PMID: 9177001May 1, 1997Paper

Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment

Journal of Chemical Information and Computer Sciences
K B Li, B C Sanctuary

Abstract

A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid coupling patterns. Both chemical shift and topologically likeness are considered. The mapping algorithm uses the amino acid type information to direct detected polypeptides to proper position onto protein primary sequence. The assignment protocol can be applied to spin systems generated by many different approaches. We designed a few computer programs to derive a protein's backbone and side chain spin systems using heteronuclear 3D NMR. The results was then input to the sequential assignment protocol. All of the algorithms were tested on NMR data of a 90-residue N-domain of chicken skeletal troponin-C.

Citations

Sep 23, 2008·European Biophysics Journal : EBJ·Peter Güntert
Sep 3, 2008·Journal of Biomolecular NMR·Dries VerdegemGuy Lippens
Jun 28, 2011·Journal of Biomolecular NMR·Jianyang ZengBruce Randall Donald
Oct 9, 2009·The Journal of Physical Chemistry. a·David A Snyder, Rafael Brüschweiler
Aug 12, 2005·Nucleic Acids Research·Hsin-Nan LinWen-Lian Hsu
Feb 18, 2010·Progress in Nuclear Magnetic Resonance Spectroscopy·Steven P Mielke, V V Krishnan
Jan 3, 2001·Journal of Magnetic Resonance·M SchubertP Schmieder
Oct 6, 1999·Current Opinion in Structural Biology·H N Moseley, G T Montelione
Mar 18, 2011·Quarterly Reviews of Biophysics·Paul Guerry, Torsten Herrmann
Apr 12, 2012·Chembiochem : a European Journal of Chemical Biology·Suhas TikolePeter Güntert
Dec 13, 2005·Journal of Biomolecular NMR·Jianyong WangGordon M Crippen
Sep 9, 2010·Bioorganicheskaia khimiia·V S KhristophorovV P Kutyshenko
Aug 12, 2004·Chemical Reviews·Michael C BaranGaetano T Montelione
Jul 17, 2012·Journal of the American Chemical Society·Elena Schmidt, Peter Güntert

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