Gromiha M Michael, Pujadas Gerard, Magyar Csaba, Selvaraj Samuel, Simon Istvan
Computational Biology Research Center (CBRC), Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
Proteins. 2004 May 1;55(2):316-29. doi: 10.1002/prot.20052.
In nature, 1 out of every 10 proteins has an (alpha/beta)(8) (TIM)-barrel fold, and in most cases, pairwise comparisons show no sequence similarity between them. Hence, delineating the key residues that induce very different sequences to share a common fold is important for understanding the folding and stability of TIM-barrel domains. In this work, we propose a new consensus approach for locating these stabilizing residues based on long-range interactions, hydrophobicity, and conservation of amino acid residues. We have identified 957 stabilizing residues in 63 proteins from a nonredundant set of 71 TIM-barrel domains. Most of these residues are located in the 8-stranded beta-sheet, with nearly one half of them oriented toward the interior of the barrel and the other half oriented toward the surrounding alpha-helices. Several stabilizing residues are found in the N- and C-terminal loops, whereas very few appear in the alpha-helices that surround the internal beta-sheet. Further, these 957 residues are placed in 434 stabilizing segments of various sizes, and each domain contains 1-10 of these segments. We found that 8 segments per domain is the most abundant one, and two thirds of the proteins have 7-9 stabilizing segments. Finally, we verified the identified residues with experimental temperature factors and found that these residues are among the ones with less mobility in the considered proteins. We suggest that our new protocol serves as a powerful tool to identify the stabilizing residues in TIM-barrel domains, which can be used as potential candidates for studying protein folding and stability by means of protein engineering experiments.
在自然界中，每10种蛋白质中就有1种具有（α/β）（8）（TIM）桶状折叠结构，而且在大多数情况下，成对比较显示它们之间没有序列相似性。因此，确定那些能使非常不同的序列共享一种共同折叠结构的关键残基，对于理解TIM桶状结构域的折叠和稳定性很重要。在这项工作中，我们基于长程相互作用、疏水性和氨基酸残基的保守性，提出了一种用于定位这些稳定残基的新的共识方法。我们从71个TIM桶状结构域的非冗余集合中，在63种蛋白质中鉴定出了957个稳定残基。这些残基大多位于8股β折叠片中，其中近一半朝向桶状结构的内部，另一半朝向周围的α螺旋。在N端和C端环中发现了几个稳定残基，而在围绕内部β折叠片的α螺旋中则很少出现。此外，这957个残基被置于各种大小的434个稳定片段中，每个结构域包含1至10个这些片段。我们发现每个结构域8个片段是最丰富的，并且三分之二的蛋白质有7至9个稳定片段。最后，我们用实验温度因子验证了所鉴定的残基，发现这些残基在所研究的蛋白质中是流动性较小的残基。我们认为，我们的新方案是识别TIM桶状结构域中稳定残基的有力工具，这些残基可作为通过蛋白质工程实验研究蛋白质折叠和稳定性的潜在候选对象。
