Research in this laboratory is centered around solution studies on the structure and dynamics of proteins, protein-protein complexes and protein-nucleic acid complexes using multidimensional NMR spectroscopy, and on the development and application of novel NMR and computational methods to aid in these studies.Over the last year we have developed novel hybrid methods combining NMR and solution scattering to solve the structures of proteins and proetin complexes in excess of 100 kDa. Structures that have been solved this year include the 128 kDa enzyme I and its 146 kDa complex with HPr from the bacterial phosphotransferase system (PTS), and the complex of IIAchitobiose with IIBchitobiose, also from the PTS. In addition, we have devoted significant efforts towards detecting, characterizing and visualizing highly transient, lowly-populated states that are invisible to conventional biophysical and structural techniques, yet play a key role in numerous biological processes including recognition, allostery, signal transduction, etc.... by means of paramagnetic relaxation enhancement (PRE) and novel relaxation methods. Using these approaches we have been able to characterize sliding and hopping of a multidomain transcription factor on NDA, to characteristics the mechanistic details involving encounter complex formation in protein-protein interactions, and to study the exchange between monomeric and protofibril forms of amyloid Abeta.

Project Start
Project End
Budget Start
Budget End
Support Year
23
Fiscal Year
2013
Total Cost
$1,761,484
Indirect Cost
City
State
Country
Zip Code
Venditti, Vincenzo; Egner, Timothy K; Clore, G Marius (2016) Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 116:6305-22
Deshmukh, Lalit; Schwieters, Charles D; Grishaev, Alexander et al. (2016) Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering. Chemphyschem 17:1548-52
Ceccon, Alberto; Tugarinov, Vitali; Bax, Ad et al. (2016) Global Dynamics and Exchange Kinetics of a Protein on the Surface of Nanoparticles Revealed by Relaxation-Based Solution NMR Spectroscopy. J Am Chem Soc 138:5789-92
Schmidt, Thomas; Ghirlando, Rodolfo; Baber, James et al. (2016) Quantitative Resolution of Monomer-Dimer Populations by Inversion Modulated DEER EPR Spectroscopy. Chemphyschem :
Schmidt, Thomas; Wälti, Marielle A; Baber, James L et al. (2016) Long Distance Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR Spectroscopy. Angew Chem Int Ed Engl 55:15905-15909
Bermejo, Guillermo A; Clore, G Marius; Schwieters, Charles D (2016) Improving NMR Structures of RNA. Structure 24:806-15
Libich, David S; Tugarinov, Vitali; Clore, G Marius (2015) Reply to Marchenko et al.: Flux analysis of GroEL-assisted protein folding/unfolding. Proc Natl Acad Sci U S A 112:E6833-4
Baber, James L; Louis, John M; Clore, G Marius (2015) Dependence of distance distributions derived from double electron-electron resonance pulsed EPR spectroscopy on pulse-sequence time. Angew Chem Int Ed Engl 54:5336-9
Anthis, Nicholas J; Clore, G Marius (2015) Visualizing transient dark states by NMR spectroscopy. Q Rev Biophys 48:35-116
Venditti, Vincenzo; Schwieters, Charles D; Grishaev, Alexander et al. (2015) Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Proc Natl Acad Sci U S A 112:11565-70

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