三种蛋白质的初步模拟与 实验，并建议这些模拟研究是值得追求的。 拟议的模拟应提供详细的动态，分子模型 折叠的中间体，超越，但又是互补的， 可以通过实验方法获得。此外， 用CI 2探索解折叠的过渡态。另外还有按 比较这两种蛋白质的解折叠特性， 确定蛋白质折叠过程中的一般作用力， 独立于所选择的模型系统。这些模拟还解决了 区分熔融球的是什么（例如，如通过α-裂解 蛋白酶）从其它折叠中间体（例如，脱辅基细胞色素b5）。后 调查这些和其他系统，我们将处于更好的位置， 将这些技术应用于与疾病直接相关的蛋白质， 可获得的实验数据较少。

The immediate goal of the proposed research is to perform realistic molecular modeling studies relating to protein folding. Although much is known of the structural details of the native folded conformation of proteins, very little is known about the actual folding process. This process has important implications for many biological processes: protein degradation, protein translocation, aging and human diseases, including cancer and amyloid diseases. Determination of the structural characteristics of intermediate states during folding are crucial for understanding the mechanism of these processes. However, the cooperative nature of folding generally results in only minute amounts of partially folded intermediates at equilibrium. Furthermore, even when relatively stable intermediates are isolated, they are difficult to characterize structurally because of the increased motion and lack of fixed structure throughout the molecules. Given that protein folding is of such widespread importance to human health and that experimental approaches provide only limited amounts of information on the structural transitions and interactions occurring during protein folding, computer simulation methods provide an avenue for elucidating the molecular details of the process. Our approach is to perform molecular dynamics simulations where the protein is "denatured" in solution. With this method, the events occurring as the protein unfolds and any intermediates in the process can be characterized at the atomic level. It is unlikely that experimental approaches will ever be able to provide structural information about these intermediates and the folding process in comparable detail to that available for native proteins. Therefore, this is an area where experiment needs theory. But, the simulations must always be compared to experiment to ensure that they are relevant. Consequently, alpha-lytic protease, and chymotrypsin inhibitor 2, and cytochrome b5 were chosen for study, as experimental studies of the folding behavior of these proteins are being pursued actively and collaborations with these experimentalists have begun. The results of preliminary simulations of all three proteins are in good agreement with experiment and suggest that these simulation studies are worth pursuing. The proposed simulations should provide detailed dynamic, molecular models of folding intermediates that go beyond, but are complementary to, what can be garnered using experimental methods. Furthermore, the nature of the transition state of unfolding is being explored with CI2. In addition, a comparison of the unfolding properties of these two proteins should allow determination of the general forces acting during protein folding that are independent of the model system chosen. These simulations also address what distinguishes a molten globule (e.g. as adopted by alpha-lytic protease) from other folding intermediates (e.g., apocytochrome b5). After investigating these and other systems, we will be in a better position to apply these techniques to proteins directly involved in diseases for which there are less experimental data available.