Role of disulfide bonds in modulating internal motions of proteins to tune their function: molecular dynamics simulation of scorpion toxin Lqh III.
A series of 1-ns MD simulations were performed on the scorpion toxin Lqh III in native and disulfide bond broken states. The removal of disulfide bonds has caused hydrogen bond network alteration in the five-residue turn, the long loop, the alpha-helix, the loop connecting strands II and III, and the C-terminal region. In addition and more importantly, it has influenced the amplitude of the fluctuations of five-residue turn, loops, and C-terminal region with a minor effect on the fluctuations of the cysteines in the broken bond sites. These findings suggest that disulfide bonds are not the most important factors in rigidifying their own locations, while they have more important effects at a global scale. Furthermore, our results reveal that disulfide bonds have considerable influence on the functionally important essential modes of motions and the correlations between the motions of the binding site residues. Therefore, we can conclude that disulfide bonds have a crucial role in modulating the function via adjusting the dynamics of scorpion toxin molecules. Although this conclusion cannot be generalized to all peptides and proteins, it demonstrates the importance of more investigations on this aspect of disulfide bond efficacy.
Moghaddam
Majid Erfani
ME
Department of Biophysics, Faculty of Science, Tarbiat Modarres University, Tehran, Iran.
Naderi-Manesh
Hossein
H
D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012604:Scorpion Venoms / Q000737:chemistry*; D012984:Software; D014118:Toxins, Biological / Q000737:chemistry*
D004220:Disulfides; C114939:Lqh III toxin; D011506:Proteins; D012604:Scorpion Venoms; D014118:Toxins, Biological