Effect of the R119G mutation on human P5CR structure and its interactions with NAD: Insights derived from molecular dynamics simulation and free energy analysis
机构:[1]Laboratory of Molecular Cardiology, Department of Cardiology,The First Affiliated Hospital of Kunming Medical University, Kunming, PR China昆明医科大学附属第一医院[2]Department of Computer Science, The Faculty of Basic Medicine, Kunming Medical University, Kunming, PR China[3]State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, PR China
Pyrroline-5-carboxylate reductase (P5CR), an enzyme with conserved housekeeping roles, is involved in the etiology of cutis laxa. While previous work has shown that the R119G point mutation in the P5CR protein is involved, the structural mechanism behind the pathology remains to be elucidated. In order to probe the role of the R119G mutation in cutis laxa, we performed molecular dynamics (MD) simulations, essential dynamics (ED) analysis, and Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on wild type (WT) and mutant P5CR-NAD complex. These MD simulations and ED analyses suggest that the R119G mutation decreases the flexibility of P5CR, specifically in the substrate binding pocket, which could decrease the kinetics of the cofactor entrance and egress. Furthermore, the MM-PBSA calculations suggest the R119G mutant has a lower cofactor binding affinity for NAD than WT. Our study provides insight into the possible role of the R119G mutation during interactions between P5CR and NAD, thus bettering our understanding of how the mutation promotes cutis laxa. (C) 2017 Elsevier Ltd. All rights reserved.
基金:
National Natural Sciences Foundation of ChinaNational Natural Science Foundation of China [30860278, 81160025, 81560075]; Leading Talent Program of Yunnan Province of China [L-201203]; Department of Science and Technology of Yunnan Province [2011CI 057]; Yunnan Province -Kunming Medical University [2012FB005]; Department of Education of Yunnan Province [ZD2010007]
第一作者机构:[1]Laboratory of Molecular Cardiology, Department of Cardiology,The First Affiliated Hospital of Kunming Medical University, Kunming, PR China
共同第一作者:
通讯作者:
通讯机构:[1]Laboratory of Molecular Cardiology, Department of Cardiology,The First Affiliated Hospital of Kunming Medical University, Kunming, PR China[3]State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, PR China
推荐引用方式(GB/T 7714):
Sang Peng,Xie Yue-Hui,Li Lin-Hua,et al.Effect of the R119G mutation on human P5CR structure and its interactions with NAD: Insights derived from molecular dynamics simulation and free energy analysis[J].COMPUTATIONAL BIOLOGY AND CHEMISTRY.2017,67:141-149.doi:10.1016/j.compbiolchem.2016.12.015.
APA:
Sang, Peng,Xie, Yue-Hui,Li, Lin-Hua,Ye, Yu-Jia,Hu, Wei...&Meng, Zhao-Hui.(2017).Effect of the R119G mutation on human P5CR structure and its interactions with NAD: Insights derived from molecular dynamics simulation and free energy analysis.COMPUTATIONAL BIOLOGY AND CHEMISTRY,67,
MLA:
Sang, Peng,et al."Effect of the R119G mutation on human P5CR structure and its interactions with NAD: Insights derived from molecular dynamics simulation and free energy analysis".COMPUTATIONAL BIOLOGY AND CHEMISTRY 67.(2017):141-149