GENERATING THE THERMALIZED AND EQUILIBRIATED UNFOLDED STATE ENSEMBLES

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 最近人们对展开状态的兴趣重新抬头，部分原因是核磁共振方法的发展，这些方法能够提供位置分辨的结构信息。测量表明，未折叠蛋白质的结构多样性比之前认为的要丰富得多。这些最近的工作似乎与坦福德及其同事的经典研究不一致，后者使用流体力学方法证明，变性蛋白质的全球尺寸表现出自我避免随机卷曲聚合物所预期的尺寸依赖关系。我们建立了一个关于未折叠状态的统计线圈模型，它成功地再现了变性状态下蛋白质的全局尺寸和局部结构，从而解决了协调问题。我们使用统计线圈模型来生成展开态系综，该统计线圈模型基于线圈库中的骨架构象频率，该线圈库是蛋白质数据库的受限子集，并且受到排除的体积约束。该模型成功地再现了多种蛋白质化学变性状态的全局尺寸(旋转半径)和局部构象偏好(核磁共振剩余偶极耦合(RDC))。未折叠状态结构系综中拉伸最大的成员对RDC信号贡献最大，而偶联的符号来自线圈库中多聚脯氨酸II和β构象的优势。当主链构象偏好包括与邻近残基的化学和构象同一性的关联时，与核磁共振数据的一致性会得到改善。使用TeraGrid上可用的计算资源，我们可以运行多个溶剂化构象的短轨迹。这些模拟将产生一个热化平衡的展开状态系综，然后供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展开启动构型。因此，展开状态的物理真实模型应该在提高精度的同时节省计算资源。

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.