Effects of ligand binding upon flexibility of proteins.
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1.
Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.
Burak
B
Erman
D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D016011:Normal Distribution; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D011505:Protein-Tyrosine Kinases / Q000737:chemistry
D008024:Ligands; D011505:Protein-Tyrosine Kinases; C403262:TNK2 protein, human
ACK1; Gaussian network model; allostery; dimerization; flexibility; ligand binding; stiffness map