Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties.
Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties.
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DOI：
10.1007/s12013-013-9553-4
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发表时间：
2013-11
影响因子：
2.6
通讯作者：
Agrawal, Alok
中科院分区：
文献类型：
--
作者：
Chakraborty, Chiranjib;Agrawal, Alok
关键词：
血清c反应蛋白（CRP）被用作多种疾病炎症的标志物，包括自身免疫性疾病和心血管疾病。CRP是戊烷素家族的一员，由五个相同的亚基组成。CRP具有不同的配体结合特性，这取决于CRP的不同结构状态。然而，对CRP的分子动力学和相互作用特性了解甚少。在本研究中，我们使用SAPS、SCRATCH蛋白预测器、PDBsum、ConSurf、ProtScale、Drawhca、ASAView、side和SRide server对CRP的分子动力学、蛋白-蛋白和残基-残基相互作用进行了综合分析。我们用1GNH。生成两个五聚体（ABCDE和FGHIJ）的人CRP晶体结构。A-B、B-C、C-D、D-E、F-G、G-H、H-I、I-J、A-E和F-J亚基之间残残相互作用的残基数分别为12、11、10、11、12、11、10、11、10。15个反平行β片参与了β片拓扑结构，5个β发夹参与了二级结构的形成。疏水段分布分析显示，CRP在不同空腔处的表面疏水性存在差异。大约33%的残留物参与了稳定中心。我们表明，生物信息学工具可以提供一种快速预测CRP分子动力学和相互作用特性的方法。我们对CRP分子动力学和相互作用特性的预测与基于已知CRP三维结构的建模数据相结合，有助于设计稳定形式的CRP突变体，用于CRP的结构-功能研究，并可能促进针对CRP治疗靶向的硅药物设计。
Serum C-reactive protein (CRP) is used as a marker of inflammation in several diseases including autoimmune disease and cardiovascular disease. CRP, a member of the pentraxin family, is comprised of five identical subunits. CRP has diverse ligand-binding properties which depend upon different structural states of CRP. However, little is known about the molecular dynamics and interaction properties of CRP. In this study, we used SAPS, SCRATCH protein predictor, PDBsum, ConSurf, ProtScale, Drawhca, ASAView, SCide and SRide server and performed comprehensive analyses of molecular dynamics, protein–protein and residue–residue interactions of CRP. We used 1GNH.pdb file for the crystal structure of human CRP which generated two pentamers (ABCDE and FGHIJ). The number of residues involved in residue–residue interactions between A–B, B–C, C–D, D–E, F–G, G–H, H–I, I–J, A–E and F–J subunits were 12, 11, 10, 11, 12, 11, 10, 11, 10 and 10, respectively. Fifteen antiparallel β sheets were involved in β-sheet topology, and five β hairpins were involved in forming the secondary structure. Analysis of hydrophobic segment distribution revealed deviations in surface hydrophobicity at different cavities present in CRP. Approximately 33 % of all residues were involved in the stabilization centers. We show that the bioinformatics tools can provide a rapid method to predict molecular dynamics and interaction properties of CRP. Our prediction of molecular dynamics and interaction properties of CRP combined with the modeling data based on the known 3D structure of CRP is helpful in designing stable forms of CRP mutants for structure–function studies of CRP and may facilitate in silico drug design for therapeutic targeting of CRP.
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影响因子：
3
作者：
Ahmad S;Gromiha M;Fawareh H;Sarai A
通讯作者：
Sarai A
影响因子：
14.9
作者：
Cheng, J;Randall, AZ;Sweredoski, MJ;Baldi, P
通讯作者：
Baldi, P
影响因子：
4.8
作者：
Gaboriaud, C;Juanhuix, J;Arlaud, GJ
通讯作者：
Arlaud, GJ
影响因子：
5.8
作者：
Dosztányi, Z;Magyar, C;Simon, I
通讯作者：
Simon, I
DOI：
10.1073/pnas.83.21.8069
发表时间：
1986-11-01
影响因子：
11.1
作者：
BALDWIN, RL
通讯作者：
BALDWIN, RL