The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

Three-dimensional (3-D) structural models of RNA are essential for understanding of the cellular roles played by RNA. Such models have been obtained by a technique based on a constraint satisfaction algorithm that allows for the facile incorporation of secondary and other structural information. The program generates 3-D structures of RNA with atomic-level resolution that can be refined by numerical techniques such as energy minimization. The precision of this technique was evaluated by comparing predicted transfer RNA loop and RNA pseudoknot structures with known or consensus structures. The root-mean-square deviation (2.0 to 3.0 angstroms before minimization) between predicted and control structures reveal this system to be an effective method in modeling RNA.

[1]  B. Sjöberg,et al.  Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA. , 1990, Biochemistry.

[2]  P G Stockley,et al.  Modeling loop structures in proteins and nucleic acids: an RNA stem-loop. , 1989, Journal of molecular graphics.

[3]  G. Fasman,et al.  Protein conformational prediction. , 1989, Trends in biochemical sciences.

[4]  D. Moras,et al.  Crystal structure of yeast tRNAAsp , 1980, Nature.

[5]  I. Tinoco,et al.  RNA pseudoknots. Stability and loop size requirements. , 1990, Journal of molecular biology.

[6]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[7]  A. Kolinski,et al.  Simulations of the Folding of a Globular Protein , 1990, Science.

[8]  H Y Mei,et al.  A computational approach to the mechanism of self-cleavage of hammerhead RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Gerald J. Sussman,et al.  Intelligence in scientific computing , 1989, CACM.

[10]  S C Harvey,et al.  Prediction of the three-dimensional structure of Escherichia coli 30S ribosomal subunit: a molecular mechanics approach. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[11]  O. Uhlenbeck,et al.  Sequence-dependent structural variations of hammerhead RNA enzymes. , 1990, Nucleic acids research.

[12]  N. Seeman,et al.  Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA , 1974, Science.

[13]  I. Tinoco,et al.  Conformation of an RNA pseudoknot , 1990, Journal of Molecular Biology.

[14]  M. Karplus,et al.  Molecular dynamics simulations in biology , 1990, Nature.

[15]  Robert M. Haralick,et al.  Increasing Tree Search Efficiency for Constraint Satisfaction Problems , 1979, Artif. Intell..

[16]  D. Turner,et al.  RNA structure prediction. , 1988, Annual review of biophysics and biophysical chemistry.

[17]  B. Clark,et al.  Structure of yeast phenylalanine tRNA at 3 Å resolution , 1974, Nature.

[18]  C. Pleij,et al.  Pseudoknots: a new motif in the RNA game. , 1990, Trends in biochemical sciences.

[19]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[20]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[21]  I. Tinoco,et al.  Solution conformation of an RNA hairpin loop. , 1990, Biochemistry.

[22]  M Mutter,et al.  Nature's rules and chemist's tools: a way for creating novel proteins. , 1988, Trends in biochemical sciences.

[23]  W. Fuller,et al.  Conformation of the Anticodon Loop in tRNA , 1967, Nature.

[24]  M. Levitt.  Detailed Molecular Model for Transfer Ribonucleic Acid , 1969, Nature.

[25]  M. Summers,et al.  High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach. , 1990, Biochemistry.