Semiautomatic sequence-specific assignment of proteins based on the tertiary structure-The program st2nmr
The sequence‐specific assignment of resonances is still the most time‐consuming procedure that is necessary as the first step in high‐resolution NMR studies of proteins. In many cases a reliable three‐dimensional (3D) structure of the protein is available, for example, from X‐ray spectroscopy or hom...
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Published in | Journal of computational chemistry Vol. 23; no. 3; pp. 335 - 340 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
New York
Wiley Periodicals, Inc
01.02.2002
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Subjects | |
Online Access | Get full text |
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Summary: | The sequence‐specific assignment of resonances is still the most time‐consuming procedure that is necessary as the first step in high‐resolution NMR studies of proteins. In many cases a reliable three‐dimensional (3D) structure of the protein is available, for example, from X‐ray spectroscopy or homology modeling. Here we introduce the st2nmr program that uses the 3D structure and Nuclear Overhauser Effect spectroscopy (NOESY) peak list(s) to evaluate and optimize trial sequence‐specific assignments of spin systems derived from correlation spectra to residues of the protein. A distance‐dependent target function that scores trial assignments based on the presence of expected NOESY crosspeaks is optimized in a Monte Carlo fashion. The performance of the program st2nmr is tested on real NMR data of an α‐helical (cytochrome c) and β‐sheet (lipocalin) protein using homology models and/or X‐ray structures; it succeeded in completely reproducing the correct sequence‐specific assignments in most cases using 2D and/or 15N/13C Nuclear Overhauser Effect (NOE) data. Additionally to amino acid residues the program can also handle ligands that are bound to the protein, such as heme, and can be used as a complementary tool to fully automated assignment procedures. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 335–340, 2002 |
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Bibliography: | ArticleID:JCC10011 ark:/67375/WNG-S6Q76RC5-3 istex:F6D6EC64609FADF30D330820FE4ADFCF3A3126C1 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 0192-8651 1096-987X |
DOI: | 10.1002/jcc.10011 |