The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm

Journal of Molecular Biology
M E HodsdonD P Cistola

Abstract

The three-dimensional solution structure of rat intestinal fatty acid-binding protein (I-FABP) complexed with palmitate has been determined using multidimensional triple-resonance NMR methods. The structure is based on 3889 conformational restraints derived mostly from 3-D 13C- and 15N-resolved nuclear Overhauser (NOESY) experiments. The 3-D NOESY data for this 15.4 kDa complex contained an average of nine possible interpretations per cross-peak. To circumvent this ambiguity, an eight-stage iterative procedure was employed to gradually interpret and introduce unambiguous distance restraints during subsequent rounds of structure calculations. The first stage of this procedure relied critically upon an initial structural model based on the consensus 1H/13C chemical shift-derived secondary structure and a set of symmetry-checked restraints derived from the 3-D 13C-resolved NOESY spectrum. The structures were calculated using DISTGEOM, a program that implements a novel distance geometry algorithm with pairwise Gaussian metrization. A central feature of this algorithm is the use of an iteratively optimized Gaussian distribution for the selection of trial distances, which overcomes the tendency of metrization to produce crushed struc...Continue Reading

Citations

Jul 9, 1998·Protein Science : a Publication of the Protein Society·R A SteeleD P Cistola
Sep 10, 1998·Nature Structural Biology·D P Cistola
Jan 15, 2000·Journal of Biomolecular Structure & Dynamics·E B StarikovE E Wanker
Mar 20, 2003·Journal of Biomolecular Structure & Dynamics·Arnd B E BrauerRobin J Leatherbarrow
Aug 19, 1999·Protein Science : a Publication of the Protein Society·V A Likić, F G Prendergast
May 29, 2010·BMC Bioinformatics·Jose M DuarteMichael Lappe
Mar 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Chao ZhangSung-Hou Kim
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·O G KisselevG R Marshall
Oct 17, 2002·Proceedings of the National Academy of Sciences of the United States of America·Krishnananda ChattopadhyayCarl Frieden
Nov 23, 2016·IEEE Transactions on Visualization and Computer Graphics·Pedro HermosillaPere-Pau Vazquez
Jan 29, 2002·Journal of Molecular Biology·Dirk Bakowies, Wilfred F van Gunsteren
Nov 24, 2004·Biophysical Journal·Krishnananda ChattopadhyayCarl Frieden
Aug 31, 2014·Drug Discovery Today·Matteo CastelliNicasio Mancini
Aug 9, 2006·The Journal of Biological Chemistry·Jitendra K GautamMichael F Smith
Apr 21, 2004·Protein Science : a Publication of the Protein Society·Benhur OgbayDavid P Cistola
Apr 4, 2008·Chemistry, an Asian Journal·Parthasarathy Ganguly, Gautam R Desiraju
Oct 22, 2009·Protein Science : a Publication of the Protein Society·Gisela R FranchiniJosé María Delfino
Oct 14, 2005·Journal of Biomolecular NMR·Agnès M JaulentRobin J Leatherbarrow
Jan 20, 2006·Proteins·Krishnananda Chattopadhyay, Carl Frieden
Apr 4, 2007·Journal of Computational Chemistry·V A LevashovM F Thorpe
May 5, 2011·Journal of Computational Chemistry·Christoph GrebnerBernd Engels
Oct 12, 2000·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·G VassilevaM J Toth
Sep 8, 2004·The Journal of Biological Chemistry·Oleg G KisselevPaul A Hargrave
Apr 14, 2016·Biochemical Society Transactions·Louise H Wong, Tim P Levine
Apr 17, 2020·Protein Science : a Publication of the Protein Society·May Poh LaiRuth E Stark
Jul 29, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Nicolas G MartinelliJérôme Cornil
Feb 22, 2005·The Journal of Biological Chemistry·Tony VelkovMartin J Scanlon
Oct 21, 2016·The Journal of Biological Chemistry·Sree V ChintapalliSean H Adams

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