Abstract
The conformational lock was a bio-thermodynamic theory to explain the characteristics of interfaces in oligomeric enzymes and their effects on catalytic activity. The previous studies on superoxide dismutases (Cu, Zn-SODs) showed that the dimeric structure contributed to the high catalytic efficiency and the stability. In this study, steered molecular dynamics simulations were used firstly to study the main interactions between two subunits of Cu, Zn-SODs. The decomposition process study showed that there were not only four pairs of hydrogen bonds but also twenty-five residue pairs participating hydrophobic interactions between A and B chains of SOD, and van der Waals interactions occupied a dominant position among these residue pairs. Moreover, the residue pairs of hydrogen bonds played a major role in maintaining the protein conformation. The analysis of the energy and conformational changes in the SMD simulation showed that there were two groups (two conformational locks) between A and B chains of SOD. The first group consisted of one hydrogen-bond residues pair and seven hydrophobic interactions residues pairs with a total average energy of −30.10 KJ/mol, and the second group of three hydrogen-bond residues pair and eighteen hydrophobic interactions residues pairs formed with a total average energy of −115.23 KJ/mol.
Highlights
The conformational lock, which was firstly proposed by Poltorak in 1998, was a bio-thermodynamic theory to explain the characteristics of interfaces in oligomeric enzymes and their effects on catalytic activity
It could be seen that the structure reached equilibration after about 60 ns and that the relative root mean square deviation (RMSD) value was stable near 0.55 nm (Fig. 1a), and structures had good convergence during last 50 ns (Fig. 1b)
Steered molecular dynamics (SMD) simulations of Cu, Zn-SOD was used to analysis the process of dissociation and conformational lock, by describing the process of energy and conformational changes during the dimeric SOD dissociations
Summary
The conformational lock, which was firstly proposed by Poltorak in 1998, was a bio-thermodynamic theory to explain the characteristics of interfaces in oligomeric enzymes and their effects on catalytic activity This theory could be applied by using the structural and kinetics data, respectively. Where, δ was obtained from the kinetic plot of residue active versus time and depending only on the number of steps (n) before loss of activity of enzyme These made it possible to estimate the minimal number of steps for a dimer enzyme in the process of thermal dissociation into inactive monomers. Conformational lock theory might provide a special explanation about the process of thermal dissociation and denaturation by obtaining the certain quantity of real number of intermediate active forms (number of conformational locks) of an oligomeric protein[1,2,3,4,5,6]. These dramatic changes probably reflect changes in the tertiary structure consequent to rearrangements of the solvent-exposed hydrophobic dimer interface
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
