CCL: re:rRNA summary

From: "DR. LIOTTA" <chemdcl3' at \`emrycc.cc.emory.edu>
Subject: CCL: re:rRNA summary
Date: 6 Jul 94 15:42:00 EST
 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' at \`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' at \`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' at \`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' at \`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' at \`launchpad.unc.edu
 6] Peter Reinert also gave reference 3 (b)
    "For obtaining the software contact tan' at \`neptune.cmc.uab.edu"
 		Peter Reinert  reinert' at \`VAX.MPIZ-KOELN.MPG.d400.de
 	These were very helpful,
 	Veronica Cornel chemdcl3' at \`emrycc.cc.emory.edu