Brunger, A.T., Clore, G.M., Gronenborn, A.M. & Karplus, M. (1986) Three-dimensional structures of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl. Acad. Sci. U.S.A. 83, 3801-3805. pubmed PDF Clore, G.M., Brunger, A.T., Karplus, M. & Gronenborn, A.M. (1986) Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: a model study of crambin. J. Mol. Biol. 191, 523-551. pubmed PDF
Clore, G.M., Gronenborn, A.M., Nilges, M. & Ryan, C.A. (1987) The three-dimensional structure of potato carboxypeptidase inhibitor in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. Biochemistry 26, 8012-8023. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1987) Determination of three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy. Protein Engineering 1, 275-288. pubmed PDF Holak, T.A., Engström, Å, Kraulis, P.J., Lindeberg, G., Bennich, H., Jones, T.A., Gronenborn, A.M. & Clore, G.M. (1988) The solution conformation of the antibacterial peptide cecropin A: a nuclear magnetic resonance and dynamical simulated annealing study. Biochemistry 27, 7620-7629. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1989) Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. CRC Critical Reviews in Biochemistry and Molecular Biology 24, 479-564. pubmed PDF Bax, A., Clore, G.M., Driscoll, P.C., Gronenborn, A.M., Ikura, M. & Kay, L.E. (1990) Practical aspects of proton-carbon-carbon-proton three-dimensional correlation spectroscopy of 13C--labeled proteins. J. Magn. Reson. 87, 620-628. PDF Driscoll, P.C., Clore, G.M., Marion, D., Wingfield, P.T. & Gronenborn, A.M. (1990) Complete resonance assignment for the polypeptide backbone of interleukin-1b using three-dimensional heteronuclear NMR spectroscopy. Biochemistry 29, 3542-3556. pubmed PDF Clore, G.M., Bax, A., Driscoll, P.C., Wingfield, P.T. & Gronenborn, A.M. (1990) Assignment of the side chain 1H and 13C resonance of interleukin-1b using double and triple resonance heteronuclear three-dimensional NMR spectroscopy. Biochemistry 29, 8172-8184. pubmed PDF Kay, L.E., Clore, G.M., Bax, A. & Gronenborn, A.M. (1990) Four-dimensional heteronuclear triple resonance NMR spectroscopy of interleukin-1b in solution. Science 249, 411-414. pubmed PDF Ikura, M., Bax, A., Clore, G.M. & Gronenborn, A.M. (1990) Detection of nuclear Overhauser effects between degenerate amide proton resonances by heteronuclear three-dimensional NMR spectroscopy. J. Am. Chem. Soc.112, 9020-9022. PDF Clore, G.M., Kay, L.E., Bax, A. & Gronenborn, A.M. (1991) Four dimensional 13C/13C-edited nuclear Overhauser enhancement spectroscopy of a protein in solution: application to interleukin-1b. Biochemistry 30, 12-18. pubmed PDF Clore, G.M., Wingfield, P.T. & Gronenborn, A.M. (1991) High resolution three dimensional structure of interleukin-1b in solution by three and four dimensional nuclear magnetic resonance spectroscopy. Biochemistry 30, 2315-2323. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1991) Applications of three- and four-dimensional heteronuclear NMR spectroscopy to protein structure determination. Progr. Nucl. Magn. Reson. Spectroscopy 23, 43-92. PDF Clore, G.M. & Gronenborn, A.M. (1991) Two-, three- and four-dimensional NMR methods for obtaining larger and more precise three-dimensional structures of proteins in solution. Ann. Rev. Biophys. Biophys. Chem. 20, 29-63. pubmed PDF Chandrasasekhar, I., Clore, G.M., Szabo, A., Gronenborn, A.M. & Brooks, B.R. (1992) A 500 ps molecular dynamics simulation study of interleukin-1b in water: correlation with nuclear magnetic resonance spectroscopy and crystallography. J. Mol. Biol. 226, 239-250. pubmed PDF Vuister, G.W., Clore, G.M., Gronenborn, A.M., Powers,
R., Garrett, D.S., Tschudin, R. & Bax, A. (1993) Increased
