Research Interests

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

 

Research Description

Structure and Dynamics of Macromolecules and their Complexes in Solution by Multidimensional Nuclear Magnetic Resonance Spectroscopy.

My research is centered upon the development and application of nuclear magnetic resonance (NMR) to study the structure and dynamics of biological macromolecules and their complexes in solution. Particular emphasis is being placed on novel approaches to extending NMR to larger and more complex systems, especially complexes involved in signal transduction and transcriptional regulation, and exploring fundamental questions associated with protein dynamics, macromolecular interactions and recognition processes. Currently we are exploiting the unique properties of NMR to detect and characterize sparsely-populated states of macromolecules. Many important biological processes proceed through transient intermediate states that comprise only a small fraction of the overall population of a molecular system at equilibrium, and, as a result, are invisible (i.e. dark) to conventional biophysical techniques (including crystallography, cryo-electron microscopy and single molecule spectroscopies). These studies, which have provided new insights into macromolecular recognition and assembly, rely on the ability of NMR to amplify, through exchange phenomena, the effect of the invisible "dark" state on some NMR observable (generally a relaxation property) so that its footprint is readily observed in measurements on the NMR visible species. Examples of such phenomena that we have studied include the search processes whereby transcription factors locate their specific DNA binding site within an overwhelming sea of non-specific DNA; the role of encounter complexes in protein-protein association; the interplay of conformational selection and induced fit in protein-ligand interactions; transient interactions of intrinsically disordered and partially folded polypeptides with large megadalton macromolecular assemblies including highly heterogeneous aggregates involved in amyloid protofibril formation and the GroEL chaperonin molecular machine; transient interactions involving the very earliest stages in the formation of huntingtin protofibrils; and transient interdomain interactions and transient oligomerization of the Hsp40 chaperone DNAJB6b.

 

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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

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

Cai, M., Huang, Y., Suh, J.-Y., Louis, J.M., Ghirlando, R., Craigie, R. & Clore, G.M. (2007) Solution NMR struture of the Barrier-to-Autointegration Factor/Emerin complex. J. Biol. Chem. 282, 14525-14535. Pubmed PDF

Tang, C., Schwieters, C.D. & Clore, G.M. (2007) Open-to-closed transition in apo maltose-binding protein visualized by paramagnetic NMR. Nature 449, 1078-1082. Pubmed PDF Supplementary Material

Clore, G.M., Tang, C. & Iwahara, J. (2007) Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr. Op. Struct. Biol. 17, 603-616. Pubmed PDF

Suh, J.-Y., Tang, C. & Clore, G.M. (2007) Role of electrostatic interactions in transient encounter complexes in protein-protein association investigated by paramagnetic relaxation enhancement. J. Am. Chem. Soc 129, 12954-12955. Pubmed PDF Supplementary Material

Clore, G.M. (2008) Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement. Molecular BioSystems 4, 1058-1069. Pubmed PDF

Doucleff, M. & Clore, G.M. (2008) Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multi-domain transcription factor Oct-1. Proc. Natl. Acad. Sci. U. S. A. 105, 13871-13876. Pubmed PDF Supplementary.

Tang, C., Louis, J.M., Aniana, A., Suh, J.-Y. & Clore, G.M (2008) Visualizing transient events in amino-terminal auto-processing of HIV-1 protease. Nature 455, 693-696. Pubmed PDF Supplementary

Tang, C., Ghirlando, R. & Clore, G. M. (2008) Visualization of transient ultra-weak protein self-association in solution using paramagnetic relaxation enhancement. J. Am. Chem. Soc. 130, 4048-4056. Pubmed PDF

Hu, J., Hu, K., Williams, D.C., Komlosh, M., Cai, M. & Clore, G.M. (2008) Solution NMR structures of productive and non-productive complexes between the A and B domains of the cytoplasmic subunit of the mannose transporter of the Escherichia coli phosphotransferase system. J. Biol. Chem. 283, 11024-11037. Pubmed PDF

Clore, G.M. (2008) Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement. Molecular BioSystems 4, 1058-1069. Pubmed PDF

