In silico screening, molecular docking, and molecular dynamics studies of SNP-derived human P5CR mutants.
Pyrroline-5-carboxylate reductase (P5CR) encoded by PYCR1 gene is a housekeeping enzyme that catalyzes the reduction of P5C to proline using NAD(P)H as the cofactor. In this study, we used in silico approaches to examine the role of nonsynonymous single-nucleotide polymorphisms in the PYCR1 gene and their putative functions in the pathogenesis of Cutis Laxa. Among the 348 identified SNPs, 15 were predicted to be potentially damaging by both SIFT and PolyPhen tools; of them two SNP-derived mutations, R119G and G206W, have been previously reported to correlate with Cutis Laxa. These two mutations were therefore selected to be mapped to the wild-type (WT) P5CR structure for further structural and functional analyses. The results of comparative computational analyses using I-Mutant and Autodock reveal reductions in both stability and cofactor binding affinity of these two mutants. Comparative molecular dynamics (MD) simulations were performed to evaluate the changes in dynamic properties of P5CR upon mutations. The results reveal that the two mutations enhance the rigidity of P5CR structure, especially that of cofactor binding site, which could result in decreased kinetics of cofactor entrance and egress. Comparison between the structural properties of the WT and mutants during MD simulations shows that the enhanced rigidity of mutants results most likely from the increased number of inter-atomic interactions and the decreased number of dynamic hydrogen bonds. Our study provides novel insight into the deleterious effects of the R119G and G206W mutations on P5CR, and sheds light on the mechanisms by which these mutations mediate Cutis Laxa.
a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China.
Peng
P
Sang
a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China.
Wei
W
Hu
a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China.
Yu-Jia
YJ
Ye
a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China.
Lin-Hua
LH
Li
a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China.
Chao
C
Zhang
b Department of Computer Science, The Faculty of Basic Medicine , Kunming Medical University , Kunming , P.R China.
Yue-Hui
YH
Xie
a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China.
Zhao-Hui
ZH
Meng
D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D003198:Computer Simulation; D003483:Cutis Laxa / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics; D006801:Humans; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009249:NADP / Q000737:chemistry / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D000072417:Protein Domains; D011762:Pyrroline Carboxylate Reductases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000097502:delta-1-Pyrroline-5-Carboxylate Reductase
D009249:NADP; D011762:Pyrroline Carboxylate Reductases; D000097502:delta-1-Pyrroline-5-Carboxylate Reductase
Cutis Laxa; P5CR; PYCR1; in silicon approaches; structure–dynamics–function relationship