Subject: CCL: re:rRNA summary

From: "DR. LIOTTA" <[email-masked]>
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  [email-masked]

 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  [email-masked]

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
		[email-masked]

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    [email-masked]

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	[email-masked]

6] Peter Reinert also gave reference 3 (b)
   "For obtaining the software contact [email-masked]"
		Peter Reinert  [email-masked]

	These were very helpful,
	Veronica Cornel [email-masked]