GENERATING THE THERMALIZED AND EQUILIBRIATED UNFOLDED STATE ENSEMBLES

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 最近的兴趣在未折叠状态的复苏，部分是由NMR方法的发展，能够提供现场解决的结构信息的动机。测量结果表明，未折叠蛋白质的结构多样性比以前认为的要丰富得多。这些最近的工作似乎与Tanford及其同事的经典研究不一致，Tanford及其同事使用流体动力学方法证明变性蛋白质的全局尺寸表现出自避免无规卷曲聚合物的尺寸依赖性。我们已经开发了一个统计线圈模型的展开状态，成功地再现了全球的尺寸和局部结构的蛋白质在变性状态，从而解决和解问题。我们生成一个未折叠的状态合奏使用的统计线圈模型，该模型是基于在一个线圈库，蛋白质数据库的一个限制性子集的骨架构象频率，并受到排除的体积约束。该模型成功地再现了各种蛋白质的化学变性状态的全局尺寸（回转半径）和局部构象偏好（NMR残余偶极耦合（RDC））。未折叠状态结构的集合的最拉伸的成员贡献最多的RDC信号，而耦合的符号如下从线圈库中的聚脯氨酸II和β构象的优势。当骨架构象偏好包括与相邻残基的化学和构象身份的相关性时，与NMR数据的一致性得到改善。利用teragrid上可用的计算资源，我们可以运行溶剂化构象的多个短轨迹。这些模拟将产生一个未折叠态的热平衡系综，然后将提供给生物物理界用于各种热力学和动力学研究。此外，我们还可以为模拟生成真实的未折叠起始构型。因此，用于展开状态的物理上真实的模型应当节省计算资源，同时提高准确度。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The recent resurgence of interest in the unfolded state is partly motivated by the development of NMR methods that are capable of providing site-resolved structural information. The measurements indicate that unfolded proteins have far richer structural diversity than earlier believed. These recent works seem at odds with classic studies by Tanford and coworkers which demonstrate using hydrodynamic methods that the global dimensions of denatured proteins exhibit the size dependence expected for self-avoiding random coil polymers. We have developed a statistical coil model for the unfolded state which successfully reproduces the global dimensions and the local structure of proteins in the denatured state thereby resolving the reconciliation problem. We generate an unfolded state ensemble using a statistical coil model that is based on backbone conformational frequencies in a coil library, a restricted subset of the protein data bank, and is subjected to excluded volume constraints. The model successfully reproduces both the global dimensions (radius of gyration) and local conformational preferences (NMR residual dipolar couplings (RDCs)) of the chemically denatured state for a variety of proteins. The most stretched members of the ensemble of unfolded state structures contribute most to the RDC signal, while the sign of the couplings follows from the preponderance of polyproline II and beta conformers in the coil library. The agreement with the NMR data improves when the backbone conformational preferences include correlations with the chemical and conformational identity of neighboring residues. Using the computational resources available on teragrid we can run multiple short trajectories of solvated conformations. These simulations will yield a thermalized equilibriated ensemble of unfolded states which will then be made availbale to the biophysics community for various thermodynamic and kinetic studies.In addition, we can also generate realistic unfolded starting configurations for simulations. Thus, a physically realistic model for the unfolded state should save computational resources while increasing accuracy.