PASA--a program for automated protein NMR backbone signal assignment by pattern-filtering approach

Journal of Biomolecular NMR
Yizhuang XuJun Qin

Abstract

We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13Calpha and/or 13Cbeta chemical shift matching. The pattern filter employs one or multiple constraints such as 13Calpha/Cbeta chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-b...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
Jul 19, 2012·Journal of Biomolecular NMR·Anna Zawadzka-KazimierczukMartin Billeter
Mar 18, 2011·Quarterly Reviews of Biophysics·Paul Guerry, Torsten Herrmann
Oct 9, 2009·The Journal of Physical Chemistry. a·David A Snyder, Rafael Brüschweiler
Dec 17, 2008·The Journal of Biological Chemistry·Sujay Subbayya IthychandaJun Qin
Aug 31, 2010·Magnetic Resonance in Chemistry : MRC·Ashok K RoutKandala V R Chary
Apr 23, 2015·Journal of Biomolecular NMR·Hesam DashtiJohn L Markley
Apr 2, 2015·Journal of Biomolecular NMR·Madeleine StricklandNico Tjandra
Apr 8, 2015·Nature Structural & Molecular Biology·Jianmin LiuJun Qin
May 24, 2014·Nature Communications·Shengyi LiuAndrew H Paterson
Sep 25, 2017·GigaScience·Wenlu YangTao Ma
Feb 15, 2020·Evolution Letters·Sonia PascoalNathan W Bailey

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