title: Sequence structure of van der Waals locks in proteins.
abstract: Recent works has suggested that proteins in early evolution have gone through a stage of closed loop elements with a typical contour size of 25-35 residues. These closed loops are still the elementary protein units to these days, and can be used to spell out protein sequence/structure relationship through a relatively small number of protein prototypes. In this study we aimed to identify the sequences that are used to lock the loop ends to one another, and to show how an extensive dictionary of such locking pairs can be created using positional correlation data from a large proteome database, and structural data from PDB databases. Such a dictionary can be used in reconstructing the evolutionary pathway the modern proteins have gone through, and in identifying closed loop elements in modern proteins with yet unknown 3D structure.
authors.affiliation: Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel.
authors.forename: Elik
authors.initials: E
authors.lastname: Aharonovsky
authors.forename: Edward N
authors.initials: EN
authors.lastname: Trifonov
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics* / Q000502:physiology; D001105:Archaea / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins