Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. 1995

R Norel, and S L Lin, and H J Wolfson, and R Nussinov
Computer Science Department, School of Mathematical Sciences, Tel Aviv University, Israel.

Rigid-body docking of two molecules involves matching of their surfaces. A successful docking methodology considers two key issues: molecular surface representation, and matching. While approaches to the problem differ, they all employ certain surface geometric features. While surface normals are routinely created with molecular surfaces, their employment has surprisingly been almost completely overlooked. Here we show how the normals to the surface, at specific, well placed points, can play a critical role in molecular docking. If the points for which the normals are calculated represent faithfully and accurately the molecular surfaces, the normals can substantially ameliorate the efficiency of the docking in a number of ways. The normals can drastically reduce the combinatorial complexity of the receptor-ligand docking. Furthermore, they can serve as a powerful filter in screening for quality docked conformations. Below we show how deploying such a straight forward device, which is easy to calculate, large protein-protein molecules are docked with unparalleled short times and with a manageable number of potential solutions. Considering the facts that here we dock (1) two large protein molecules, including several large immunoglobulin-lysozyme complexes; (2) that we use the entire molecular surfaces, without a predefinition of the active sites, or of the epitopes, of neither the ligand nor the receptor; that (3) the docking is completely automated, without any labelling, or pre-specification, of the input structural database, and (4) with a single set of parameters, without any further tuning whatsoever, such results are highly desirable. This approach is specifically geared towards matching of the surfaces of large protein molecules and is not applicable to small molecule drugs.

UI MeSH Term Description Entries
D008024 Ligands A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed) Ligand
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D003196 Computer Graphics The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation. Computer Graphic,Graphic, Computer,Graphics, Computer
D013499 Surface Properties Characteristics or attributes of the outer boundaries of objects, including molecules. Properties, Surface,Property, Surface,Surface Property

Related Publications

R Norel, and S L Lin, and H J Wolfson, and R Nussinov
January 1994, Proteins,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
September 2018, Journal of molecular graphics & modelling,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
May 1996, Proteins,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
May 1997, Journal of molecular biology,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
December 1993, Journal of molecular biology,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
March 2010, FEBS letters,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
November 2010, Proteins,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
June 2008, Proceedings of the National Academy of Sciences of the United States of America,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
November 1990, Physical review letters,
R Norel, and S L Lin, and H J Wolfson, and R Nussinov
November 1996, Journal of molecular biology,
Copied contents to your clipboard!