Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms
Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms
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DOI：
10.1093/bioinformatics/btm345
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发表时间：
2007-09-01
期刊：
影响因子：
5.8
通讯作者：
Galzitskaya, Oxana V.
中科院分区：
文献类型：
--
作者：
Glyakina, Anna V.;Garbuzynskiy, Sergiy O.;Galzitskaya, Oxana V.
动机：了解嗜热生物体中蛋白质稳定性的基础提出了一个普遍问题：与来自嗜温生物体的蛋白质相比，蛋白质的哪些结构特性导致来自嗜热生物体的蛋白质比来自嗜温生物体的蛋白质具有更高的热稳定性？结果：构建了一个包含来自嗜热和嗜温生物体的 373 个结构良好的蛋白质对的独特数据库。对来自嗜热生物和嗜温生物的蛋白质的比较表明，第一组的外部可接触水的残基比第二组的更紧密。在这两种情况下，蛋白质内部部分（水分子无法接近的残基）的包装是相同的。对嗜热生物蛋白质外部残基的氨基酸组成分析表明，Lys、Arg和Glu等氨基酸比例增加，而Ala、Asp、Asn、Gln、Thr、Ser和His等氨基酸比例减少。我们对折叠/展开行为的理论研究证实了实验观察结果，即嗜热和嗜温蛋白质中不同的相互作用仅在折叠过程中过渡态通过后才形成。因此，外部残基的不同包装可以解释来自嗜热和嗜温生物体的蛋白质的热稳定性差异。 可用性：373个结构排列良好的蛋白质对的数据库可在http://phys.protres.ru/resources/termo_ meso_base.html联系：ogalzit@vega.protres.ru补充信息：补充数据可在生物信息学在线获得。
Motivation: Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms?Results: A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins ( residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms.Availability: The database of 373 structurally well-aligned protein pairs is available at http://phys.protres.ru/resources/termo_ meso_base.htmlContact: ogalzit@ vega.protres.ruSupplementary information: Supplementary data are available at Bioinformatics online.