Molecular dynamics simulations of pea (Pisum sativum) lectin structure with octyl glucoside detergents: the ligand interactions and dynamics.
The mitogenic pea (Pisum sativum) lectin is a legume protein of non-immunoglobulin nature capable of specific recognition of glucose derivatives without altering its structure. Molecular dynamics simulations were performed in a realistic environment to investigate the structure and interaction properties of pea lectin with various concentrations of n-octyl-beta-d-glucopyranoside (OG) detergent monomers distributed inside explicit solvent cell. In addition, the diffusion coefficients of the ligands (OG, Ca2+, Mn2+, and Cl-) and the water molecules were also reported. The structural flexibility of the lectin was conserved in all simulations. The self-assembly of OG monomers into a small micelle at the hydrophobic site of the lectin was noticed in the simulation with 20 OG monomers. The interaction energy analysis concludes that the lectin was appropriately termed an adaptive structure. One or rarely two binding sites were observed at an instant in each simulation that were electrostatically favoured for the OG to interact with the surface amino acid residues. Enhanced binding of OG to the pea lectin was quantified in the system containing only Ca2+ divalent ions. Interestingly, no binding was observed in the simulation without divalent ions. Furthermore, the lectin-ligand complex was stabilized by multiple hydrogen bonds and at least one water bridge. Finally, the work was also in accordance with the published work elsewhere that the simulations performed with different initial conditions and using higher nonbonded cutoffs for the van der Waals and electrostatic interactions provide more accurate information and clues than the single large simulation of the biomolecular system of interest.
Konidala
Praveen
P
Institute of Thermodynamics, Helmut-Schmidt-University / University of the Federal Armed Forces Hamburg, Holstenhofweg 85, D-22043 Hamburg, Germany.
Niemeyer
Bernd
B
D003198:Computer Simulation; D003902:Detergents / Q000737:chemistry* / Q000494:pharmacology; D005960:Glucosides / Q000737:chemistry* / Q000494:pharmacology; D006017:Glycolipids / Q000737:chemistry; D006860:Hydrogen Bonding / Q000187:drug effects; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D018532:Pisum sativum / Q000737:chemistry*; D037121:Plant Lectins / Q000737:chemistry*; D011487:Protein Conformation / Q000187:drug effects; D014867:Water
D003902:Detergents; D005960:Glucosides; D006017:Glycolipids; D008024:Ligands; D037121:Plant Lectins; D014867:Water; C018619:octyl-beta-D-glucoside