Structural analysis of heme proteins: implications for design and prediction.
Structural analysis of heme proteins: implications for design and prediction.
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DOI：
10.1186/1472-6807-11-13
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发表时间：
2011-03-03
影响因子：
--
通讯作者：
Guo JT
中科院分区：
文献类型：
--
作者：
Li T;Bonkovsky HL;Guo JT
血红素是一种重要的分子，在许多生物过程中起着重要作用。大量血红素蛋白的结构测定使得研究血红素结合环境的详细化学和结构特性成为可能。这些特性的知识可以提供有价值的指导方针，在设计新的血红素蛋白，并帮助我们预测未知的血红素结合蛋白。本文构建了一个包含125条血红素结合蛋白链的非冗余数据集，发现这些血红素蛋白至少包含31个不同的结构折叠，所有的-α类都是主要的骨架。血红素结合口袋富含芳香族和非极性氨基酸，带电残基较少。血红素蛋白的脱辅基形式和全血红素形式在结构和结合口袋方面的差异已被研究。在大多数情况下，蛋白质在血红素结合时经历小的构象变化。我们还研究了CP（半胱氨酸-脯氨酸）血红素调控基序，并证明了保守的二肽在蛋白质-血红素相互作用中具有结构上的意义。我们的分析表明，血红素结合口袋显示出特殊的功能，大多数血红素蛋白在血红素结合后发生了小的构象变化，这表明载脂蛋白结构可以用于基于结构的血红素蛋白预测和作为未来血红素蛋白设计的支架。
Heme is an essential molecule and plays vital roles in many biological processes. The structural determination of a large number of heme proteins has made it possible to study the detailed chemical and structural properties of heme binding environment. Knowledge of these characteristics can provide valuable guidelines in the design of novel heme proteins and help us predict unknown heme binding proteins. In this paper, we constructed a non-redundant dataset of 125 heme-binding protein chains and found that these heme proteins encompass at least 31 different structural folds with all-α class as the dominating scaffold. Heme binding pockets are enriched in aromatic and non-polar amino acids with fewer charged residues. The differences between apo and holo forms of heme proteins in terms of the structure and the binding pockets have been investigated. In most cases the proteins undergo small conformational changes upon heme binding. We also examined the CP (cysteine-proline) heme regulatory motifs and demonstrated that the conserved dipeptide has structural implications in protein-heme interactions. Our analysis revealed that heme binding pockets show special features and that most of the heme proteins undergo small conformational changes after heme binding, suggesting the apo structures can be used for structure-based heme protein prediction and as scaffolds for future heme protein design.
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影响因子：
4.8
作者：
Coste, H;Rodríguez, JC
通讯作者：
Rodríguez, JC
影响因子：
--
作者：
Kim R;Guo JT
通讯作者：
Guo JT
DOI：
10.1107/s0907444906052024
发表时间：
2007-03-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Carson, Mike;Johnson, David H.;DeLucas, Lawrence J.
通讯作者：
DeLucas, Lawrence J.
影响因子：
2.9
作者：
Brylinski, Michal;Skolnick, Jeffrey
通讯作者：
Skolnick, Jeffrey
DOI：
10.1073/pnas.78.2.780
发表时间：
1981-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
LEUTZINGER, Y;BEYCHOK, S
通讯作者：
BEYCHOK, S