The coiled coil is a widespread and biologically important structural motif that mediates specific protein-protein interactions. Although coiled coils had previously been assumed to be parallel, recent structural studies have highlighted the importance of antiparallel-coiled coils in nature. Due to the prevalence of coiled-coil domains and to the recent explosion in genome sequence information, the ability to predict coiled-coil function from sequence data would be extremely valuable. Because the orientation within a coiled coil affects strand-pairing specificity, an understanding of the interactions that affect helix orientation is necessary to accurately predict interaction partners. We have recently developed a genetic method for selecting coiled coils that associate with a given relative helix orientation from a randomized pool of proteins. We will apply this approach to identify sequence features that specify one orientation over the other. In addition, because more than half of the structurally characterized coiled coil domains are intramolecular, we will use a combination of rational design and selection methods to probe the structural determinants for helical hairpin formation. Such information will aid in the prediction of coiled coil function, as the helical hairpin appears to be a versatile motif for protein-protein or protein-nucleic acid interactions. We will also probe the interactions of three proteins involved in the maintenance of muscle integrity that appear to contain helical hairpin domains: dystrophin, dystrobrevin, and dysbindin. Finally, one of the most surprising recent findings in this area is that structural maintenance of chromosome (SMC) proteins contains two antiparallel-coiled coils that are several hundred amino acid residues in length. We propose a combination of biophysical and functional studies that explore the importance of coiled-coil length and sequence for function of bacterial SMC proteins in vivo.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM057571-09
Application #
7060738
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Program Officer
Basavappa, Ravi
Project Start
1998-05-01
Project End
2008-04-30
Budget Start
2006-05-01
Budget End
2008-04-30
Support Year
9
Fiscal Year
2006
Total Cost
$262,950
Indirect Cost
Name
Indiana University Bloomington
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
006046700
City
Bloomington
State
IN
Country
United States
Zip Code
47401
Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra et al. (2015) Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins. Proteins 83:1027-45
Weitzel, Christopher S; Waldman, Vincent M; Graham, Travis A et al. (2011) A repeated coiled-coil interruption in the Escherichia coli condensin MukB. J Mol Biol 414:578-95
Li, Yinyin; Schoeffler, Allyn J; Berger, James M et al. (2010) The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB. J Mol Biol 395:11-9
Li, Yinyin; Stewart, Nichole K; Berger, Anthony J et al. (2010) Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction. Proc Natl Acad Sci U S A 107:18832-7
Li, Yinyin; Weitzel, Christopher S; Arnold, Randy J et al. (2009) Identification of interacting regions within the coiled coil of the Escherichia coli structural maintenance of chromosomes protein MukB. J Mol Biol 391:57-73
McClain, D L; Binfet, J P; Oakley, M G (2001) Evaluation of the energetic contribution of interhelical Coulombic interactions for coiled coil helix orientation specificity. J Mol Biol 313:371-83