Computational methods for defining the allowed conformational space of 16S rRNA based on chemical footprinting data

RNA

Volumn 2, Issue 9, 1996, Pages 851-866

  Fink, Doran L ^a   Chen, Richard O ^a   Noller, Harry F ^b   Altman, Russ B ^a  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

computational methods; molecular modeling; ribosome active sites; ribosome structure; tRNA binding

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

ALGORITHM; ARTICLE; CALCULATION; GENETIC ENGINEERING; PRIORITY JOURNAL; RNA CONFORMATION;

BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, RIBOSOMAL, 16S;

EID: 0029949592     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (21)

1. Agrawal RK, Penczek P, Grassucci RA, Li Y, Leith A, Nierhaus KH, Frank J. 1996. Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science 271:1000-1002.
2. Altman RB, Weiser B, Noller HF. 1994. Constraint satisfaction tech-niques for modeling large complexes: Application to the central domain of 16S ribosomal RNA. ISMB 2:10-18.
3. Arrowsmith C, Pachter R, Altman R, Jardetzky O. 1991. The solution structures of E. coli trp repressor and trp aporepressor at an intermediate resolution. Eur J Biochem 202:53-66.
4. Brimacombe R. 1991. RNA-protein interactions in the Escherichia coli ribosome. Biochimie 73:927-936.
5. Brimacombe R. 1995. The structure of ribosomal RNA: A three-dimensional jigsaw puzzle. Eur J Biochem 230:365-833.
6. Brimacombe R, Atmadja J, Stiege W, Schuler D. 1988. A detailed model of the three-dimensional structure of Escherichia coli 16 S ribosomal RNA in situ in the 30 S subunit. J Mol Biol 199:115-136.
7. Brimacombe R, Greuer B, Mitchell P, Osswald M, Rinke-Appel J, Schüler D, Stade K. 1990. Three-dimensional structure and function of Escherichia coli 16S and 23S rRNA as studied by cross-linking techniques. In: Hill WE, Dahlberg A, Garrett RA, Moore PB, Schlessinger D, Warner JR, eds. The ribosome: Structure, function, and evolution. Washington, DC: ASM Press, pp 93-106.
8. Brinkley J, Cornelius C, Altman R, Brugge J, Pachter R, Buchanan B, Jardetzky O. 1990. PROTEAN/I and PROTEAN/II. Quantum Chemistry Program Exchange Newsletter X:596. (Catalog section VIII).
9. Brinkley JF, Altman RB, Duncan BS, Buchanan BG, Jardetzky O. 1987. Heuristic refinement method for the derivation of protein solution structures: Validation on cytochrome b562. J Chem Informational Comput Sci 28:194-210.
10. Brosius J, Dull TJ, Sleeter DD, Noller HF. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107-127.
11. Capel MS, Engelman DM, Freeborn BR, Kjeldgaard M, Langer JA, Ramakrishnan V, Schindler DG, Schneider DK, Schoenborn BP, Sillers IY, et al. 1987. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science 238:1403-1406.
12. Chen R, Fink D, Altman RB. 1995. Computing the structure of large complexes: Applying constraint satisfaction techniques to modeling the 16S ribosomal RNA. In: Markley JL, Opella SJ, eds. Biomolecular NMR spectroscopy. Oxford: Oxford University Press, pp 279-299.
13. Expert-Bezancon A, Wollenzien PL. 1985. Three-dimensional arrangement of the Escherichia coli 16s ribosomal RNA. J Mol Biol 184:53-66.
14. Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK. 1995. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome [see comments]. Nature 376:441-444.
15. Golden BL, Hoffman DW, Ramakrishnan V, White SW. 1993. Ribosomal protein S17: Characterization of the three-dimensional structure by 1H and 15N NMR. Biochemistry 32:12812-12820.
16. Greuer B, Osswald M, Brimacombe R, Stöffler G. 1987. RNA-protein cross-linking in Escherichia coli ribosomal subunits; determination of sites on 16S RNA that are cross-linked to proteins S3, S4, S7, S9, S10, S11, S17, S18 and S21 by treatment with bis-(2-chloroethyl)-methylamine. Nucleic Acids Res 15:3241-3255.
17. Hubbard JM, Hearst JE. 1991. Computer modeling 16 S ribosomal RNA. J Mol Biol 221:889-907.
18. Latham JA, Cech TR. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245:276-282.
19. Lichtarge O, Cornelius C, Buchanan B, Jardetzky O. 1987. Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data. Proteins Struct Fund Genet 2:340-358.
20. Liljas A, Garber M. 1995. Ribosomal proteins and elongation factors. Curr Opin Struct Biol 5:721-727.
21. Lindahl M, Svensson LA, Liljas A, Sedelnikova SE, Eliseikina IA, Fomenkova NP, Nevskaya N, Nikonov SV, Garber MB, Muranova TA, et al. 1994. Crystal structure of the ribosomal protein S6 from Thermus thermophilus. EMBO J 33:1249-1254.