Bioinformatics Analysis for Structure and Function of Common and Novel Cytochrome P4502C9 Variants
10.11969/j.issn.1673-548X.2024.10.013
- VernacularTitle:CYP2C9常见及新变异体结构和功能的生物信息学分析
- Author:
Qiuyue LAN
1
;
Jianping CAI
;
Dapeng DAI
Author Information
1. 100730 北京医院国家老年医学中心、国家卫生健康委北京老年医学研究所、国家卫生健康委老年医学重点实验室、中国医学科学院老年医学研究院
- Keywords:
Cytochrome P4502C9(CYP2C9);
Bioinformatics;
Molecular docking;
Protein structure and function
- From:
Journal of Medical Research
2024;53(10):67-73
- CountryChina
- Language:Chinese
-
Abstract:
Objective Bioinformatics tools were used to conduct a prediction analysis of common CYP2C9 variants(*3)and new variants(*76-*85)in our population,aiming to illustrate the impact of amino acid variants on the multidimensional aspects of CYP2C9 protein structure,properties,and functions.Methods The physicochemical properties,glycosylation and phosphorylation mod-ification,important structural domains,spatial structure and functional changes,and docking mode with the probe drug,tolbutamide,were predicted for each variant by applying various analytical tools.Results Compared with CYP2C9*1,the variants showed different degrees and multiple levels of alterations in amino acid sequence,local structural domains,phosphorylation sites,physicochemical proper-ties,tertiary structure,and docking patterns with substrates.*76 and*84 showed local structure,overall spatial structure,and function disruptions,and they were also correlated with disease outbreaks.*78-*79 and*81-*82 variants showed significant heterogeneity in the predicted results at different levels;*85 had an early termination codon and deletion of most critical structural domains due to a code-shift mutation,and the results suggested that it might affect the protein translation and the assembly of the whole enzyme.The pre-dicted results of the physicochemical properties,local structural domains,and stability of*3 were all non-significantly altered in com-parison with*1;however,docking results showed that*3 protein and tolbutamide were significantly changed in the shape,three-di-mensional size,and contact pattern of the docking pocket.Conclusion This study analyzed the effects of amino acid variants on pheno-types from multiple perspectives and levels,including protein primary,secondary,and tertiary structures,holoenzyme-drug docking,physicochemical properties,and functions,which provides essential references and new interpretative perspectives for future structural elu-cidation,ex vivo and in vivo drug metabolism experiments,and individualized dosing of CYP2C9 variants.
