Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures.
Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures.
复制标题
DOI：
10.1371/journal.pone.0024533
复制
发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Esposito L
中科院分区：
文献类型：
--
作者：
Improta R;Vitagliano L;Esposito L
结合量子力学分析和肽/蛋白质结构数据库的统计调查，我们在这里报告了一个深入的调查的构象依赖性的蛋白质结构的基本元素的肽键的几何形状。采用DFT、MP2和CCSD（T）计算方法，对不同的肽模型体系进行了水溶液和气相的量子力学研究。此外，在不存在残基间相互作用的情况下，平面性的小变形更是一种规则而不是例外，并且它们主要由主链的反二面角决定。这些迹象完全证实了准确的蛋白质/肽结构的统计调查。轨道分析表明，C α取代基的σ系统和酰胺键的π系统之间的轨道相互作用对调节肽键畸变是至关重要的。因此，我们的研究表明，虽然长程分子间相互作用可以明显影响肽的平面性，其影响是统计平均。因此，蛋白质中的肽键几何形状的可变性可以通过极其简化的系统显着再现，因为局部因素是这些观察到的趋势的主要驱动力。本研究结果的蛋白质结构的测定，验证和预测的影响进行了讨论。
By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed.
登录
查看更多内容
影响因子：
15
作者：
Hu, JS;Bax, A
通讯作者：
Bax, A
影响因子：
5.6
作者：
Esposito, L;Vitagliano, L;Mazzarella, L
通讯作者：
Mazzarella, L
DOI：
10.1039/ft9938902631
发表时间：
1993-08-07
期刊：
JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS
影响因子：
--
作者：
BURTON, NA;CHIU, SSL;VINCENT, MA
通讯作者：
VINCENT, MA
蛋白质中主链几何形状的构象依赖性。
DOI：
10.1016/j.str.2009.08.012
发表时间：
2009-10-14
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Berkholz DS;Shapovalov MV;Dunbrack RL Jr;Karplus PA
通讯作者：
Karplus PA
影响因子：
15
作者：
HEADGORDON, T;HEADGORDON, M;POPLE, JA
通讯作者：
POPLE, JA