This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. PDS conducted on spin-labeled proteins at low temperatures yields distance distributions. However, it is not well understood to what extent protein conformations represented by these distributions correspond to conformations in solution. In general there is an argument that the structure determined at such conditions may be a poor model for highly dynamic (flexible) proteins. Similar arguments, such as protein confinement by the crystal lattice and using cryogenic temperatures for collecting diffraction pattern could be (and are) applied to X-ray crystallography. But we do know that there is often significant correspondence between X-ray and NMR derived structures. Therefore it is important to test what the distance distributions from PDS conducted on proteins in solution in the absence of confinement by crystal contacts may represent. One argument is that the range of conformations given by the distribution of end-to-end distances depends mainly on spring constants and the number of connecting chemical bonds. One would expect to find this for example for a rod like organic molecule or long alpha-helix, however one would need to take a sufficiently long helix in order be able determine the extent of its flexibility and may also need to use conformationally-persistent spin-labels, such as TOAC. This was the approach used in our collaborative paper with D. Budil et al. However, for a folded protein or a protein complex the picture may be more complex, since many bonds allow for substantial freedom and may produce an ensemble of conformations that exchange slow and can get trapped. Therefore, sufficiently rapid freezing that brings the solvent into the glassy state as a matter of microseconds is expected to preserve the ensemble of such conformers, but may depopulate those that exchange with faster rates in microsecond range. We are going to apply freeze-quenching technique, developed in Scholes lab, using different freezing rates on doubly labeled model proteins and to compare distances distributions obtained by PDS with the goals to delineate conformational exchange rates and to test the relevance of distance distributions from PDS to the range of conformations sampled by a protein in solution. .

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
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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
Smith, Andrew K; Freed, Jack H (2012) Dynamics and ordering of lipid spin-labels along the coexistence curve of two membrane phases: an ESR study. Chem Phys Lipids 165:348-61
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
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
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

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