Carboxyl Peptide Plane Stacking Is Important for Stabilization of Buried E305 of Trichoderma reesei Cel5A | |
He, Chunyan; Chen, Jingfei; An, Liaoyuan; Wang, Yefei; Shu, Zhiyu; Yao, Lishan | |
2015 | |
发表期刊 | JOURNAL OF CHEMICAL INFORMATION AND MODELING |
卷号 | 55期号:1页码:104-113 |
摘要 | Hydrogen bonds or salt bridges are usually formed to stabilize the buried ionizable residues. However, such interactions do not exist for two buried residues D271 and E305 of Trichoderma reesei Cel5A, an endoglucanase. Mutating D271 to alanine or leucine improves the enzyme thermostability quantified by the temperature T-50 due to the elimination of the desolvation penalty of the aspartic acid. However, the same mutations for E305 decrease the enzyme thermostability. Free energy calculations based on the molecular dynamics simulation predict the thermostability of D271A, D271L, and E305A (compared to WT) in line with the experimental observation but overestimate the thermostability of E305L. Quantum mechanical calculations suggest that the carboxylpeptide plane stacking interactions occurring to E305 but not D271 are important for the carboxyl group stabilization. For the protonated carboxyl group, the interaction energy can be as much as about -4 kcal/mol for parallel stacking and about -7 kcal/mol for T-shaped stacking. For the deprotonated carboxyl group, the largest interaction energies for parallel stacking and T-shaped stacking are comparable, about -7 kcal/mol. The solvation effect generally weakens the interaction, especially for the charged system. A search of the carboxylpeptide plane stacking in the PDB databank indicates that parallel stacking but not T-shaped stacking is quite common, and the most probable distance between the two stacking fragments is close to the value predicted by the QM calculations. This work highlights the potential role of carboxyl amide pi-pi stacking in the stabilization of aspartic acid and glutamic acid in proteins. |
文章类型 | Article |
WOS标题词 | Science & Technology ; Life Sciences & Biomedicine ; Physical Sciences ; Technology |
DOI | 10.1021/ci500610m |
关键词[WOS] | PARTICLE MESH EWALD ; FREE-ENERGY ; MOLECULAR-DYNAMICS ; SALT BRIDGES ; BASIS-SETS ; PROTEIN ; SIMULATION ; STABILITY ; EFFICIENT ; SYSTEMS |
收录类别 | SCI |
语种 | 英语 |
WOS研究方向 | Pharmacology & Pharmacy ; Chemistry ; Computer Science |
WOS类目 | Chemistry, Medicinal ; Chemistry, Multidisciplinary ; Computer Science, Information Systems ; Computer Science, Interdisciplinary Applications |
WOS记录号 | WOS:000348619400010 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://ir.qibebt.ac.cn/handle/337004/6101 |
专题 | 蛋白质设计研究组 |
作者单位 | Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Lab Biofuels, Qingdao 266061, Peoples R China |
推荐引用方式 GB/T 7714 | He, Chunyan,Chen, Jingfei,An, Liaoyuan,et al. Carboxyl Peptide Plane Stacking Is Important for Stabilization of Buried E305 of Trichoderma reesei Cel5A[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2015,55(1):104-113. |
APA | He, Chunyan,Chen, Jingfei,An, Liaoyuan,Wang, Yefei,Shu, Zhiyu,&Yao, Lishan.(2015).Carboxyl Peptide Plane Stacking Is Important for Stabilization of Buried E305 of Trichoderma reesei Cel5A.JOURNAL OF CHEMICAL INFORMATION AND MODELING,55(1),104-113. |
MLA | He, Chunyan,et al."Carboxyl Peptide Plane Stacking Is Important for Stabilization of Buried E305 of Trichoderma reesei Cel5A".JOURNAL OF CHEMICAL INFORMATION AND MODELING 55.1(2015):104-113. |
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