Clore, G.M. & Iwahara, J. (2009) Theory, practice and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem. Rev. 109, 4108-4139. Pubmed PDF

Ryabov, Y., Suh, J.-Y., Grishaev, A., Clore, G.M. & Schwieters, C.D. (2009) Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes. J. Am. Chem. Soc. 131, 9522-9531. Pubmed PDF Supplementary

Fawzi, N.L., Doucleff, M., Suh, J.-Y. & Clore, G.M. (2010) Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements. Proc. Natl. Acad. Sci. U. S. A. 121, 1379-1384. Pubmed PDF Supplementary

Yung, Y.-S., Cai, M. & Clore, G.M. (2010) Solution structure of the IIA^Chitobiose-IIB^Chitobiose complex of the N,N'-diacetylchitobiose branch of the Eschrichia coli phosphotransferase system. J. Biol. Chem. 285, 4173-4184. Pubmed PDF

Ryabov, Y., Clore, G.M. & Schwieters, C.D. (2010) Direct use of ¹⁵N relaxation rates as experimental restraints on molecular shape and orientation for docking of protein-protein complexes. J. Am. Chem. Soc. 132, 5987-5989 Pubmed PDF Supplementary

Fawzi, N., Ying, J., Torchia, D, A., Clore, G. M. (2010) Kinetics of amyloid b monomer to oligomer exchange by NMR relaxation. J. Am. Chem. Soc. 132, 9948-9951 Pubmed PDF Supplementary

Schwieters, C.D., Suh, J.-Y., Grishaev, A., Ghirlando, R., Takayama, Y. & Clore, G.M. (2010) Solution structure of the 128 kDa Enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small and wide angle X-ray scattering. J. Am. Chem. Soc. 132, 13026-13045. Pubmed PDF Supplementary

Iwahara, J. & Clore, G.M. (2010) Structure-independent analysis of the breadth of the positional distribution of disordered groups in macromolecules from order parameters for long variable-length vectors using NMR paramagnetic relaxation enhancement. J. Am. Chem. Soc. 132, 13346-13356. Pubmed PDF

Ryabov, Y., Schwieters, C.D. & Clore, G.M. (2011) Impact of ¹⁵N R₂/R₁ relaxation restraints on molecular size, shape and bond vector orientation for NMR protein structure determination with sparse distance restraints. J. Am. Chem. Soc. in press. Pubmed PDF Supplementary

Clore, G.M. (2011) Exploring sparsely-populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Protein Sci. 20, 229-246. pubmed PDF

Takayama, Y., Schwieters, C. D., Grishaev, A., Ghirlando, R. & Clore, G.M. (2011) Combined use of residual dipolar couplings and solution X-ray scattering to rapidly probe rigid body conformational transitions in a non-phosphorylatable active site mutant of the 128 kDa enzyme I dimer. J. Am. Chem. Soc. 133, 424-427. pubmed PDF Supplementary

Takayama, Y. & Clore, G.M. (2011) Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR. Proc. Natl Acad. Sci. U. S. A. 108, E169-E176. pubmed PDF Supplementary Author summary

Clore, G.M. (2011) Exploring translocation of proteins on DNA by NMR. J. Biomol. NMR 51, 209-219. pubmed PDF

Fawzi, N.L., Ying, J., Ghirlando, R, Torchia, D.A. & Clore, G.M. (2011) Atomic resolution dynamics on the surface of amyloid ß protofibrils probed by solution NMR. Nature 480, 268-272. pubmed PDF Supplementary Software for fitting DEST data

Anthis, N.J., Doucleff, M. & Clore, G.M. (2011) Transient sparsely-populated compact states of apo and calcium-loaded calmodulin probed by paramagnetic relaxation enhancement: interplay of conformational selection and induced fit. J. Am. Chem. Soc. 133, 18976-18974. pubmed PDF Supplementary

Takayama, Y. & Clore, G.M. (2012) Interplay between minor and major groove-binding transcription factors Sox2 and Oct1 in translocation on DNA studied by paramagnetic and diamagnetic NMR. J. Biol. Chem. 287, 14349-14363. pubmed PDF

