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Nucleic Acids Research Pages 187-189  

The Database of Ribosomal Cross links (DRC)
Introduction
Description
Future Prospects
Availability
Acknowlegements
References

The Database of Ribosomal Cross links (DRC)

The Database of Ribosomal Cross links (DRC)

Pavel V. Baranov, Petr V. Sergiev, Olga A. Dontsova, Alexey A. Bogdanov, Richard Brimacombe1,*

A. N. Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Moscow State University, Moscow 119899, Russia and 1Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany

Received October 15, 1997; Accepted October 24, 1997

ABSTRACT

The Database of Ribosomal Cross-links (DRC) provides a complete collection of all the published data produced by cross-linking studies on the Escherichia coli ribosome, as well as on its components and functional ligands. The DRC currently includes data on 986 cross-links from >100 research papers, yielded by >40 different reagents. For each cross-link, information is given concerning its location in the ribosome, the chemical or photochemical reagent applied, a brief description of the method(s) used to locate the cross-link, and the literature reference. The DRC is freely available via the World Wide Web at: http://Ribosome.Genebee.MSU.SU/DRC/ or at http://WWW:MPIMG-Berlin-Dahlem.MPG.DE/~baranov/DRC/

INTRODUCTION

During the last 30 years a vast amount of structural data has accumulated on the ribosome and its components, as well as on interactions between the ribosome and its functional ligands (see e.g. refs 1-4 for reviews). A substantial proportion of the data concerned has been derived from cross-linking studies of various types. Over the years the technology of cross-linking has changed dramatically, and the methods applied have become more accurate and reliable. Furthermore, the newer approaches allow the cross-links to be localized more precisely within the ribosomal components. At the same time it has also become clear that there are many contradictions both within and between the various data sets. Thus, it is very difficult to keep track of all the available information and to assess its reliability. Here we present a new database which offers an easy and rapid way for collating cross-linking data related to the ribosome structure.

DESCRIPTION

The Database of Ribosomal Cross-links (DRC) is currently located at the Moscow State University, Moscow and also at the Max-Planck-Institut für Molekulare Genetik, Berlin. This database was created in order to offer workers in the field a means for rapid searching and comparison of the different types of ribosomal cross-linking data, together with the appropriate literature references. In order to allow a rough estimation of the reliability of the data, each cross-link is listed together with the following information, in addition to the information defining the nature of the cross-linked components. (i) The name of the cross-linking reagent (or method) applied. (ii) A brief description of the techniques used to localize the cross-link site (or to identify the cross-linked components). (iii) Relevant literature reference (in most cases with hyperlinks to the corresponding medline abstracts). An example is shown in Figure 1.


Figure 1 An example of the DRC format, showing some of the intra-RNA cross-links within the 16S rRNA.


Figure 2 The first main page of the DRC, listing the different types of cross-links contained in the Tables.

The DRC contains separate html Tables, each of which deals with a specific type of cross-linking data (Fig. 2). All the data in these Tables are sorted according to the positions of the cross-links within the rRNA, ribosomal proteins, or ribosomal ligands (mRNA, tRNA, factors, etc.). This method of ordering provides an easy way for searching for cross-links located in particular regions of the biomolecules concerned.

FUTURE PROSPECTS

In the near future we plan to enter descriptions for all of the cross-linking reagents that are listed in the database. These descriptions will include the following information in each case: (i) the IUPAC nomenclature for the reagent; (ii) any abbreviations or non-IUPAC names; (iii) the structure of the molecule; (iv) the extended cross-linking length of the reagent; (v) the method of incorporation into the ribosome or ligand; (vi) the method of generation of the cross-link; (vii) the specifity of the reagent.

At the same time we plan to create a simple search system to allow a search for the cross-linking data via positions in the rRNA, proteins or functional ligands. As new approaches in cross-liking methodology become available, these will of course be added to the database.

AVAILABILITY

The DRC is available via two mirror www sites at the Moscow State University at http://Ribosome.GeneBee.MSU.SU/DRC/ and at the Max-Planck-Institut für Molekulare genetik at http://WWW.MPIMG-Berlin-Dahlem.MPG.DE/~baranov/DRC/

Please send any suggestions, questions, corrections or omissions to Pavel Baranov via e-mail: Baranov@MPIMG-Berlin-Dahlem.MPG.DE

ACKNOWLEGEMENTS

We are grateful to Olga Gurvich (Molecular Biology Program, University of Utah, Salt Lake City) for her careful corrections and useful suggestions during the development of this database. We also thank the www administrators at the Max-Planck-Institute for providing access to their WWW server.

REFERENCES

1. Traut,R.R., Lambert,J.M., Boileau,G. and Kenny,J.W. (1980) In Chambliss,G., Craven,G.R., Davies,J., Davis,K., Kahan,L. and Nomura,M. (eds), Ribosomes: Structure, Function and Genetics. University Park Press, Baltimore, pp. 89-110.Wower,J., Sylvers,L.A., Rosen,K.V., Hixon,S.S. and Zimmermann,R.A. (1993) In Nierhaus,K.H., Franceschi,F., Subramanian,A.R., Erdmann,V.A. and Wittmann-Liebold,B. (eds), The translational Apparatus. Plenum Press, New York, pp. 455-464.Brimacombe,R. (1995) Eur. J. Biochem. 230, 365-383.

2. Green,R. and Noller,H.F. (1997) Annu. Rev. Biochem. 66, 679-716. MEDLINE Abstract

*To whom correspondence should be addressed. Tel: +49 30 8413 1592; Fax: +49 30 8413 1690; Email: mueller_f@mping-berlin-dahlem.mpgo.de

This page is run by Oxford University Press, Great Clarendon Street, Oxford OX2 6DP, as part of the OUP Journals Comments and feedback: www-admin{at}oup.co.uk
Last modification: 17 Dec 1997
Copyright© Oxford University Press, 1998.

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