title: The response of Ω-loop D dynamics to truncation of trimethyllysine 72 of yeast iso-1-cytochrome c depends on the nature of loop deformation.
abstract: Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70-85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild-type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild-type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA.
authors.forename: Levi J
authors.initials: LJ
authors.lastname: McClelland
authors.forename: Sean M
authors.initials: SM
authors.lastname: Seagraves
authors.forename: Md Khurshid Alam
authors.initials: MK
authors.lastname: Khan
authors.forename: Melisa M
authors.initials: MM
authors.lastname: Cherney
authors.forename: Swati
authors.initials: S
authors.lastname: Bandi
authors.forename: Justin E
authors.initials: JE
authors.lastname: Culbertson
authors.forename: Bruce E
authors.initials: BE
authors.lastname: Bowler
mesh_terms: D045304:Cytochromes c / Q000737:chemistry / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008239:Lysine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000378:metabolism; D012965:Sodium Chloride / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics
chemical_list: C003712:trimethyllysine; D012965:Sodium Chloride; D045304:Cytochromes c; D008239:Lysine