赖氨酰氧化酶LOXL2稳定性的理论计算研究  

Insight into the Stability of LOXL2:a Computational Study

作　　者：林李锐 林凯 邹海鹰 许丽艳[4,5] 李恩民 东庚 LIN Li-Rui;LIN Kai;ZOU Hai-Ying;XU Li-Yan;LI En-Min;DONG Geng(Department of Biochemistry and Molecular Biology,Shantou University Medical College,Shantou 515041,China;Department of Bioinformatics,Shantou University Medical College,Shantou 515041,China;Medical Informatics Research Center,Shantou University Medical College,Shantou 515041,China;Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes,Shantou University Medical College,Shantou 515041,China;Cancer Research Center,Shantou University Medical College,Shantou 515041,China;Shantou Academy Medical Sciences,Shantou 515041,China)

机构地区：[1]汕头大学医学院生物化学与分子生物学教研室,广东汕头515041 [2]汕头大学医学院生物信息学教研室,广东汕头515041 [3]汕头大学医学院医学信息学研究中心,广东汕头515041 [4]汕头大学医学院广东省沿海高发地区分子生物学重点实验室,广东汕头515041 [5]汕头大学医学院肿瘤研究中心,广东汕头515041 [6]汕头市医学科学院,广东汕头515041

出　　处：《中国生物化学与分子生物学报》2024年第5期685-695,共11页Chinese Journal of Biochemistry and Molecular Biology

基　　金：国家自然科学青年基金(No.21907063,No.81472613);李嘉诚基金会(No.LD0101,No.2020LKSFG07B);广东省普通高校创新团队项目(No.2021KCXTD005);汕头大学医学院科研启动经费项目(No.510858063)资助。

摘　　要：赖氨酰氧化酶LOXL2是一种依赖于铜离子的胺氧化酶,催化胶原蛋白和弹性蛋白的赖氨酸残基侧链发生氧化脱氨,发挥着稳固细胞外基质的作用。而稳定性是蛋白质的一个重要特性,直接影响蛋白质的分子动态及其正常功能发挥,这与人类的健康和疾病密切相关。然而,关于LOXL2的稳定性目前鲜有报道,哪些位点对其稳定性有显著影响尚不清楚。本研究采用冷冻电镜和Alphafold2的数据,建立LOXL2的全长结构,通过分子动力学模拟得到其优化构象。再通过4种方法(mCSM,PremPS,DeepDDG和FoldX),计算所有位点的稳定性属性,筛选出对稳定性有显性影响的位点(定义为关键位点)。结果表明,95个关键位点对LOXL2的稳定性具有显著影响,在5个结构域上的分布数量依次为14、13、8、11和26,而结构域间的连接肽段上也有23个关键位点。在这些关键位点中,类型及数量分别为Leu(24个)、Val(20个)、Ile(12个)、Trp(11个)、Phe(11个)、Tyr(6个)、Cys(6个)、Met(4个)和Arg(1个)。其中大部分关键位点(88个)为疏水性质,这与蛋白质折叠的主要力量为疏水作用的情况是一致的,而Cys两两成对,构成二硫键,对LOXL2的结构及功能发挥重要作用。讨论中,我们将预测结果与实验值进行比较,并用自由能微扰方法,对部分关键位点进行比较,从多方面论证此项工作的可信度。此项研究,可为靶向LOXL2的疾病治疗研究,提供重要指导。Lysyl oxidase-like 2(LOXL2)is a Cu^(2+)-dependent amine oxidase,and it catalyzes the oxidative deamination of theε-amino group of Lys residues on elastin and collagen,which is critical for extracellular matrix modeling.Stability is an important property for protein and it directly affects the dynamics and function of protein,which strongly relates to the human health and disease.However,the stability of LOXL2 is not well defined,i.e.,which residues are important for its stability is unclear.In this paper,protein stability of LOXL2 was calculated by four methods,viz.mCSM,PremPS,DeepDDG and FoldX.Our results indicate that 95 residues(key residues)are important for the stability of LOXL2,with the amount of 14,13,8,11,26 in domain 1,2,3,4,5,respectively,while 23 in the linker between domains.Among these key residues,the types(numbers)are Leu(24),Val(20),Ile(12),Trp(11),Phe(11),Tyr(6),Cys(6),Met(4)and Arg(1).Most of the key residues are hydrophobic(88 in 95),which is consistent with the fact that hydrophobic interaction is the main force in protein folding.Cys residues are paired to constitute disulfide bonds,which play an important role in the structure and function of LOXL2.In the discussion,we compare the results with experimental data,and use the free energy perturbation for verification,which prove the reliability of this work.Thus,this study provides important insight for the research of disease treatment targeting LOXL2.

关 键 词：赖氨酰氧化酶样2 稳定性 分子动力学模拟 计算预测 吉布斯自由能 

分 类 号：Q180[生物学—普通生物学]