Protein Science
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by SIPPL, M. J.
Right arrow Articles by LACKNER, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by SIPPL, M. J.
Right arrow Articles by LACKNER, P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Protein Science, Vol 1, Issue 5 625-640, Copyright © 1992 by Cold Spring Harbor Laboratory Press

ARTICLE

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin {beta}(4)

M. J. SIPPL, M. HENDLICH and P. LACKNER
Institute for General Biology, Biochemistry & Biophysics, Department of Biochemistry, University of Salzburg, Hellbrunnerstra{szlig}e 34, A-5020 Salzburg, Austria

Recently we developed methods for the construction of knowledge-based mean fields from a data base of known protein structures. As shown previously, this approach can be used to calculate ensembles of probable conformations for short fragments of polypeptide chains. Here we develop procedures for the assembly of short fragments to complete three-dimensional models of polypeptide chains. The amino acid sequence of a given protein is decomposed into all possible overlapping fragments of a given length, and an ensemble of probable conformations is calculated for each fragment. The fragments are assembled to a complete model by choosing appropriate conformations from the individual ensembles and by averaging over equivalent angles. Finally a consistent model is obtained by rebuilding the conformation from the average angles. From the average angles the local variability of the structure can be calculated, which is a useful criterion for the reliability of the model. The procedure is applied to the calculation of the local backbone conformations of myoglobin and lysozyme whose structures have been solved by X-ray analysis and thymosin {beta}(4), a polypeptide of 43 amino acid residues whose structure was recently investigated by NMR spectroscopy. We demonstrate that substantial fractions of the calculated local backbone conformations are similar to the experimentally determined structures.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Protein Sci.Home page
J. B. Holmes and J. Tsai
Some fundamental aspects of building protein structures from fragment libraries
Protein Sci., June 1, 2004; 13(6): 1636 - 1650.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. Wiedemann, K. Giehl, S. C. Almo, A. A. Fedorov, M. Girvin, P. Steinberger, M. Rudiger, M. Ortner, M. Sippl, C. Dolecek, et al.
Molecular and Structural Analysis of a Continuous Birch Profilin Epitope Defined by a Monoclonal Antibody
J. Biol. Chem., November 22, 1996; 271(47): 29915 - 29921.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1992 by The Protein Society.