Structural investigation of human wild-type Cu, Zn superoxide dismutase – a biomolecular case study using DL_POLY_3

Abstract

This article demonstrates the capability of DL_POLY_3 to study protein molecules at long time scales. The example shown here is the study of early stages of structural destabilisation of human superoxide dismutase (SOD1) as a result of metal depletions. Simulations of up to 4 ns have been carried out on wild-type SOD1. It is shown that the removal of metal ions from the active site essentially destabilises loop structures and provides a potential precursor for unintended protein–protein interactions to take place, as observed experimentally. The results reveal early stages of the destabilisation of structures that may enhance subsequent protein aggregations. It is found that the removal of Zn ion at the active sites of the protein enzyme causes a disruption to the Zn-loop and subsequently the electrostatic-loop (e-loops) with an increase in flexibility and mobility of the structures. The Zn ion is important to maintain structural integrity of the channel loops, whereas the Cu ions apparently play a lesser role in this aspect.

Keywords:

• Superoxide dismutase
• Molecular dynamics
• Protein unfolding
• Amyotrophic lateral sclerosis
• DL_POLY_3