Semiautomatic sequence-specific assignment of proteins based on the tertiary structure--the program st2nmr

Journal of Computational Chemistry
Primoz PristovsekRoman Jerala

Abstract

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 alpha-helical (cytochrome c) and beta-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 aut...Continue Reading

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Citations

Sep 23, 2008·European Biophysics Journal : EBJ·Peter Güntert
Sep 3, 2008·Journal of Biomolecular NMR·Dries VerdegemGuy Lippens
Dec 31, 2010·Journal of Biomolecular NMR·Xingsheng WangFang Tian
Mar 31, 2011·Journal of Biomolecular NMR·Teppei IkeyaPeter Güntert
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Richard JangMing Li
Jul 1, 2008·Bioinformatics·Fei XiongChris Bailey-Kellogg
Dec 22, 2009·Journal of Biomolecular NMR·Dirk StratmannCarine van Heijenoort
Nov 26, 2008·Biochimica Et Biophysica Acta·Mateja ZorkoRoman Jerala
Feb 18, 2011·Journal of Bioinformatics and Computational Biology·Babak AlipanahiMing Li
Feb 3, 2005·The Journal of Biological Chemistry·Bostjan JapeljRoman Jerala
Mar 10, 2006·Journal of Computational Chemistry·Primoz Pristovsek, Lorella Franzoni
May 13, 2003·The Journal of Biological Chemistry·Primoz PristovsekFrank Bernhard
Aug 4, 2016·Journal of Biomolecular NMR·Matthias TrautweinThomas E Exner
Feb 8, 2006·Biochemistry·Rafael M MartinsSergio Schenkman

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