MOLECULAR DYNAMICS SIMULATIONS OF PROTEIN UNFOLDING

Daggett博士请求继续支持， 模拟蛋白质在溶液中的变性。取得了相当大的进展， 在上一个供资期间展开模拟描述， 建立方法，设计识别和测试模型的方法， 发展分析工具，以评价 部分未折叠和变性蛋白质的结构， 将模拟结果与实验结果进行比较， 实验结果。但是，仍然有一些问题需要解决。 处理。高温分子动力学模拟的解折叠 小的球状蛋白质将继续存在，但巨大的差异， 蛋白质解折叠的实验时间尺度以及 目前的计算机电源。该方法的有效性将通过以下方式进行评估： 在各种温度下进行模拟，使用化学 变性剂，并进行温度淬火模拟。此外，虽然它是 希望有能力随着时间的推移跟踪单一蛋白质，现在， 将进行多次模拟，以确保观察到的效果 代表了更大的合奏探测实验，和 从严格测试的模拟中识别的过渡态系综， 以确保它们是合理的。该项目将扩展到自由能源 微扰计算提供更直接的比较与实验 结果最后，具有改变的折叠行为的突变蛋白正在被 设计，完全基于分子动力学生成的模型。变种人 正在一个合作者的实验室里进行生产和实验评估， 英国著名剑桥酶学家艾伦·弗什特教授。

Dr. Daggett requests continuation support to perform computer simulations of protein denaturation in solution. Considerable progress with unfolding simulations during the last funding period is described, with respect to establishing the methods, devising ways to identify and test models of transition states, developing analysis tools for the evaluation of residual structure in partially unfolded and denatured proteins, developing approaches for comparison of simulation results with experiment, and predicting experimental outcomes. But, there are still a number of issues that need to be addressed. High temperature molecular dynamics simulations of the unfolding of small globular proteins will continue continue, but huge differences between the experimental time scale of protein unfolding and what is accessible with current computer power. The validity of this approach will be evaluated by performing simulations at a variety of temperatures, using chemical denaturants, and performing temperature-quenched simulations. Also, while it is desirable to have the ability to follow a single protein over time, now multiple simulations will be performed to ensure that the effects observed are representative of the much larger ensemble probed experimentally, and the transition state ensembles identified from the simulations tested rigorously, to ensure that they are reasonable. The project will be extended to free energy perturbation calculations to provide more direct comparisons with experimental results. Finally, mutant proteins with altered folding behavior are being designed, based solely on the molecular dynamics-generated models. The mutants are being produced and experimentally evaluated in the lab of a collaborator, Prof Alan Fersht, an eminent Cambridge UK enzymologist.