resolution and improved spectral quality in four-dimensional 13C/13C-separated HMQC-NOE-HMQC spectra
using pulsed field gradients. J. Magn. Reson. Series B 101,
210-213. PDF J. Magn. Reson. Varley, P., Gronenborn, A.M., Christensen, H., Wingfield, P.T., Pain, R.H. & Clore, G.M. (1993) Kinetics of folding of the all b-sheet protein interleukin-1b studied by nuclear magnetic resonance, circular dichroism and fluorescence. Science 240, 1110-1113. pubmed PDF Sakaguchi, K., Zambrano, N., Baldwin, E.T., Shapiro, B.A., Erickson, J.W., J.G. Omichinski, G.M. Clore, A.M. Gronenborn & E. Appella (1993) Identification of a binding site for the human immunodeficiency virus type I nucleocapsid protein. Proc. Natl. Acad. Sci. U.S.A. 90, 5219-5223. pubmed PDF Clore, G.M., Robien, M.A. & Gronenborn, A.M. (1993) Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J. Mol. Biol. 231, 82-102. pubmed PDF Clore, G.M., Omichinski, J.G., Sakaguchi, K., Zambrano, N., Sakamoto, H., Appella, E. & Gronenborn, A.M. (1994) High-resolution solution structure of the oligomerization domain of p53 by multi-dimensional NMR. Science 265, 386-391. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1994) Multidimensional heteronuclear nuclear magnetic resonance of proteins. Meth. Enzymol. 239, 349-363. pubmed PDF Rozwarski, D.A., Gronenborn, A.M., Clore, G.M., Bazan, J.F., Bohm, A., Wlodawer, A., Hatada, M. & Karplus, P.A. (1994) Structural comparison among the short-chain helical cytokines. Structure 2, 159-173. pubmed PDF Lodi, P.J., Garrett, D.S., Kuszewski, J., Tsang, M.L.S., Weatherbee, J.A., Leonard, W.J., Gronenborn, A.M. & Clore, G.M. (1994) High resolution solution structure of the b chemokine hMIP-1beta by multi-dimensional NMR. Science 263, 1762-1767. pubmed PDF Lodi, P.J., Ernst, J.A., Kuszewski, J., Hickman, A.B., Engelman, A., Craigie, R., Clore, G.M. & Gronenborn, A.M. (1995) Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry 34, 9826-9833. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1995) Three-dimensional structures of alpha and beta chemokines. FASEB Journal 9, 57-62. pubmed PDF Qin, J., Clore, G.M. Kennedy, W.M.P., Huth, J.R. & Gronenborn, A.M. (1995) Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NFkB. Structure 3, 289-297. pubmed PDF Ernst, J.A., Clubb, R.T., Zhou, H.-X., Gronenborn, A.M. & Clore, G.M. (1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267, 1813-1817. pubmed PDF Makhatadze, G.I., Clore, G.M. & Gronenborn, A.M. (1995) Solvent isotope effect and protein stability. Nature Struct. Biol. 2, 852-855. pubmed PDF Clore, G.M., Ernst, J., Clubb, R.T., Omichinski, J.G., Kennedy, W.M.P., Sakaguchi, K., Appella, E. & Gronenborn, A.M. (1995) Refined solution structure of the oligomerization domain of the tumour suppressor p53. Nature Struct. Biol. 2, 321-332. pubmed PDF Grzesiek, S., Bax, A., Clore, G.M., Gronenborn, A.M., Hu, J.-H., Kaufman, J., Palmer, I., Stahl, S.J. & Wingfield, P.T. (1996) The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase. Nature Struct. Biol. 3, 340-345. pubmed PDF Werner, M.H., Gronenborn, A.M. & Clore, G.M. (1996) Intercalation, DNA kinking and the control of transcription. Science 271, 778-784. pubmed PDF Trainor, C.D., Omichinski, J.G., Vandergon, T.L., Gronenborn, A.M., Clore, G.M. & Felsenfeld, G. (1996) A palyndromic regulatory site with vertebrate GATA-1 promoters requires both zinc fingers of the GATA-1 DNA binding domain for high affinity interaction. Mol. Cell. Biol. 16, 2238-2247. pubmed PDF Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1996) Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Science 5, 1067-1080. pubmed PDF Qin, J., Clore, G.M., Kennedy W.P., Kuszewski, J. & Gronenborn, A.M. (1996) The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal. Structure 4, 613-620. pubmed PDF