This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. ESR studies of nitroxide spin labels have become a valuable tool for the investigation of protein structure and dynamics. The spectra reflect mobility and chemical environment of the spin label. Different motions, covering a wide range of amplitudes and different timescales, are simultaneously present: they comprise overall protein tumbling and refolding processes, backbone fluctuations, and side-chain isomerizations. Recognition of the motion of the spin label about its tether, even though it is not the objective of the investigation, is a prerequisite for extracting useful information. We have developed a theoretical approach to analyze the conformations and dynamics of the side-chain of the MTSSL spin-label attached to a model alpha-helix in order to identify general features, which can be useful for the interpretation of ESR spectra of spin-labeled proteins. Torsional energy profiles have been obtained by quantum mechanical methods taking into account the constraints imposed by the local environment. This enables a description of the system in terms of a limited number of rotamers, undergoing conformational jumps and librations about the minima of the side-chain torsional potential. A diffusive treatment of the dynamics is used which takes account of the energetic and frictional features of the flexible tail. This yields estimates of the amplitude and time-scale of the chain motions of the tether. Rotations around the chi1, chi2, and chi3 bonds are very unlikely, and only the chi 4 and chi 5 conformational transitions (and torsional oscillations) affect the ESR spectrum. The results of this analysis have been incorporated into an approximate form of the stochastic Liouville equation, that is reasonable for 9 GHz ESR spectra. With virtually all the parameters determined independently, the 9 GHz spectra from T4 Lysozyme spin-labeled at the 72 residue are well fit by this theory. For the methyl substituted MTSSL spin label, only a few non-interconverting conformers are possible whose mobility is limited to torsional oscillations, yielding almost identical spectra, typical of slightly mobile nitroxides. The standard MTSSL spin label yields more complex spectra which result from the simultaneous presence of constrained and mobile chain conformers. There is good agreement between experiment and theory.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
2P41RR016292-11
Application #
8363973
Study Section
Special Emphasis Panel (ZRG1-BCMB-K (40))
Project Start
2011-09-01
Project End
2012-08-31
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
11
Fiscal Year
2011
Total Cost
$3,659
Indirect Cost
Name
Cornell University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Jain, Rinku; Vanamee, Eva S; Dzikovski, Boris G et al. (2014) An iron-sulfur cluster in the polymerase domain of yeast DNA polymerase ?. J Mol Biol 426:301-8
Pratt, Ashley J; Shin, David S; Merz, Gregory E et al. (2014) Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes. Proc Natl Acad Sci U S A 111:E4568-76
Georgieva, Elka R; Borbat, Peter P; Ginter, Christopher et al. (2013) Conformational ensemble of the sodium-coupled aspartate transporter. Nat Struct Mol Biol 20:215-21
Airola, Michael V; Sukomon, Nattakan; Samanta, Dipanjan et al. (2013) HAMP domain conformers that propagate opposite signals in bacterial chemoreceptors. PLoS Biol 11:e1001479
Airola, Michael V; Huh, Doowon; Sukomon, Nattakan et al. (2013) Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling. J Mol Biol 425:886-901
Sun, Yan; Zhang, Ziwei; Grigoryants, Vladimir M et al. (2012) The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge. Biochemistry 51:8530-41
Yu, Renyuan Pony; Darmon, Jonathan M; Hoyt, Jordan M et al. (2012) High-Activity Iron Catalysts for the Hydrogenation of Hindered, Unfunctionalized Alkenes. ACS Catal 2:1760-1764
Dzikovski, Boris; Tipikin, Dmitriy; Freed, Jack (2012) Conformational distributions and hydrogen bonding in gel and frozen lipid bilayers: a high frequency spin-label ESR study. J Phys Chem B 116:6694-706
Gaffney, Betty J; Bradshaw, Miles D; Frausto, Stephen D et al. (2012) Locating a lipid at the portal to the lipoxygenase active site. Biophys J 103:2134-44
Maeda, Kiminori; Lodge, Matthew T J; Harmer, Jeffrey et al. (2012) Electron tunneling in lithium-ammonia solutions probed by frequency-dependent electron spin relaxation studies. J Am Chem Soc 134:9209-18

Showing the most recent 10 out of 72 publications