Research Interests

Structural Biology / Macromolecular NMR / Protein-Protein Interactions / Protein-Nucleic Acid Interactions / Computational NMR

 

Research Description

Determination of Three-Dimensional Structures of Proteins and Protein Complexes in Solution by Multidimensional Nuclear Magnetic Resonance Spectroscopy.

Current research is principally focused on 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.

Particular emphasis is being placed on complexes involved in signal transduction and transcriptional regulation, and on AIDS and AIDS-related proteins. Recent accomplishments include the extension of the applicability of the NMR method to structures larger than 40 kDa, including the determination of the 3D solution structures of the complete 44 kDa trimeric ectodomain of SIV gp41, the 42 kDa ternary Oct1·Sox2·Hoxb1-DNA complex, and the 40 kDa phosphoryl transfer complex of enzyme I and the histidine-containing phosphocarrier protein (HPr) of the bacterial PTS system. Other systems whose structures have recently been solved include: a variety of complexes from the bacterial PTS system including complexes of enyme IIA^Glc with HPr and the IIB domain of enzyme IICB^Glc and a complex of enyzme IIA^Mtl with HPr; complexes of the transcription factors GATA-1, AREA, HMG-I/Y and MEF2A with dsDNA, complexes of wild-type SRY (the mammalian male sex determining factor) and a sex reversal mutant of SRY with dsDNA; specific complexes of FBP and hnRNP K with ssDNA; the anti-HIV protein cyanovirin in monomeric and domain-swapped dimeric forms; the cellular factor BAF which is responsible for protecting retroviral DNA from autointegration; and the N- and C-terminal domains of HIV integrase. Examples of methodological developments include the whole suite of 3D and 4D heteronuclear NMR experiments that have been developed at NIH and are essential for studying larger proteins where overlapping resonances pose a formidable problem; methods that make use of anisotropy of the alignment tensor or the diffusion tensor to provide long-range structural information that is not available from other NMR parameters that rely entirely on close spatial proximity of atoms; novel methods for long range distance determination using paramagnetic relaxation enhancement; and the development of fast and efficient algorithms for the analysis of NMR spectra and for the computation of 3D structures based on all available experimental NMR restraints.

In addition to our NMR work, we are also engaged in a major effort relating to the development of potential HIV Env-mediated fusion inhibitors and vaccines using chimeric gp41 proteins designed on the basis of the NMR structure of gp41 solved in our laboratory.

 

Publications

 

Selected Recent Publications (2004-)

Kuszewski, J., Schwieters, C.D., Garrett, D.S., Byrd, R.A., Tjandra, N. & Clore, G. M. (2004) Completely automated, highly error tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments. J. Am. Chem. Soc. 126, 6258-6273. Pubmed PDF

Clore, G.M. & Schwieters, C. D. (2004) Amplitudes of protein backbone dynamics and correlated motions in a small a/b protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43, 10678-10691. Pubmed PDF Supplementary Information

Legler, P. M., Cai, M., Peterkofsky, A. & Clore, G. M. (2004) Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter II^Mannitol of the Escherichia coli phosphotransferase system. J. Biol. Chem. 279, 39115-39121. Pubmed PDF

Iwahara, J., Schwieters, C.D. & Clore, G.M. (2004) Characterization of non-specific protein-DNA interactions by ¹H paramagnetic relaxation enhancement. J. Am. Chem. Soc. 126, 12800-12808. Pubmed PDF

Williams, D.C., Cai, M., Suh, J.-Y., Peterkofsky, A. & Clore, G. M. (2005) Solution NMR structure of the 48 kDa IIA^Mannose-HPr complex of the Escherichia coli mannose phosphotransferase system. J. Biol. Chem. 280, 20775-20784. Pubmed PDF

Clore, G.M. & Schwieters, C.D. (2006) Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small a/b protein: a unified picture of high probability, fast atomic motions in proteins. J. Mol. Biol. 355, 879-886. Pubmed PDF

Iwahara, J. & Clore, G.M. (2006) Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440, 1227-1230. Pubmed PDF Supplementary Information

Iwahara, J. & Clore, G.M. (2006) NMR structural and kinetic characterization of a homeodomain diffusing and hopping on non-specific DNA. Proc. Natl. Acad. Sci. U.S.A. 103, 15062-15067. Pubmed PDF Supplementary Material

Tang, C., Iwahara, J. & Clore, G.M. (2006) Visualization of transient encounter complexes in protein-protein association. Nature 444, 383-386. Pubmed PDF Supplementary Material Movie1 Movie2
News & Views (Blundell & Fernandez-Recio, Nature 444, 279-280)
Leading Edge Molecular Biology Selects, Cell 127, 653 (2006)

Schwieters, C.D. & Clore, G.M. (2007) A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large angle X-ray scattering data. Biochemistry 46, 1152-1166. Pubmed PDF Supplementary Material

Suh, J.-Y., Iwahara, J. & Clore, G.M. (2007) Intramolecular domain-domain association/dissociation and phosphoryl transfer in the mannitol transporter of Escherichia coli are not coupled. Proc. Natl. Acad. Sci. U.S.A. 104, 3153-3158. Pubmed PDF Supplementary Material

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