Fawzi, N.L., Ying, J., Torchia, D.A. & Clore, G.M. (2012) Probing exchange kinetics and atomic resolution dynamics in high molecular weight complexes: dark-state exchange saturation transfer NMR spectroscopy. Nature Protocol 7, 1523-1533. pubmed PDF

Jung, Y.-S., Cai, M. & Clore, G.M. (2012) Solution structure of the IIA^Chitobiose-HPr complex of the N,N’-diacetylchitobiose branch of the Escherichia coli phosphotransferase system. J. Biol. Chem. 287, 23819-23829. pubmed PDF

Takayama, Y. & Clore, G.M. (2012) Impact of protein-protein interactions on global intermolecular translocation rates of the transcription factors Sox2 and Oct1 between DNA cognate sites studied by z-exchange NMR spectroscopy. J. Biol. Chem. 287, 26962-26970. Pubmed PDF

Venditti, V. & Clore, G.M. (2012) Conformational selection and substrate binding regulate the monomer/dimer equilibrium of the C-terminal domain of Escherichia coli Enzyme I. J. Biol. Chem. 287, 26989-26998. Pubmed PDF

Grishaev, A., Anthis, N.J. & Clore, G.M. (2012) Contrast-matched small angle X-ray scattering from a heavy atom-labeled protein in structure determination: application to a lead-substituted calmodulin-peptide complex. J. Am. Chem. Soc. 134, 14686-14689. Pubmed PDF Supplementary

Libich, D.S., Fawzi, N.L., Ying, J. & Clore, G.M. (2013) Probing the transient ‘dark-state’ of substrate binding to GroEL by relaxation-based solution NMR. Proc. Natl. Acad. Sci. U.S.A. 110, 11361-11366. Pubmed PDF

Anthis, N.J. & Clore, G.M. (2013) The length of the calmodulin linker determines the extent of transient interdomain association and target affinity. J. Am. Chem. Soc. 135, 9648-9651. Pubmed PDF Supplementary

Clore, G.M. & Venditti, V. (2013) Structure, dynamics and biophysics of the cytoplasmic protein-protein complexes of the bacterial phosphoenolpyruvate:sugar phosphotransferase system. Trends Biochem. 38, 515-530. Pubmed PDF

Deshmukh, L., Schwieters, C.D., Grishaev, A., Ghirlando, R., Baber, J.L. & Clore, G.M. (2013) Structure and dynamics of full length HIV-1 capsid protein in solution. J. Am. Chem. Soc. 133, 16133-16147. Pubmed PDF Supplementary

Clore, G.M. (2013) Seeing the invisible by paramagnetic and diamagnetic NMR. Centenary Award and Frederick Gowland Hopkins Memorial Lecture. Biochem. Soc. Trans. 41, 1343-1354. Pubmed PDF

Clore, G.M. (2014) Interplay between conformational selection and induced fit in multidomain protein-ligand binding probed by paramagnetic relaxation enhancement. Biophysical Chemistry. 186, 3-12. Pubmed PDF

Deshmukh, L., Ghirlando, R. & Clore, G.M. (2014) Investigation of the structure and dynamics of the capsid-spacer peptide 1-nucleocapsid fragment of the HIV-1 Gag polyprotein by solution NMR spectroscopy. Angwandte Chimie Int. Ed. 53, 1025-1028. Pubmed PDF Supplementary

Schwieters, C.D. & Clore, G.M. (2014) Using small angle solution scattering data in Xplor-NIH structure calculations. Progr. Nucl. Magn. Reson. Spectroscopy 80, 1-11 Pubmed PDF

Fawzi, N.L., Libich, D.S., Ying, J., Tugarinov, V. & Clore, G.M. (2014) Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid beta protofibril interactions using ¹³C_methyl-DEST and lifetime line broadening. Angewandte Chemie Int. Ed. 53, 10345-10349. Pubmed PDF Supplementary

Ryu, K.-S., Tugarinov, V. & Clore, G.M. (2014) Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by ¹⁵N_z-exchange NMR spectroscopy. J. Am. Chem. Soc. 136, 14369-14372. Pubmed PDF Supplementary

