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Integrating State-of-the-Art in silico Tools With Molecular Docking to Predict the Impact of the Most Deleterious Amino Acid Substitutions on TRAPPC6A Protein


Affiliations
1 Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil 51001, Iraq
2 Babylon Directorate of Education, Ministry of Education, Babil 51001, Iraq
 

Trafficking Protein Particle Complex subunit 6A (TRAPPC6A) is an important molecule that is mainly involved in the transport of vesicles to the cis-Golgi membrane. Loss of function in this protein leads to a variety of severe disorders. The present study was conducted to prioritize the most deleterious effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on TRAPPC6A protein. Two approaches were employed, sequence-based and structure-based, to predict which nsSNP has the most harmful effects on TRAPPC6A. Docking was performed to compare the ability of normal TRAPPC6A and its most delete-rious mutants to bind with the corresponding recep-tor. All utilized in silico tools indicated highly damaging impacts of three nsSNPs, viz. W74C, G125S and G129D. Docking showed remarkable alterations in the atomic contact energy of TRAPPC6A binding with its receptor. The present finding provides a cost effective method for assessing the damaging effects of nsSNPs on TRAPPC6A, which may help in under-standing the impact of this protein on neurodevelop-mental disorders.

Keywords

Deleterious Mutants, in silico Tools, Molec-ular Docking, Protein Particle Complex, Single Nucleotide Polymorphism.
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  • Integrating State-of-the-Art in silico Tools With Molecular Docking to Predict the Impact of the Most Deleterious Amino Acid Substitutions on TRAPPC6A Protein

Abstract Views: 329  |  PDF Views: 113

Authors

Mohammed Baqur S. Al-Shuhaib
Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil 51001, Iraq
Jafar M. B. Al-Shuhaib
Babylon Directorate of Education, Ministry of Education, Babil 51001, Iraq

Abstract


Trafficking Protein Particle Complex subunit 6A (TRAPPC6A) is an important molecule that is mainly involved in the transport of vesicles to the cis-Golgi membrane. Loss of function in this protein leads to a variety of severe disorders. The present study was conducted to prioritize the most deleterious effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on TRAPPC6A protein. Two approaches were employed, sequence-based and structure-based, to predict which nsSNP has the most harmful effects on TRAPPC6A. Docking was performed to compare the ability of normal TRAPPC6A and its most delete-rious mutants to bind with the corresponding recep-tor. All utilized in silico tools indicated highly damaging impacts of three nsSNPs, viz. W74C, G125S and G129D. Docking showed remarkable alterations in the atomic contact energy of TRAPPC6A binding with its receptor. The present finding provides a cost effective method for assessing the damaging effects of nsSNPs on TRAPPC6A, which may help in under-standing the impact of this protein on neurodevelop-mental disorders.

Keywords


Deleterious Mutants, in silico Tools, Molec-ular Docking, Protein Particle Complex, Single Nucleotide Polymorphism.

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DOI: https://doi.org/10.18520/cs%2Fv120%2Fi2%2F398-405