Huth, J.R., Bewley, C.A., Nissen, M.S., Evans, J.N.S., Reeves, R., Gronenborn, A.M. & Clore, G.M. (1997) The solution structure of an HMG-I(Y)/DNA complex defines a new architectural minor groove binding motif. Nature Sruct. Biol. 4, 657-665. pubmed PDF Huth, J.R., Bewley, C.A., Jackson, B.M., Hinnebusch, A.G., Clore, G.M. & Gronenborn, A.M. (1997) Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. Protein Sci. 6, 2359-2364. pubmed PDF Cai, M., Zheng, R., Caffrey, M., Craigie, R., Clore, G.M. & Gronenborn, A.M. (1997) Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nature Struct. Biol. 4, 567-577. pubmed PDF Omichinski, J.G., Pedone, P.V., Felsenfeld, G., Gronenborn, A.M. & Clore, G.M. (1997) The solution structure of a specific GAGA factor/DNA complex reveals a modular binding mode. Nature Struct. Biol. 4, 122-132. pubmed PDF Tjandra, N., Garrett, D.S., Gronenborn, A.M., Bax, A. & Clore, G.M. (1997) Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nature Struct. Biol.4, 443-449. pubmed PDF Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1997) Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J. Magn. Reson. 125, 171-177. pubmed PDF Garrett, D.S., Seok, Y.J., Liao, D.I., Peterkofsky, A., Gronenborn, A.M. & Clore, G.M. (1997) Solution structure of the 30 kDa N-terminal domain of Enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. Biochemistry 36, 2517-2530. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1997) NMR structures of proteins and protein complexes beyond 20,000 Mr.Nature Struct. Biol. 4, 849-853 pubmed PDF Bewley, C.A., Gustafson, K.R., Boyd, M.R., Covell, D.G., Bax, A., Clore, G.M. & Gronenborn, A.M. (1998) Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nature Struct. Biol. 5, 571-578. pubmed PDF Bewley, C.A., Gronenborn, A.M. & Clore, G.M. (1998) Minor-groove binding architectural proteins: structure, function and DNA recognition. Ann. Rev. Biophys. Biomolec. Struct. 27, 105-131. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1998) Determining structures of large proteins and protein complexes by NMR. Trends in Biotechnology 16, 22-34. pubmed PDF Clore, G.M., Gronenborn, A.M. & Tjandra, N. (1998) Direct refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson. 131, 159-162. pubmed PDF Clore, G.M., Gronenborn, A.M. & Bax, A. (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Magn. Reson. 133, 216-221. pubmed PDF Clore, G.M. & Gronenborn, A. M. (1998) New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl. Acad. Sci. U.S.A. 95, 5891-5898. pubmed PDF Clore, G.M., Starich, M.R., Gronenborn, A.M. (1998) Measurement of residual dipolar couplings of macromolecules aligned in the nematic phase of a colloidal suspension of rod-shaped viruses. J. Am. Chem. Soc. 120, 10571-10572. PDF Cai, M., Huang, Y., Sakaguchi, K., Clore, G.M., Gronenborn, A.M. & Craigie, R. (1998) An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli. J. Biomol. NMR 11, 97-102. pubmed PDF Cai, M., Huang, Y., Sakaguchi, K., Clore, G.M., Gronenborn, A.M. & Craigie, R. (1998) An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli. J. Biomol. NMR 11, 97-102. pubmed PDF Cornilescu, G., Ramirez, B.E., Frank, M.K., Clore, G.M., Gronenborn,
A.M. & Bax, A. (1999) Correlation between 3hJNC and hydrogen bond length in proteins. J. Am. Chem. Soc. 121,
6275-6279. PDF ACS Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1999) Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J. Am. Chem. Soc. 121, 2337-2338. PDF ACS Clore, G.M. & Garrett, D.S. (1999) R-factor, Free
R and complete cross-validation for dipolar coupling refinement