Venditti, V., Tugarinov, V., Schwieters, C.D., Grishaev, A. & Clore, G.M. (2015) Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I. Nature Communications 6, 5960. Pubmed PDF Supplementary

Anthis, N.J. & Clore, G.M. (2015) Visualizing transient dark states by NMR spectroscopy. Q. Rev. Biophys. 48, 35-116. Pubmed PDF

Deshmukh, L., Ghirlando, R. & Clore, G.M. (2015) Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 112, 3374-3379. Pubmed PDF

Baber, J. L., Louis, J. M. & Clore, G. M. (2015) Dependence of distance distributions derived from double electron-electron resonance pulsed EPR spectroscopy on pulse-sequence time. Angewandte Chemie Int. Ed. 54. 5336-5339. Pubmed PDF Supplementary

Libich, D.S., Tugarinov, V. & Clore, G.M. (2015) Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR. Proc. Natl. Acad. Sci. U. S. A. 112, 8817-8823. Pubmed PDF

Venditti, V., Schwieters, C.D., Grishaev, A. & Clore, G.M. (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, 11565-11570. Pubmed PDF

Venditti, V., Egner, T.K. & Clore, G.M. (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. 11, 6305-6322. Pubmed PDF

Bermejo, G., Clore, G.M. & Schwieters, C.D. (2016) Improving NMR structures of RNA. Structure 24, 806-815. Pubmed PDF Supplementary

Deshmukh, L., Schweiters, C.D.Grishaev, A. & Clore, G.M. (2016) Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR, X-ray scattering and protein engineering. ChemPhysChem, 17, 1548-1552. Pubmed PDF Supplementary

Ceccon, A., Tugarinov, V., Bax, A. & Clore, G.M. (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, 5789-5792. Pubmed PDF Supplementary
C&E News (Borman S., vol 94, issue 20, p.11)
J. Am. Chem. Soc. Spotlight (2016, 138, 7199)

Schmidt, T., Ghirlando, R., Baber, J. & Clore, G.M. (2016) Quantitative resolution of monomer-dimer populations by inversion modulated DEER EPR spectroscopy. ChemPhysChem 17, 2987-2991. Pubmed PDF Supplementary

Deshmukh, L., Louis, J.M., Ghirlando, R. & Clore, G.M. (2016) Transient Gag-protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations in HIV-1. Proc. Natl. Acad. Sci. U. S. A. 113, 12456-12461. Pubmed PDF

Schmidt, T., Walti, M.A., Baber, J.L., Hustedt, E.J. & Clore, G.M. (2016) Long distance measurements up to 160 A in the GroEL tetradecamer using Q-band DEER EPR spectroscopy. Angewandte Chemie Int. Ed.55, 15905-15909. Pubmed PDF Supplementary

Libich, D.S., Tugarinov, V., Ghirlando, R. & Clore, G.M. (2017) Confinement and stabilization of Fyn SH3 folding intermediate mimetics within the cavity of the chaperonin GroEL by relaxation-based NMR. Biochemistry 56, 903-906. Pubmed PDF Supplementary

Kotler, S.A, Tugarinov, V., Schmidt, T., Ceccon, A., Libich, D.S., Ghirlando, R., Schwieters, C.D. and Clore, G.M. (2019) Probing initial transient oligomerization events facilitating Huntingtin fibril nucleation at atomic resolution by relaxation-based NMR. Proc. Natl. Acad. Sci. U. S. A. 116, 3562-3571. Pubmed PDF Supplementary

Ceccon, A., Tugarinov, V., Ghirlando, R. & Clore, G.M. (2020) Abrogation of pre-nucleation, transient oligomerization of the Huntingtin exon-1 protein by human profilin-I. Proc. Natl. Acad. Sci. U.S.A. 117, 5844-5852 . Pubmed PDF Supplementary

Ceccon, A., Tugarinov, V. & Clore, G.M. (2021) Quantitative exchange NMR-based analysis of Huntingtin-SH3 interactions suggests an allosteric mechanism of inhibition of Huntingtin aggregation. J. Am. Chem. Soc. 143, 9672-9681. Pubmed PDF Supplementary

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