Sudarsanam S, DuBose R F, March C J, Srinivasan S
Department of Protein Chemistry, Immunex Corporation, Seattle, Washington 98101, USA.
Protein Sci. 1995 Jul;4(7):1412-20. doi: 10.1002/pro.5560040715.
We present an automated method for modeling backbones of protein loops. The method samples a database of phi i + 1 and psi i angles constructed from a nonredundant version of the Protein Data Bank (PDB). The dihedral angles phi i + 1 and psi i completely define the backbone conformation of a dimer when standard bond lengths, bond angles, and a trans planar peptide configuration are used. For the 400 possible dimers resulting from 20 natural amino acids, a list of allowed phi i + 1, psi i pairs for each dimer is created by pooling all such pairs from the loop segments of each protein in the nonredundant version of the PDB. Starting from the N-terminus of the loop sequence, conformations are generated by assigning randomly selected pairs of phi i + 1, psi i for each dimer from the respective pool using standard bond lengths, bond angles, and a trans peptide configuration. We use this database to simulate protein loops of lengths varying from 5 to 11 amino acids in five proteins of known three-dimensional structures. Typically, 10,000-50,000 models are simulated for each protein loop and are evaluated for stereochemical consistency. Depending on the length and sequence of a given loop, 50-80% of the models generated have no stereochemical strain in the backbone atoms. We demonstrate that, when simulated loops are extended to include flanking residues from homologous segments, only very few loops from an ensemble of sterically allowed conformations orient the flanking segments consistent with the protein topology. The presence of near-native backbone conformations for loops from five different proteins suggests the completeness of the dimeric database for use in modeling loops of homologous proteins. Here, we take advantage of this observation to design a method that filters near-native loop conformations from an ensemble of sterically allowed conformations. We demonstrate that our method eliminates the need for a loop-closure algorithm and hence allows for the use of topological constraints of the homologous proteins or disulfide constraints to filter near-native loop conformations.
我们提出了一种用于构建蛋白质环骨架模型的自动化方法。该方法对从蛋白质数据库（PDB）的非冗余版本构建的φi + 1和ψi角数据库进行采样。当使用标准键长、键角和反式平面肽构型时，二面角φi + 1和ψi完全定义了二聚体的骨架构象。对于由20种天然氨基酸产生的400种可能的二聚体，通过汇总PDB非冗余版本中每个蛋白质环段的所有此类对，为每个二聚体创建了允许的φi + 1、ψi对列表。从环序列的N端开始，使用标准键长、键角和反式肽构型，为每个二聚体从各自的库中随机分配选定的φi + 1、ψi对来生成构象。我们使用这个数据库来模拟已知三维结构的五种蛋白质中长度从5到11个氨基酸不等的蛋白质环。通常，为每个蛋白质环模拟10,000 - 50,000个模型，并对其立体化学一致性进行评估。根据给定环的长度和序列，生成的模型中有50 - 80%在骨架原子中没有立体化学应变。我们证明，当模拟环扩展以包括来自同源片段的侧翼残基时，在空间允许的构象集合中，只有极少数环能使侧翼片段的取向与蛋白质拓扑结构一致。来自五种不同蛋白质的环存在近天然骨架构象，这表明用于同源蛋白质环建模的二聚体数据库是完整的。在此，我们利用这一观察结果设计了一种方法，该方法从空间允许的构象集合中筛选近天然环构象。我们证明，我们的方法无需环闭合算法，因此允许使用同源蛋白质的拓扑约束或二硫键约束来筛选近天然环构象。
