Kamal Md Mostafa, Shantanu Kazi Fahmida Haque, Teeya Shamiha Tabassum, Rahman Md Motiar, Hasan A K M Munzurul, Chivers Douglas P, Wani Tanveer A, Alshammari Atekah Hazzaa, Rachamalla Mahesh, da Silva Junior Francisco Carlos, Hossen Md Munnaf
Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
Department of Botany, National University, Gazipur, Bangladesh.
PLoS One. 2025 Jan 24;20(1):e0316465. doi: 10.1371/journal.pone.0316465. eCollection 2025.
The cytotoxic T-lymphocyte antigen-4 (CTLA4) is essential in controlling T cell activity within the immune system. Thus, uncovering the molecular dynamics of single nucleotide polymorphisms (SNPs) within the CTLA4 gene is critical. We identified the non-synonymous SNPs (nsSNPs), examined their impact on protein stability, and identified the protein sequences associated with them in the human CTLA4 gene. There were 3134 SNPs (rsIDs) in our study. Out of these, 186 missense variants (5.93%), 1491 intron variants (47.57%), and 91 synonymous variants (2.90%), while the remaining SNPs were unspecified. We utilized SIFT, PolyPhen-2, PROVEAN, and SNAP for identifying deleterious nsSNPs, and SNPs&GO, PhD SNP, and PANTHER for verifying risk nsSNPs in the CTLA4 gene. Following SIFT analysis, six nsSNPs were identified as deleterious and reporting second and third nsSNPs as probably damaging and one as benign, respectively. From upstream analysis, rs138279736, rs201778935, rs369567630, and rs376038796 were found to be deleterious, probably damaging, and disease associated. ConSurf predicted conservation scores for four nsSNPs, and Project Hope suggested that all mutations could disrupt protein interactions. Furthermore, mCSM and DynaMut2 analyses indicated a decrease in ΔΔG stability for the mutants. GeneMANIA and STRING networks highlighted correlations with CD86 and CD80 genes. Finally, MD simulation revealed consistent fluctuation in RMSD and RMSF, consequently Rg, hydrogen bonds, and PCA in the mutant proteins compared with wild-type, which might alter the functional and structural stability of CTLA4 protein. The current comprehensive study shows how various nsSNPs in the CTLA4 gene can modify the structural and functional characteristics of the protein, potentially influencing the pathogenesis of diseases in humans. Further, experimental studies are needed to analyze the effect of these nsSNPs on the susceptibility of pathological phenotype populations.
细胞毒性T淋巴细胞抗原4（CTLA4）在控制系统内的T细胞活性方面至关重要。因此，揭示CTLA4基因内单核苷酸多态性（SNP）的分子动力学至关重要。我们鉴定了非同义SNP（nsSNP），研究了它们对蛋白质稳定性的影响，并确定了人类CTLA4基因中与之相关的蛋白质序列。我们的研究中有3134个SNP（rsID）。其中，186个错义变异（5.93%）、1491个内含子变异（47.57%）和91个同义变异（2.90%），其余SNP未明确分类。我们利用SIFT、PolyPhen-2、PROVEAN和SNAP来鉴定有害的nsSNP，并利用SNPs&GO、PhD SNP和PANTHER来验证CTLA4基因中的风险nsSNP。经过SIFT分析，鉴定出6个nsSNP为有害，另外分别有第二个和第三个nsSNP被报告为可能有害和良性。从上游分析来看，rs138279736、rs201778935、rs369567630和rs376038796被发现是有害的、可能有害的且与疾病相关。ConSurf预测了4个nsSNP的保守性得分，Project Hope表明所有突变都可能破坏蛋白质相互作用。此外，mCSM和DynaMut2分析表明突变体的ΔΔG稳定性降低。GeneMANIA和STRING网络突出了与CD86和CD80基因的相关性。最后，分子动力学模拟显示，与野生型相比，突变蛋白的均方根偏差（RMSD）和均方根波动（RMSF）存在一致波动，因此其回旋半径（Rg）、氢键和主成分分析（PCA）也有变化，这可能会改变CTLA4蛋白的功能和结构稳定性。当前的综合研究表明，CTLA4基因中的各种nsSNP如何改变蛋白质的结构和功能特征，可能影响人类疾病的发病机制。此外，需要进行实验研究来分析这些nsSNP对病理表型人群易感性的影响。