of NMR structures. J. Am. Chem. Soc. 121, 9008-9012. PDF ACS Louis, J.M., Clore, G.M. & Gronenborn, A.M. (1999) Regulation of HIV-1 protease: autoprocessing is tightly coupled to protein folding. Nature Struct. Biol. 6, 868-875. pubmed PDF Clore, G.M. (2000) Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization. Proc. Natl. Acad. Sci. U.S.A. 97, 9021-9025. pubmed PDF Cai, M., Huang, Y., Ghirlando, R., Wilson, K.L., Craigie, R. and Clore, G.M. (2001) Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA. EMBO J. 20, 4399-4407. pubmed PDF Schwieters, C.D. & Clore, G.M. (2001) Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J. Magn. Reson. 152, 288-302. pubmed PDF Braddock, D.T., Louis, J.M., Baber, J.L., Levens, D. & Clore, G.M. (2002) Structure and dynamics of KH domains from FBP bound to single stranded DNA. Nature 415, 1051-1056. pubmed PDF SupplementaryIwahara, J., Schwieters, C. D., Clore, G. M. (2004) Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J. Am. Chem. Soc. 126, 5879-5896. Pubmed PDF Supplementary Information Clore, G.M. & Schwieters, C.D. (2004) How much backbone motion in ubiquitin is required to be consistent with dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation. J. Am. Chem. Soc. 126, 2923-2938. pubmed PDF Supplementary Information Iwahara, J. & Clore, G.M. (2006) Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440, 1227-1230. Pubmed PDF Supplementary Information 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 Iwahara, J., Zweckstetter, M. & 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., 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 Iwahara, J., Tang, C. & Clore, G.M. (2007) Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules. J. Magn. Reson. 184, 185-195. pubmed PDF 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 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. & Clore, G.M. (2015) Visualizing transient dark states by NMR spectroscopy. Q. Rev. Biophys. 48, 35-116. Pubmed PDF Schwieters, C.D., Bermejo, G.A. & Clore, G.M. (2018) Xplor-NIH for molecular structure determination from NMR and other data sources. Protein Sci. 27, 26-40. Pubmed PDF
Clore, G.M., Andreasson, L.E., Karlsson, B., Aasa, R. & Malstrom, B.G. (1980) Characterization of the low temperature intermediates of the reaction of fully reduced soluble cytochrome oxidase with oxygen by electron paramagnetic resonance and optical spectroscopy. Biochem. J. 185, 139-154. pubmed PDF Clore, G.M., Andreasson, L.E., Karlsson, B., Aasa, R. & Malmstrom, B.G. (1980) Characterization of the intermediates in the reaction of mixed valence state soluble cytochrome oxidase with oxygen at low temperatures by optical and electron paramagnetic resonance spectroscopy. Biochem. J. 185, 155-167. pubmed PDF Clore, G.M., Kimber, B.J. & Gronenborn, A.M. (1983) The 1-1 hard pulse: a novel, simple and effective method of water resonance suppression in FT-1H-NMR. J. Magn. Reson. 54, 170-173. PDF Gronenborn, A.M. & Clore, G.M. (1985) Investigations into the solution structures of short nucleic acid fragments by means of nuclear Overhauser enhancement measurements. Progr. Nucl. Magn. Reson. Spectroscopy 17, 1-32. PDF Perutz, M.F., Gronenborn, A.M., Clore, G.M., Hogg, J.H. & Shi, T. (1985) The pKa's of two histidines in human haemoglobin, the Bohr effect and the dipole moment of a-helices. J. Mol. Biol. 183, 491-498. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1985) Assessment of
errors involved in the determination of interproton distance
ratios and distances by means of one- and two-dimensional NOE
