In silico analysis predicting effects of deleterious SNPs of human RASSF5 gene on its structure and functions

Md Shahadat Hossain,Arpita Singha Roy,Md Sajedul Islam

doi:10.1038/s41598-020-71457-1

Md Shahadat Hossain, Arpita Singha Roy + Show 1 more

Open Access

https://doi.org/10.1038/s41598-020-71457-1

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Abstract

Ras association domain-containing protein 5 (RASSF5), one of the prospective biomarkers for tumors, generally plays a crucial role as a tumor suppressor. As deleterious effects can result from functional differences through SNPs, we sought to analyze the most deleterious SNPs of RASSF5 as well as predict the structural changes associated with the mutants that hamper the normal protein–protein interactions. We adopted both sequence and structure based approaches to analyze the SNPs of RASSF5 protein. We also analyzed the putative post translational modification sites as well as the altered protein–protein interactions that encompass various cascades of signals. Out of all the SNPs obtained from the NCBI database, only 25 were considered as highly deleterious by six in silico SNP prediction tools. Among them, upon analyzing the effect of these nsSNPs on the stability of the protein, we found 17 SNPs that decrease the stability. Significant deviation in the energy minimization score was observed in P350R, F321L, and R277W. Besides this, docking analysis confirmed that P350R, A319V, F321L, and R277W reduce the binding affinity of the protein with H-Ras, where P350R shows the most remarkable deviation. Protein–protein interaction analysis revealed that RASSF5 acts as a hub connecting two clusters consisting of 18 proteins and alteration in the RASSF5 may lead to disassociation of several signal cascades. Thus, based on these analyses, our study suggests that the reported functional SNPs may serve as potential targets for different proteomic studies, diagnosis and therapeutic interventions.

Highlights

Ras association domain-containing protein 5 (RASSF5) is the leading member of Ras effector super family protein that prevents tumor growth by facilitating G 1/S arrest of cell c ycle[1,2,3,4,5,6]
The RASSF5A protein structure includes an N-terminal proline-rich section containing prospective SH3-binding sites, and a nuclear localization signal, a cysteine-rich C1-type zinc finger (C1) domain, a Ras-association (RA) domain that interacts with GTP-bound H-Ras or several other Ras subfamily GTPases, and a Salvador-RASSF-Hippo[9] domain that contains C-type carboxy-terminal tail (Fig. 1), which is essential for binding to pro-apoptotic kinases MST1/215 and interaction factors WW45/SAV110,11
It revealed 20 nsSNPs in three different domains of the protein, where two nsSNPs were positioned in the Zinc finger domain that interacts with Ras association (RA) domain[38], eleven (11) nsSNPs were located in the RA domain[3], which serves as the binding site for active GTP-bound Ras, and the rest seven (7) nsSNPs were present in the SARAH domain that is crucial for cell apoptosis[39]

Summary

Introduction

Ras association domain-containing protein 5 (RASSF5) is the leading member of Ras effector super family protein that prevents tumor growth by facilitating G 1/S arrest of cell c ycle[1,2,3,4,5,6]. Human genome shares about 99.9% identical DNA sequences globally and the rest 0.1% of the genome contains individual variations. This variation in the individual genome is resulted from random m utations[12]. Alterations in the protein sequence may affect alteration of protein charge, geometry, hydrophobicity[22], dynamics, translation, and inter/intra protein interaction[6,23,24] putting cells in danger[25]. This information confirms that nsSNPs, especially missense SNPs, are associated with various human diseases. In the present study, we explored various bioinformatics tools and servers to find out the functional effects of nsSNPs of RASSF5 protein

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