Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA.
The secondary and 3D structure of the active site of the self-splicing T4 nrdB RNA has been modeled on a graphics workstation by use of the suggested 3D arrangement of the active site of the Tetrahymena IVS [Kim, S.H., & Cech, T.R. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8788-8792] as a guideline. The initially obtained crude structure was then subjected to molecular mechanics energy minimization and molecular dynamics simulation to relax tensions. In this process the energy decreased considerably and gave a final structure that deviated by 3 A [root mean square (rms)] from the initial structure. The cofactor guanosine (and the competitive inhibitor arginine) was docked to a proposed [Michel, F., Hanna, M., Green, R., Bartel, D.P., & Szostak, J.W. (1989) Nature 342, 391-395] binding site, where it was found to fit rather well. A minor modification of the binding mode easily brought the O3' end of the guanosine within 2 A of the phosphodiester bond where the primary cleavage occurs.
Nilsson
L
L
Department of Medical Biophysics, Karolinska Institutet, Stockholm, Sweden.
Ahgren-Stålhandske
A
A
Sjögren
A S
AS
Hahne
S
S
Sjöberg
B M
BM
D000818:Animals; D001120:Arginine / Q000494:pharmacology; D001483:Base Sequence; D001665:Binding Sites / Q000187:drug effects; D003198:Computer Simulation; D007438:Introns; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D013237:Stereoisomerism; D013604:T-Phages / Q000235:genetics*; D013768:Tetrahymena / Q000235:genetics; D013816:Thermodynamics
D012333:RNA, Messenger; D001120:Arginine