title: Side-chain pairing preferences in the parallel coiled-coil dimer motif: insight on ion pairing between core and flanking sites.
abstract: A new strategy for rapid evaluation of sequence-stability relationships in the parallel coiled-coil motif is described. The experimental design relies upon thiol-thioester exchange equilibria, an approach that is particularly well suited to examination of heterodimeric systems. Our model system has been benchmarked by demonstrating that it can quantitatively reproduce previously reported trends in interhelical a-a' side-chain pairing preferences at the coiled-coil interface. This new tool has been used to explore the role of Coulombic interactions between a core position on one helix and a flanking position on the other helix (a-g'). This type of interhelical contact has received relatively little attention to date. Our results indicate that such interactions can influence coiled-coil partner preferences.
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Steinkruger
authors.forename: Derek N
authors.initials: DN
authors.lastname: Woolfson
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Gellman
mesh_terms: D020816:Amino Acid Motifs; D007477:Ions / Q000737:chemistry; D008954:Models, Biological; D055503:Protein Multimerization; D055550:Protein Stability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D007477:Ions; D011506:Proteins
references.citation: Biochemistry. 2006 Sep 26;45(38):11324-32
references.pmid: 16981692
references.citation: Nat Struct Biol. 1996 Dec;3(12):1011-8
references.pmid: 8946854
references.citation: J Mol Biol. 2006 Feb 3;355(5):1125-42
references.pmid: 16359704
references.citation: ACS Chem Biol. 2008 Jan 18;3(1):38-50
references.pmid: 18205291
references.citation: Annu Rev Biochem. 1978;47:251-76
references.pmid: 354496
references.citation: Proteins. 1994 Dec;20(4):301-11
references.pmid: 7731949
references.citation: Proteins. 1990;7(1):1-15
references.pmid: 2184436
references.citation: J Mol Biol. 2000 Jul 7;300(2):377-402
references.pmid: 10873472
references.citation: Adv Protein Chem. 2005;70:79-112
references.pmid: 15837514
references.citation: Nature. 2009 Apr 16;458(7240):859-64
references.pmid: 19370028
references.citation: Curr Opin Struct Biol. 2008 Aug;18(4):477-83
references.pmid: 18555680
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D315-22
references.pmid: 18842638
references.citation: J Struct Biol. 2008 Sep;163(3):258-69
references.pmid: 18342539
references.citation: Adv Protein Chem. 1995;46:141-76
references.pmid: 7771317
references.citation: Science. 1990 Nov 2;250(4981):646-51
references.pmid: 2237415
references.citation: Science. 1993 Nov 26;262(5138):1401-7
references.pmid: 8248779
references.citation: J Mol Biol. 2002 Nov 22;324(2):257-70
references.pmid: 12441105
references.citation: Biochemistry. 1995 Jul 11;34(27):8642-8
references.pmid: 7612604
references.citation: Nat Struct Biol. 2003 Jan;10(1):45-52
references.pmid: 12459719
references.citation: Biochemistry. 2002 Apr 16;41(15):4866-71
references.pmid: 11939781
references.citation: Protein Sci. 1995 Aug;4(8):1596-607
references.pmid: 8520486
references.citation: J Am Chem Soc. 2007 Aug 22;129(33):10255-60
references.pmid: 17661469
references.citation: Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):530-5
references.pmid: 18184807
references.citation: Biochemistry. 2002 Dec 3;41(48):14122-31
references.pmid: 12450375
references.citation: Biophys J. 1998 Jul;75(1):422-7
references.pmid: 9649402
references.citation: Nature. 1990 Mar 15;344(6263):268-70
references.pmid: 2314462
references.citation: Science. 1990 Nov 2;250(4981):669-73
references.pmid: 2237416
references.citation: Chembiochem. 2004 Feb 6;5(2):170-6
references.pmid: 14760737
references.citation: Biochemistry. 1997 Oct 14;36(41):12567-73
references.pmid: 9376362
references.citation: J Am Chem Soc. 2004 Sep 15;126(36):11172-4
references.pmid: 15355097
references.citation: J Am Chem Soc. 2006 Dec 27;128(51):16444-5
references.pmid: 17177361
references.citation: Protein Sci. 1999 Nov;8(11):2312-29
references.pmid: 10595534