From chemdcl3@emrycc.cc.emory.edu Wed Jul 6 15:50:56 1994 Received: from emoryu1.cc.emory.edu for chemdcl3@emrycc.cc.emory.edu by www.ccl.net (8.6.9/930601.1506) id PAA03830; Wed, 6 Jul 1994 15:43:35 -0400 Received: from emrycc.cc.emory.edu by emoryu1.cc.emory.edu (5.65/Emory_cc.3.5.2) via SMTP id AA04531 ; Wed, 6 Jul 94 15:44:35 -0400 Message-Id: <9407061944.AA04531@emoryu1.cc.emory.edu> Date: 6 Jul 94 15:42:00 EST From: "DR. LIOTTA" Subject: CCL: re:rRNA summary To: "chemistry" Thank you to the various people who responded to the following message: >We would like to model the secondary structure of ribosomal >RNA and would like to contact anybody who has done similar >work or who can lead us to useful references. Are there any >crystollographic structures of rRNA available? Here is a summary of the responses: 1] "I have mostly used Michael Zukers MFold software to predict RNA secondary structure." ... and "Here is one paper:" Baldridge, G.D.; Dalton, M.W.; Fallon, A.M.; Is higher order Structure Conserved in Eukaryotic Ribosomal DNA Intergenic spacers?, Journal of Molecular Evolution, vol 35, (1992) Mark Dalton mwd@cray.com 2] "We are doing NMR spectroscopy of ions in ribosomal solutions, and would be interested in any information you get from the net about crystal structures etc.. of rRNA. A few articles that deal with ribosomal structure in general are: Crichton et al. 1977. PNAS 74:5547 Tardieu and Vachette 1982. EMBO J. 1?:35 Wittmann 1983. Ann. Rev. Biochem. 52:35" Harry J. Guttman guttman@poly.nn.wisc.edu 3] "Perhaps the following articles will be of interest: (a) Malhotra, Arun; Gabb, H.A; Harvey, S.C.; Modelling large nucleic -acids; Current Opinion in Structural Biology; vol 3 (2) p241-246 (1993)" (b) Malhotra, Arun; Tan, R.K.-Z.; Harvey, S.C.; Modelling large RNAs and ribonucleoprotein particles using molecular mechanics techniques, Biophysical Journal, vol 66; p1777-1795 (1994) Eberhard von Kitzing vkitzing@sunny.mpimf-Heidelberg.mpg.de 4] "There is extensive noncrystollographic work from the labs of Woese, Noller and Gutell. A quick medline search should turn these up. There is reasonable literature on ribosomal structure, by chemical cross- linking (labs of Wool and Wittman), electron micrography and maybe neutron scattering. There are probably some clues there. I doubt if there are crystals of isolated rRNAs, but if there are they should be in nucleic acids database (NDB) at Rutgers." Toni Kazic toni@athe.wustl.edu 5] "To the best of my knowledge there are two items in the PDB that might interest you: (a) theoretical model of 5s rRNA and (b) NMR structures of rRNA. Here are the headers for your information: HEADER RIBONUCLEIC ACID COMPND 5s RIBOSOMAL RNA (HELIX I) (NMR, 6 STRUCTURES) SOURCE (ESCHERICHIA COLI) EXPDTA NMR AUTHOR S.WHITE, P.MOORE REVDAT 31-JAN-94 1ELH 0 JRNL AUTH S.A.WHITE,M.NILGES,A.HUANG,A.T.BRUNGER,P.B.MOORE JRNL TITL NMR ANALYSIS OF HELIX I FROM THE 5s RNA OF JRNL TITL 2 ESCHERICHIA COLI JRNL REF BIOCHEMISTRY V. 31 1610 1992 JRNL REFN ASTM BICHAW US ISSN 0006-2960 033 HEADER RIBONUCLEIC ACID COMPND 5 s RIBOSOMAL RNA (THEORETICAL MODEL) SOURCE (XENOPUS LAEVIS) OOCYTES EXPDTA THEORETICAL MODEL AUTHOR E.WESTHOF, P.ROMBY, C.EHRESMANN REVDAT 2 31-JAN-94 1RRNA 1 REMARK REVDAT 1 31-OCT-93 1RRN 0 JRNL AUTH E.WESTHOF, P.ROMBY, P.J. ROMANUIK, J.-*P.EBEL, JRNL AUTH C.EHRESMANN, B.EHRESMANN JRNL TITL COMPUTER MODELLING FROM SOLUTION DATA OF SPINACH JRNL TITL 2 CHLOROPLAST AND OF XENOPUS LAEVIS SOMATIC AND JRNL TITL 3 OOCYTE 5 S $R/RNA$S JRNL REF J.MOL.BIOL V. 207 417 1989 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070" C.S. Ramen raman@launchpad.unc.edu 6] Peter Reinert also gave reference 3 (b) "For obtaining the software contact tan@neptune.cmc.uab.edu" Peter Reinert reinert@VAX.MPIZ-KOELN.MPG.d400.de These were very helpful, Veronica Cornel chemdcl3@emrycc.cc.emory.edu