SIMULATION OF PROTEIN DYNAMICS AND UNFOLDING IN SOLUTION

溶液中蛋白质的计算机模拟方法 在第一个资助期内测试的系统将应用于 积极开展实验研究。我们的计算协议使用 周期框，明确包括溶剂分子，允许完全键合 长度和角度灵活，可顺畅地截断远程交互 并节约总能量。它提供了行为良好的轨迹，可以 计算效率高。我们新获得的跑得更长的能力， 更逼真的模拟，将帮助我们形成与 标准大学、美国国立卫生研究院、麻省理工学院和洛斯阿拉莫斯大学的实验合作者。 具体目标是： 1.我们能模拟尿素和三氟乙醇吗？我们将分子化为 动力学来模拟这些变性和复性溶液 不同的浓度和温度，并对它们进行校准 实验数据，以获得实际解决方案，用于展开和 重新折叠模拟。 2.α-螺旋和β-发夹结构是如何展开的？多长时间 螺旋展开的镜头？螺旋和发夹的成核中心是什么？ 队形？贝塔发夹是如何展开的，它的长程氢 键，不同于阿尔法螺旋的展开？这些问题将是 在持续1至10纳秒(Ns)的展开模拟中回答 在一定的温度范围内完成。通过缓慢降温，我们将 还试图重新折叠部分变性的α-螺旋和贝塔- 发夹。 3.蛋白质进化最早的事件是什么？我们小心翼翼地 选择了一组五种蛋白质，它们(A)小，(B)根据 不同的建筑原则，以及(C)正在进行实验研究。 短模拟(&lt；100ps)将在一定温度和范围内运行 密度。水的相互作用、填料接触和填料体积 将对变化进行分析，以揭示结构是如何被破坏的。这个 还将研究浓缩尿素和TFe的影响。 4.展开途径如何依赖于蛋白质的结构？正在运行 在高温下长时间(1-5 ns)的模拟应导致 在这里研究的每一种小蛋白都是为了揭示。这个世界的本质 将分析展开过程中的中间体及其形成方式 并进行了比较。 5.中间状态的流动性有多大？中间态的动力学 通过解开这五种蛋白质产生的蛋白质将在房间里运行 温度。半胱氨酸、疏水残基和电荷之间的距离 PARS将被监控。 6.我们能恢复部分α-乳清蛋白的天然折叠吗？我们会 使用我们的包装方法和模拟来预测稳定突变 对于已知的在低温下是熔化球体的部分。

Methods for computer simulation of proteins in solution developed and tested during the first funding period will be applied to systems under active experimental investigation. Our calculation protocol uses a periodic box, includes solvent molecules explicitly, allows full bond length and angle flexibility, truncates long-range interactions smoothly and conserves total energy. It gives well-behaved trajectories that can be computed efficiently. Our newly gained ability to run much longer, more realistic simulations, will help us form strong interactions with experimental collaborators at Standard, NIH, MIT and Los Alamos. Specific aims are: 1. Can we simulate urea and trifluoroethanol? We will molecular dynamics to simulate these denaturing and renaturing solutions at different concentrations and temperatures and calibrate them against experimental data to obtain realistic solutions for use in unfolding and refolding simulations. 2. How do alpha-helix and Beta-hairpin structures unfold? How long does helix unfolding take? What is the nucleation center for helix and hairpin formation? How does Beta-hairpin unfolding, with its long-rang hydrogen bonds, differ from alpha-helix unfolding? These questions will be answered in unfolding simulations lasting 1 to 10 nanoseconds (ns) to be done at a range of temperatures. By reducing temperature slowly, we will also attempt to refold partially denatured alpha-helices and Beta- hairpins. 3. What are the earliest events in protein unfolding? We have carefully chosen a set of five proteins that are (a) small, (b) built according to different architectural principles, and (c) under experimental study. Short simulations (<100ps) will be run at a range of temperatures and densities. Water interactions, packing contacts and packing volume changes will be analyzed to reveal how structure is disrupted. The effects of concentrated urea and TFE will also be investigated. 4. How do unfolding pathways depend on protein architecture? Running prolonged (1-5 ns) simulations at elevated temperatures should caused each of the small proteins studied here to unfold. The nature of the intermediates in unfolding and the way they are formed will be analyzed and compared. 5. How mobile are intermediate states? Dynamics of intermediate states generated by unfolding these five proteins will be run at room temperature. Distances between cysteine, hydrophobic residues and charge pairs will be monitored. 6. Can we restore a native fold to a part of alpha-lactalbumin? We will use our packing methods and simulations to predict stabilizing mutations for a part known to be a molten globule at low temperature.