REFINEMENT OF PREDICTED LOW-RESOLUTION PROTEIN MODELS TO HIGH-RESOLUTION ALL-AT

该子项目是利用 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来源获得主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 蛋白质结构预测中的一个主要挑战是将低分辨率预测模型（例如，与天然结构的骨架均方根偏差（RMSD）约为5的模型）细化为RMSD小于2的高分辨率全原子结构。到目前为止，只有少数记录的例子，在原子细节的结构已改善相对于其最初的起始构象。即使目标蛋白质的原始结构的RMSD约为5的低分辨率模型可用，但要精确到RMSD小于2的高分辨率结构可能很难实现。鉴于蛋白质结构预测算法（如我们实验室开发的TASSER）组装近似正确的天然结构的能力不断提高，应努力完善此类模型，以便它们可用于配体筛选以及更一般类型的功能注释。高分辨率结构在详细研究机制以及药物分子设计中是有用的，其中小（药物）分子的（原子）局部环境需要精确表征。虽然在生成和选择低分辨率结构方面取得了重大进展，但结构调整的最后一步仍然存在重大困难。尽管付出了相当大的努力，但从具有接近天然结构的蛋白质中进行结构精修已被证明是非常困难的，特别是如果使用所有原子模型和原子势的话。这是必要的低分辨率模型的成功改进，力场识别的天然结构的蛋白质作为最低的自由能最小值，它显示能量和天然相似的诱饵结构之间的相关性。目前的全原子力场在许多情况下不能识别天然结构作为最低的自由能最小值，并且诱饵的能量不会随着接近天然构象而单调降低。这种不准确性的来源可能是：a）。势B的数学形式）。在电势中缺乏重要的物理相互作用，例如极化或相关效应（多体相互作用），或c）。力场参数化不充分，其中没有包括关于能源景观全球形状的足够信息。大多数全原子力场依赖于这样的假设，即每个残基的构象对其相邻残基的构象在能量上不敏感（即它们不包含相邻残基的骨架构象（扭转角）的明确相关项）。然而，有实验和统计数据从解决蛋白质结构，表明氨基酸链中的残基的骨架构象与相邻残基的构象和身份相关。这些数据反映了蛋白质环境的影响，其中局部效应与溶剂和非局部效应的相关性是不可分离的。因此，重要的是确定局部相互作用（氨基酸序列中接近的残基之间）在多大程度上改变了可接近的构象空间，以及这种效应有多少来自非局部相互作用（空间上接近但序列上远离的残基之间）和溶剂化，以及当前现存的力场（不明确包括骨架相关性和极化）是否可以重现这些效应。可以想象，忽略一些重要的相互作用可能导致相对构象能的不准确，从而影响将天然结构鉴定为最低能量最小值的能力。然而，如果当前分子力学势的函数形式在数学上是正确的，那么无法将天然结构识别为全局能量最小值可能是由于力场参数的不正确细节引起的，这些力场参数应该可以通过重新参数化来修复。该项目的长期目标是评估和提高当前全原子力场的准确性，并开发方法来改进低分辨率蛋白质模型，这是由Skolnick及其同事开发的蛋白质结构预测方法导致的，以全原子表示的高分辨率结构。

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. A major challenge in protein structure prediction is the refinement of low-resolution predicted models (e.g. those with a backbone root-mean-square-deviation, RMSD, from the native structure of about 5 ), to high-resolution all-atom structures with a RMSD of less than 2 . To date, there have only been a few documented instances where structures at atomic detail have improved relative to their initial starting conformation. Even if low-resolution models with a RMSD from the native structure of about 5 were available for a target protein, the refinement to a high-resolution structure with a RMSD of less than 2 can be difficult to achieve. Given the increasing ability of protein structure prediction algorithms, such as TASSER developed in our laboratory, to assemble approximately correct native structures, the effort should be made to refine such models so that they can be used for ligand screening as well as more general types of functional annotation. High-resolution structures are useful in detailed studies of mechanisms as well as in the design of drug molecules in which the (atomic) local environment of the small (drug) molecule requires accurate characterization. While significant progress has been made in the generation of low-resolution structures and their selection, the final step of structural adjustment still poses significant difficulties. Despite considerable effort, structure refinement from proteins having near native structures has proven to be very difficult, especially if all atom models and atomic potentials are used. It is necessary for successful refinement of low-resolution models that the force field recognizes the native structure of a protein as the lowest free energy minimum, and it shows correlation between energy and the native-likeness of decoy structures. Current all-atom force fields in many cases fail to recognize the native structure as the lowest free energy minimum and energy of the decoys do not monotonically decreases as the native conformation is approached. The source of this inaccuracy may be: a). the mathematical form of the potential b). lack of important physical interactions in the potential, e.g. polarization or correlation effects (many body interactions), or c). inadequate parameterization of the force field, which does not include sufficient information about the global shape of the energy landscape. Most all-atom force fields rely on the assumption that the conformation of each residue is energetically insensitive to the conformation of its neighbors (i.e. they do not contain explicit correlation terms for the backbone conformation (torsional angles) of the neighboring residues). However, there are experimental and statistical data from solved protein structures, showing that the backbone conformation of a residue in the amino acid chain is correlated with the conformation and identity of the neighboring residues. These data reflect the influence of the environment of the protein, where the correlations of local effects with solvent and non-local effects are non-separable. Therefore, it is important to determine to what extent the local interactions (between residues close in amino acid sequence) alter the accessible conformational space and how much of this effect originates from non-local interactions (between residues close in space but distant in sequence) and solvation, and whether current extant force fields, that do not explicitly include backbone correlation and polarization can reproduce these effects. Conceivably, ignoring some important interactions could result in inaccuracies of the relative conformational energies thereby affecting the ability to identify the native structure as the lowest energy minimum. However, if the functional form of current molecular mechanics potentials is mathematically correct, then the failure to recognize the native structure as the global energy minimum could arise from incorrect details of the force field parameters that should be fixable by reparameterization. The long-term goal of this project is to evaluate and improve accuracy of current all-atom force fields and develop methodology to refine the low-resolution protein models, resulted from the protein structure prediction approaches developed by Skolnick and coworkers, to high-resolution structures in all-atom representation.