measurements. J. Magn. Reson. 61, 158-164. PDF J. Magn. Reson. Nilsson, L., Clore, G.M., Gronenborn, A.M., Brunger, A.T. & Karplus, M. (1986) Structure refinement of oligonucleotides by molecular dynamics with NOE interproton distance restraints: application to 5'd(CGTACG)2. J. Mol. Biol. 188, 455-475. pubmed PDF Clore, G.M., Martin, S.R. & Gronenborn, A.M. (1986) The solution structure of human growth hormone releasing factor: combined use of circular dichroism and nuclear magnetic resonance spectroscopy. J. Mol. Biol. 191, 553-561. pubmed PDF Clore, G.M., Gronenborn, A.M. Carlson, G. & Meyer, E.F. (1986) Stereochemistry of binding of the tetrapeptide Acetyl-Pro-Ala-Pro-TyrNH2 to porcine pancreatic elastase: combined use of two-dimensional transferred nuclear Overhauser enhancement measurements, restrained molecular dynamics, X-ray crystallography and molecular modelling. J. Mol. Biol. 190, 259-267. pubmed PDF Clore, G.M., Gronenborn, A.M., Nilges, M., Sukumaran, D.K. & Zarbock, J. (1987) The polypeptide fold of the globular domain of histone H5 in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 6, 1833-1842. pubmed PDF Bax, A., Sklenar, V., Clore, G.M. & Gronenborn, A.M. (1987) Water suppression in two-dimensional spin-locked NMR experiments using a novel phase cycling procedure. J. Am. Chem. Soc. 109, 6511-6513. PDF Oschkinat, H., Griesinger, C., Kraulis, P.J., Sørensen, O.W., Ernst, R.R., Gronenborn, A.M. & Clore, G.M. (1988) Three-dimensional NMR spectroscopy of a protein in solution. Nature 332, 374-376. pubmed PDF Clore, G.M., Sukumaran, D.K., Nilges, M., Zarbock, J. & Gronenborn, A.M. (1987) The conformations of hirudin in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 6, 529-537. PDF Holak, T.A., Nilges, M., Prestegard, H., Gronenborn, A.M. & Clore, G.M. (1988) Three-dimensional structure of acyl carrier protein in solution determined by nuclear magnetic resonance and the combined use of dynamical simulated annealing and distance geometry. Eur. J. Biochem. 175, 9-15. pubmed PDF Driscoll, P.C., Clore, G.M., Beress, L. & Gronenborn, A.M. (1989) A proton nuclear magnetic resonance study of the anti-hypertensive and anti-viral protein BDS-I from the sea anemone Anemonia sulcata: sequential and stereospecific assignment and secondary structure. Biochemistry 28, 2178-2187. pubmed PDF Driscoll, P.C., Gronenborn, A.M., Beress, L. & Clore, G.M. (1989) Determination of the three-dimensional structure of the anti-hypertensive and anti-viral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. Biochemistry 28, 2188-2198. pubmed PDF Folkers, P.J.M., Clore, G.M., Driscoll, P.C., Dodt, J., Köhler, S. & Gronenborn, A.M. (1989) The solution structure of recombinant hirudin and the Lys-47ÆGlu mutant: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. Biochemistry 28, 2601-2617. pubmed PDF Clore, G.M., Appella, E., Yamada, M., Matsushima, K. & Gronenborn, A.M. (1989) Determination of the secondary structure of interleukin-8 by nuclear magnetic resonance spectroscopy. J. Biol. Chem. 264, 18907-18911. pubmed PDF Gronenborn, A.M., Bax, A., Wingfield, P.T. & Clore, G.M. (1989) A powerful method of sequential proton resonance assignment in proteins using relayed 15N-1H multiple quantum coherence spectroscopy. FEBS Letters 243, 93-98. pubmed PDF Clore, G.M., Bax, A., Wingfield, P.T. & Gronenborn, A.M. (1990) Identification and localization of bound internal water in the solution structure of interleukin-1b by heteronuclear three-dimensional 1H rotating frame Overhauser 15N-1H multiple quantum coherence NMR spectroscopy. Biochemistry 29, 5671-5676. pubmed PDF Omichinski, J., Clore, G.M., Appella, E., Sakaguchi, K. & Gronenborn, A.M. (1990) High resolution three-dimensional solution structure of a single zinc finger from a human enhancer binding protein in solution. Biochemistry 29, 9324-9334. pubmed PDF Nilges, M., Clore, G.M. & Gronenborn, A.M. (1990) 1H-NMR stereospecific assignments by conformational database searches. Biopolymers 29, 813-822. pubmed PDF Clore, G.M., Bax, A. & Gronenborn, A.M. (1991) Stereospecific assignment of beta-methylene protons in larger proteins using