NMRKIN: simulating line shapes from two-dimensional spectra of proteins upon ligand binding.
The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Gunther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT).
Günther
Ulrich L
UL
Biozentrum N230, Institut für Biophysikalische Chemie, J. W Goethe Universität, Frankfurt, Germany. ugunt@bpc.uni-frankfurt.de
Schaffhausen
Brian
B
D000465:Algorithms; D000818:Animals; D000952:Antigens, Polyomavirus Transforming / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D008024:Ligands; D008390:Markov Chains; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D012984:Software; D018909:src Homology Domains
D000952:Antigens, Polyomavirus Transforming; D008024:Ligands; D010446:Peptide Fragments; D019869:Phosphatidylinositol 3-Kinases