title: ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily.
abstract: Members of the extracellular immunoglobulin superfamily (IgSF) play a key role in immune regulation through the control of the co-stimulatory pathway, and have emerged as potent drug targets in cancers, infectious diseases, and autoimmunity. Despite the difficult experimental access to this class of proteins, single structures of ectodomains of IgSF proteins are solved with regularity. However, the most biologically critical challenge for this class of proteins is the identification of their cognate ligands that communicate intercellular signals. We describe a conceptually novel method, protein-ligand interface design (ProtLID), to identify cognate ligands from a subproteome for a given target receptor protein. ProtLID designs an optimal protein interface for a given receptor by running extensive molecular dynamics simulations of single-residue probes. The type and location of residue preferences establish a residue-based pharmacophore, which is subsequently used to find potential matches among candidate ligands within a subproteome.
authors.affiliation: Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
authors.forename: Eng-Hui
authors.initials: EH
authors.lastname: Yap
authors.affiliation: Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. Electronic address: andras.fiser@einstein.yu.edu.
authors.forename: Andras
authors.initials: A
authors.lastname: Fiser
mesh_terms: D006801:Humans; D007136:Immunoglobulins / Q000737:chemistry* / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D020543:Proteome / Q000378:metabolism*
chemical_list: D007136:Immunoglobulins; D008024:Ligands; D020543:Proteome
keywords: ProtLID; Protein ligand interface design; immunoglobulin superfamily; receptor-ligand identification