Department of Zoology, GC University, Lahore, Pakistan.
Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
J Biomol Struct Dyn. 2024;42(22):12214-12227. doi: 10.1080/07391102.2023.2268198. Epub 2023 Oct 10.
TGF-β1 is a potent immunoregulatory cytokine that plays diverse roles in development, bone healing, fibrosis, and cancer. However, characterizing gene variants is challenging because the structural and functional consequences of these variants are still undetermined. In this study, we aimed to perform an analysis of non-synonymous variants and their pathogenic effects on the TGF-β1 protein. A total of 10,252 SNPs were collected from the NCBI dbSNP database and tools (SIFT, PROVEAN, Mutation Taster, ClinVar, PolyPhen-2, CScape, MutPred, and ConSurf) were used. The predicted potential variants were further investigated for their binding to the TGF-β1 targeting drug "Fresolimumab". Molecular docking was performed using HADDOCK and confirmed by PRODIGY and PDBsum. The analysis predicted four potential nsSNPs: E47G in the LAP domain of the propeptide and I22T, L28F, and E35D in the mature TGF-β1 peptide. HADDOCK and molecular dynamics simulations revealed that the I22T and E35D variants have higher binding affinity for Fresolimumab as compared to the wild type and L28F variants. Molecular dynamics simulations (100 ns) and principal component analysis showed that variants influenced the protein structure and caused variations in the internal dynamics of protein complexes with the antibody. Among them, the E35D variant significantly destabilized the TGF-β1 protein structure, resulting in rearrangement in the binding site and affecting the interactions with the Fresolimumab. This study identified four variants that can affect the TGF-β1 protein structure and result in functional consequences such as impaired response to Fresolimumab.Communicated by Ramaswamy H. Sarma.
TGF-β1 是一种有效的免疫调节细胞因子，在发育、骨愈合、纤维化和癌症中发挥着多种作用。然而，对基因变异进行特征分析具有挑战性，因为这些变异的结构和功能后果仍未确定。在这项研究中，我们旨在分析非同义变异及其对 TGF-β1 蛋白的致病效应。从 NCBI dbSNP 数据库中收集了总共 10252 个 SNP，并使用了 SIFT、PROVEAN、Mutation Taster、ClinVar、PolyPhen-2、CScape、MutPred 和 ConSurf 等工具。预测的潜在变异进一步研究了它们与 TGF-β1 靶向药物“Fresolimumab”的结合。使用 HADDOCK 进行分子对接，并通过 PRODIGY 和 PDBsum 进行验证。分析预测了四个潜在的 nsSNP：前肽 LAP 结构域中的 E47G 和成熟 TGF-β1 肽中的 I22T、L28F 和 E35D。HADDOCK 和分子动力学模拟表明，与野生型和 L28F 变体相比，I22T 和 E35D 变体与 Fresolimumab 具有更高的结合亲和力。分子动力学模拟（100ns）和主成分分析表明，变体影响蛋白质结构，并导致与抗体的蛋白质复合物内部动力学发生变化。其中，E35D 变体显著破坏了 TGF-β1 蛋白质结构，导致结合位点重新排列，并影响与 Fresolimumab 的相互作用。这项研究鉴定了四个可能影响 TGF-β1 蛋白质结构并导致功能后果的变体，例如对 Fresolimumab 的反应受损。由 Ramaswamy H. Sarma 交流。
