In-silico analysis of nonsynonymous genomic variants within CCM2 gene reaffirm the existence of dual cores within typical PTB domain

Akhil Padarti; Ofek Belkin; Johnathan Abou-Fadel; Jun Zhang

doi:10.1016/j.bbrep.2022.101218

In-silico analysis of nonsynonymous genomic variants within CCM2 gene reaffirm the existence of dual cores within typical PTB domain

Biochem Biophys Rep. 2022 Jan 27:29:101218. doi: 10.1016/j.bbrep.2022.101218. eCollection 2022 Mar.

Authors

Akhil Padarti^{1

2}, Ofek Belkin¹, Johnathan Abou-Fadel¹, Jun Zhang¹

Affiliations

¹ Departments of Molecular & Translational Medicine (MTM), Texas Tech University Health Science Center El Paso (TTUHSCEP), El Paso, TX, 79905, USA.
² Department of Neurology, University of South Alabama School of Medicine, 5795 USA N Dr., Mobile, AL, 36608, USA.

Abstract

Purpose: The objective of this study is to validate the existence of dual cores within the typical phosphotyrosine binding (PTB) domain and to identify potentially damaging and pathogenic nonsynonymous coding single nuclear polymorphisms (nsSNPs) in the canonical PTB domain of the CCM2 gene that causes cerebral cavernous malformations (CCMs).

Methods: The nsSNPs within the coding sequence for PTB domain of human CCM2 gene, retrieved from exclusive database searches, were analyzed for their functional and structural impact using a series of bioinformatic tools. The effects of mutations on the tertiary structure of the PTB domain in human CCM2 protein were predicted to examine the effect of nsSNPs on the tertiary structure of PTB Cores.

Results: Our mutation analysis, through alignment of protein structures between wildtype CCM2 and mutant, predicted that the structural impacts of pathogenic nsSNPs is biophysically limited to only the spatially adjacent substituted amino acid site with minimal structural influence on the adjacent core of the PTB domain, suggesting both cores are independently functional and essential for proper CCM2 PTB function.

Conclusion: Utilizing a combination of protein conservation and structure-based analysis, we analyzed the structural effects of inherited pathogenic mutations within the CCM2 PTB domain. Our results predicted that the pathogenic amino acid substitutions lead to only subtle changes locally, confined to the surrounding tertiary structure of the PTB core within which it resides, while no structural disturbance to the neighboring PTB core was observed, reaffirming the presence of independently functional dual cores in the CCM2 typical PTB domain.

Keywords: Amino acid substitution; CCMs, cerebral cavernous malformations; CSC, CCM signaling complex; CUPSAT, Cologne University Protein Stability Analysis Tool; HOPE, Have (y)Our Protein Explained; I-TASSER, the iterative threading assembly refinement; INDELs, insertions/deletions; In-silico analysis; MAF, minor allele frequency; Nonsynonymous single nucleotide polymorphisms (nsSNPs); PANTHER, Protein ANalysis THrough Evolutionary Relationship; PDB, protein data bank; PH, pleckstrin homology; POLYPHEN-2, Polymorphism Phenotyping; PROVEAN, Protein Variation Effect Analyzer; PTB, phosphotyrosine binding; PTCs, premature termination codons; SIFT, Sorting Intolerant From Tolerant; Single nucleotide polymorphisms (SNPs); Superimposition of protein structures; Tertiary structure; nsSNP, nonsynonymous single nucleotide polymorphism.