title: Proteins with similar architecture exhibit similar large-scale dynamic behavior.
abstract: We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior.
authors.affiliation: Chemical Engineering Department and Polymer Research Center, Bogazici University, and TUBITAK Advanced Polymeric Materials Research Center, Bebek 80815, Istanbul, Turkey.
authors.forename: O
authors.initials: O
authors.lastname: Keskin
authors.forename: R L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: I
authors.initials: I
authors.lastname: Bahar
mesh_terms: D001059:Apoproteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D002352:Carrier Proteins / Q000737:chemistry; D003207:Conalbumin / Q000737:chemistry; D029968:Escherichia coli Proteins; D011163:Hydroxymethylbilane Synthase / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D009038:Motion; D033902:Periplasmic Binding Proteins; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D001059:Apoproteins; D001426:Bacterial Proteins; D002352:Carrier Proteins; C062886:CysB protein, Bacteria; D029968:Escherichia coli Proteins; D008024:Ligands; C488923:LivJ protein, E coli; D033902:Periplasmic Binding Proteins; D011506:Proteins; C028003:RbsB protein, E coli; C028332:leucine-isoleucine-valine binding protein, bacteria; C033849:lysyl-arginyl-ornithine-binding protein, bacteria; D003207:Conalbumin; D011163:Hydroxymethylbilane Synthase