Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
The analysis of the dynamic behavior of enzymes is fundamental to structural biology. A direct relationship between protein flexibility and biological function has been shown for bovine pancreatic ribonuclease (RNase A) (Rasmussen et al., Nature 1992;357:423-424). More recently, crystallographic studies have shown that functional motions in RNase A involve the enzyme beta-sheet regions that move concertedly on substrate binding and release (Vitagliano et al., Proteins 2002;46:97-104). These motions have been shown to correspond to intrinsic dynamic properties of the native enzyme by molecular dynamics (MD) simulations. To unveil the occurrence of these collective motions in other members of pancreatic-like superfamily, we carried out MD simulations on human angiogenin (Ang). Essential dynamics (ED) analyses performed on the trajectories reveal that Ang exhibits collective motions similar to RNase A, despite the limited sequence identity (33%) of the two proteins. Furthermore, we show that these collective motions are also present in ensembles of experimentally determined structures of both Ang and RNase A. Finally, these subtle concerted beta-sheet motions were also observed for other two members of the pancreatic-like superfamily by comparing the ligand-bound and ligand-free structures of these enzymes. Taken together, these findings suggest that pancreatic-like ribonucleases share an evolutionary conserved dynamic behavior consisting of subtle beta-sheet motions, which are essential for substrate binding and release.
Merlino
Antonello
A
Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Napoli, Italy.
Vitagliano
Luigi
L
Ceruso
Marc Antoine
MA
Mazzarella
Lelio
L
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003198:Computer Simulation; D004795:Enzyme Stability; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009038:Motion; D017433:Protein Structure, Secondary; D012259:Ribonuclease, Pancreatic / Q000737:chemistry* / Q000145:classification / Q000378:metabolism
C046366:angiogenin; D012259:Ribonuclease, Pancreatic