Reproducing the three-dimensional structure of a tRNA molecule from structural constraints

Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9408-12. doi: 10.1073/pnas.90.20.9408.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computer Simulation
  • Hydrogen Bonding
  • In Vitro Techniques
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • RNA, Transfer, Asp / ultrastructure*
  • RNA, Transfer, Phe / ultrastructure*

Substances

  • RNA, Transfer, Asp
  • RNA, Transfer, Phe