Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.
The three-dimensional structure of yeast tRNA(Phe) was reproduced at atomic resolution with the automated RNA modeling program MC-SYM, which is based on a constraint-satisfaction algorithm. Structural constraints used in the modeling were derived from the secondary structure, four tertiary base pairs, and other information available prior to the determination of the x-ray crystal structure of the tRNA. The program generated 26 solutions (models), all of which had the familiar "L" form of tRNA and root-mean-square deviations from the crystal structure in the range of 3.1-3.8 A. The interaction between uridine-8 and adenosine-14 was crucial in the modeling procedure, since only this among the tertiary pairs is necessary and sufficient to reproduce the L form of tRNA. Other tertiary interactions were critical in reducing the number of solutions proposed by the program.
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National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.
Gautheret
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Cedergren
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D001483:Base Sequence; D003198:Computer Simulation; D006860:Hydrogen Bonding; D066298:In Vitro Techniques; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012349:RNA, Transfer, Asp / Q000648:ultrastructure*; D012360:RNA, Transfer, Phe / Q000648:ultrastructure*
D012349:RNA, Transfer, Asp; D012360:RNA, Transfer, Phe