Vitamin B12 binding to mutated human transcobalamin, in-silico study of TCN2 alanine scanning and ClinVar missense mutations/SNPs

Abstract

Many missense mutations/SNPs of the TCN2 gene (which yield Transcobalamin (TC)) were reported in the literature but no study is available about their effect on binding to vitamin B12(B12) at the structural level experimentally nor computationally. Predict the effect of TC missense mutations/SNPs on binding affinity to B12 and characterize their contacts to B12 at the structural level. TC-B12 binding energy difference from the wildtype (ΔΔGmut) was calculated for 378 alanine scanning mutations and 76 ClinVar missense mutations, repeated on two distinct X-ray structures of holoTC namely 2BB5 and 4ZRP. Destabilizing mutations then went through 100 ns molecular dynamics simulation to study their effect on TC-B12 binding at the structural level employing 2BB5 structure. Out of the studied 454 mutations (378 alanine mutations + 76 ClinVar mutations), 19 were destabilizing representing 17 amino acid locations. Mutation energy results show a neutral effect on B12 binding of several missense SNPs reported in the literature including I23V, G94S, R215W, P259R, S348F, L376S, and R399Q. Compared to the wildtype, all the destabilizing mutations have higher average RMSD-Ligand in the last 25% of the MD simulation trajectories and lower average hydrogen bond count while the other parameters vary. Previously reported TCN2 SNPs with an unknown effect on TC-B12 binding were found to have a neutral effect in the current study based on mutation energy calculations. Also, we reported 17 possible amino acids that destabilize TC-B12 binding upon mutation (four listed in ClinVar) and studied their structural effect computationally.

Graphical Abstract

Communicated by Ramaswamy H. Sarma

Keywords:

• Vitamin B12
• cobalamin
• molecular dynamics
• transcobalamin
• ClinVar
• missense mutation
• TCN2 gene
• TCN2 polymorphism
• I23V
• G94S
• R215W
• P259R
• S348F
• L376S
• R399Q

Acknowledgments

The authors thank the Hashemite University for funding this project. Also, we thank Prof. Ebba Nexo, Denmark for her valuable comments and guidance in relation to our vitamin B12 research projects.

Disclosure statement

No potential conflict of interest was reported by the authors.