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Semiautomatic sequence‐specific assignment of proteins based on the tertiary structure—The program st2nmr
Author(s) -
Pristovšek Primož,
Rüterjans Heinz,
Jerala Roman
Publication year - 2002
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10011
Subject(s) - nuclear overhauser effect , two dimensional nuclear magnetic resonance spectroscopy , nuclear magnetic resonance spectroscopy , chemistry , homology modeling , protein structure , protein tertiary structure , sequence (biology) , protein secondary structure , crystallography , stereochemistry , biochemistry , enzyme
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 15 N/ 13 C 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