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Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study

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Abstract

Cu–Zn superoxide dismutase 1 (SOD1) is a highly conserved bimetallic protein enzyme, used for the scavenging the superoxide radicals (O2 −) produced due to aerobic metabolism in the mitochondrial respiratory chain. Over 100 mutations have been identified and found to be in the homodimeric structure of SOD1. The enzyme has to be maintained in its dimeric state for the structural stability and enzymatic activity. From our investigation, we found that the mutations apart from the dimer interface residues are found to affect the dimer stability of protein and hence enhancing the aggregation and misfolding tendency of mutated protein. The homodimeric state of SOD1 is found to be held together by the non-covalent interactions. The molecular dynamics simulation has been used to study the hydrogen bond interactions between the dimer interface residues of the monomers in native and mutated forms of SOD1 in apo- and holo-states. The results obtained by this analysis reveal the fact that the loss of hydrogen bond interactions between the monomers of the dimer is responsible for the reduced stability of the apo- and holo-mutant forms of SOD1. The conformers with dimer interface residues in native and mutated protein obtained by the molecular dynamics simulation is subjected to quantum mechanical study using M052X/6-31G(d) level of theory. The charge transfer between N–H···O interactions in the dimer interface residues were studied. The weak interaction between the monomers of the dimer accounts for the reduced dimerization and enhanced deformation energy in the mutated SOD1 protein.

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Acknowledgments

The authors express their sincere thanks to HPCF Centre (High Performance Computing Facility) of DST Government of India at Hyderabad for allowing us to use the facility, where most of the calculations have been performed.

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  1. Department of Physics, Bharathiar University, Coimbatore, 641 046, India

    S. P. Keerthana & P. Kolandaivel

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  1. S. P. Keerthana
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  2. P. Kolandaivel
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Correspondence to P. Kolandaivel.

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Keerthana, S.P., Kolandaivel, P. Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study. J Biol Inorg Chem 20, 509–522 (2015). https://doi.org/10.1007/s00775-014-1235-1

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