title: Prediction of protein binding regions.
abstract: Identifying protein binding sites provides important clues to the function of a protein. Experimental methods to identify the binding sites such as determining the crystal structures of protein complexes are extremely laborious and expensive. Here, we present a computational technique called spatial aggregation propensity (SAP) based on molecular simulations to predict protein binding sites. We apply this technique to two model proteins, an IgG1 antibody and epidermal growth factor receptor (EGFR) and demonstrate that SAP predicts protein binding regions with very good accuracy. In the case of the IgG1 antibody, SAP accurately predicts binding regions with the Fc-receptor, protein-A, and protein-G. For EGFR, SAP accurately predicts binding regions with EGF, TGFα, and with another EGFR. The resolution of SAP is varied to obtain a detailed picture of these binding sites. We also show that some of these binding sites overlap with protein self-aggregation prone regions. We demonstrate how SAP analysis can be used to engineer the protein to remove unfavorable aggregation prone regions without disturbing protein binding regions. The SAP technique could be also used to predict the yet unknown binding sites of numerous proteins, thereby providing clues to their function.
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Naresh
authors.initials: N
authors.lastname: Chennamsetty
authors.forename: Vladimir
authors.initials: V
authors.lastname: Voynov
authors.forename: Veysel
authors.initials: V
authors.lastname: Kayser
authors.forename: Bernhard
authors.initials: B
authors.lastname: Helk
authors.forename: Bernhardt L
authors.initials: BL
authors.lastname: Trout
mesh_terms: D001665:Binding Sites; D066246:ErbB Receptors / Q000737:chemistry / Q000378:metabolism*; D007074:Immunoglobulin G / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D011485:Protein Binding
chemical_list: D007074:Immunoglobulin G; D066246:ErbB Receptors