A relation between the principal axes of inertia and ligand binding.
The principal axes of inertia are eigenvectors that can be calculated for any rigid body. We report studies of the position of the principal axes in crystallographically solved protein molecules. We find with high frequency that at least one principal axis penetrates the surface of the respective protein in a region used for ligand binding. In antibody variable regions, an axis goes through the third hypervariable loop of the heavy chain. In major histocompatibility complex proteins, an axis goes through the peptide-binding groove. In protein-protein heterodimers, a principal axis of one subunit will often penetrate the interface formed with the other subunit. In many of these protein-protein complexes, the axis specifically intersects residues known to be critical for molecular recognition.
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Program in Molecular Medicine, Fred Hutchinson Cancer Research Center, C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. jfoote@fhcrc.org
Raman
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D000465:Algorithms; D000818:Animals; D000937:Antigen-Antibody Reactions; D000941:Antigens / Q000378:metabolism; D007611:Aprotinin / Q000737:chemistry / Q000378:metabolism; D002417:Cattle; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D002645:Chickens; D002918:Chymotrypsin / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D003574:Cytochrome c Group / Q000737:chemistry / Q000378:metabolism; D003578:Cytochrome-c Peroxidase / Q000737:chemistry / Q000378:metabolism; D045304:Cytochromes c; D019281:Dimerization; D007128:Immunoglobulin Fragments / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008956:Models, Chemical; D009113:Muramidase / Q000276:immunology; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins; D013329:Structure-Activity Relationship
D000941:Antigens; C014059:CYC1 protein, S cerevisiae; D003574:Cytochrome c Group; D007128:Immunoglobulin Fragments; D008024:Ligands; D029701:Saccharomyces cerevisiae Proteins; C055966:immunoglobulin Fv; D045304:Cytochromes c; D007611:Aprotinin; D003578:Cytochrome-c Peroxidase; D009113:Muramidase; D002918:Chymotrypsin