title: NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model.
abstract: The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent, are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on (13)Cα, (1)Hα, and (1)HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water).
authors.affiliation: Department of Chemistry, California State University, Fresno, CA, 93740.
authors.forename: Kurt A
authors.initials: KA
authors.lastname: Heisel
authors.forename: V V
authors.initials: VV
authors.lastname: Krishnan
mesh_terms: D000595:Amino Acid Sequence; D002244:Carbon; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D028861:Nuclear Pore Complex Proteins / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011522:Protons; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D012997:Solvents / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D064267:Intrinsically Disordered Proteins; D028861:Nuclear Pore Complex Proteins; D010455:Peptides; D011522:Protons; D012997:Solvents; C040500:phenylalanylglycine; D002244:Carbon; D004121:Dimethyl Sulfoxide
keywords: intrinsically disordered protein; nuclear magnetic resonance; nucleoporins; solvent perturbation
references.citation: Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2450-5
references.pmid: 12604785
references.citation: Prog Biophys Mol Biol. 2010 Jun-Jul;102(2-3):73-84
references.pmid: 20097220
references.citation: J Biomol NMR. 1995 Nov;6(3):277-93
references.pmid: 8520220
references.citation: BMC Genomics. 2008 Sep 16;9 Suppl 2:S1
references.pmid: 18831774
references.citation: Methods Mol Biol. 2004;278:353-78
references.pmid: 15318003
references.citation: J Biomol NMR. 1995 Sep;6(2):135-40
references.pmid: 8589602
references.citation: J Biomol NMR. 1996 Jul;8(1):93-7
references.pmid: 8810526
references.citation: Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2008-11
references.pmid: 7892216
references.citation: J Biomol NMR. 2010 Apr;46(4):257-70
references.pmid: 20213252
references.citation: Prog Nucl Magn Reson Spectrosc. 2009 Apr 5;54(3-4):141-165
references.pmid: 20160946
references.citation: J Biomol NMR. 2004 Oct;30(2):143-53
references.pmid: 15666561
references.citation: Mol Biol Cell. 2002 Feb;13(2):425-34
references.pmid: 11854401
references.citation: Mol Cell Proteomics. 2010 Oct;9(10):2205-24
references.pmid: 20368288
references.citation: Biochemistry. 1981 Dec 8;20(25):7278-84
references.pmid: 6274396
references.citation: J Am Chem Soc. 2001 Apr 4;123(13):2970-8
references.pmid: 11457007
references.citation: Cell. 2007 Apr 6;129(1):83-96
references.pmid: 17418788
references.citation: PLoS Comput Biol. 2008 Aug 08;4(8):e1000145
references.pmid: 18688269
references.citation: Angew Chem Int Ed Engl. 2003 Aug 25;42(33):3938-41
references.pmid: 12949874
references.citation: Biochem Biophys Res Commun. 1983 Dec 16;117(2):479-85
references.pmid: 6661238
references.citation: J Cell Biol. 2000 Feb 21;148(4):635-51
references.pmid: 10684247
references.citation: J Biol Chem. 1995 Jul 14;270(28):16499-502
references.pmid: 7622450
references.citation: J Biol Chem. 2002 Dec 27;277(52):50597-606
references.pmid: 12372823
references.citation: Cochlear Implants Int. 2002 Mar;3(1):54-67
references.pmid: 18792111
references.citation: Protein Sci. 2002 Apr;11(4):739-56
references.pmid: 11910019
references.citation: J Mol Graph Model. 2001;19(1):26-59
references.pmid: 11381529
references.citation: Cell. 2000 Jul 7;102(1):99-108
references.pmid: 10929717