three-dimensional 15N-separated Hartmann-Hahn and 13C-separated rotating frame Overhauser spectroscopy. J. Biomol. NMR 1, 13-22. pubmed PDF Forman-Kay, J.D., Clore, G.M., Wingfield, P.T. & Gronenborn, A.M. (1991) The high resolution three-dimensional structure of reduced recombinant human thioredoxin in solution. Biochemistry 30, 2685-2698. pubmed PDF Omichinski, J.G., Clore, G.M., Sakaguchi, K., Appella, E. & Gronenborn, A.M. (1991) Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy. FEBS Lett. 292, 25-30. pubmed PDF Robien, M.A., Clore, G.M., Omichinski, J.G., Perham, R.N., Appella, E., Sakaguchi, K. & Gronenborn, A.M. (1992) Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli. Biochemistry 31, 3463-3471. pubmed PDF Forman-Kay, J.D., Clore, G.M. & Gronenborn, A.M. (1992) The relationship between electrostatics and redox function in human thioredoxin: charaterization of pH titration shifts using two-dimensional homo- and heteronuclear NMR. Biochemistry 31, 3442-3452. pubmed PDF Powers, R., Garrett, D.S., March, C.J., Frieden. E.A., Gronenborn, A.M. & Clore, G.M. (1992) Three-dimensional solution structure of human interleukin-4 by multi-dimensional heteronuclear magnetic resonance spectroscopy. Science 256, 1673-1677. pubmed PDF Achari, A., Hale, S.P, Howard, A.J., Clore, G.M., Gronenborn, A.M., Hardman, K.D. & Whitlow, M. (1992) The 1.67 Å X-ray structure of the B2 immunoglobulin domain of streptococcal protein G and comparison to the NMR structure of the B1 domain. Biochemistry 31, 10449-10457. pubmed PDF Brünger, A.T., Clore, G.M., Gronenborn, A.M., Saffrich, R. & Nilges, M. (1993) Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 261, 328-331. pubmed PDF Powers, R., Garrett, D.S., March, C.J., Frieden, E.A., Gronenborn, A.M. & Clore, G.M. (1993) The high resolution three-dimensional solution structure of human interleukin-4 determined by multi-dimensional heteronuclear magnetic resonance spectroscopy. Biochemistry 32, 6744-6762. pubmed PDF Gronenborn, A.M. & Clore, G.M. (1993) Identification of the contact surface of a Streptococcal protein G domain complexed with a human Fc fragment. J. Mol. Biol.233, 331-335. pubmed PDF Omichinski, J.G., Trainor, C., Evans, T., Gronenborn, A.M., Clore, G.M. & Felsenfeld, G. (1993) A small single-'finger' peptide from the erythroid factor GATA-1 binds specifically to DNA as a zinc or iron complex. Proc. Natl. Acad. Sci. U.S.A. 90, 1676-1680. pubmed PDF Clubb, R.T., Omichinski, J.G., Clore, G.M. & Gronenborn, A.M. (1994) Mapping the binding surface of interleukin-8 complexed with an N-terminal fragment of the type I human interleukin-8 receptor. FEBS Lett. 338, 93-97. pubmed PDF Garrett, D.S., Kuszewski, J., Hancock, T.J., Lodi, P.J., Vuister, G.W., Gronenborn, A.M. & Clore, G.M. (1994) The impact of direct refinement against three-bond HN-CalphaH coupling constants on protein structure determination by NMR. J. Magn. Reson. Series B 104, 99-103. pubmed PDF Qin, J., Clore, G.M. & Gronenborn, A.M. (1994) The high resolution three-dimensional solution structure of the oxidized and reduced states of human thioredoxin: delineation of conformational differences between the two redox states. Structure 2, 503-522. pubmed PDF Werner, M.H., Clore, G.M., Gronenborn, A.M., Kondoh, A. & Fisher, R.J. (1994) Refolding proteins by gel filtration chromatography. FEBS Lett. 345, 125-130. pubmed PDF Kuszewski, J., Clore, G.M. & Gronenborn, A.M. (1994) Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of Streptococcal Protein G. Protein Science 3, 1945-1952. pubmed PDF Kuszewski, J., Qin, J., Gronenborn, A.M. & Clore, G.M. (1995) The impact of direct refinement against 13Calpha and 13Cbeta chemical shifts on protein structure determination by NMR. J. Magn. Reson Series B 106, 92-96. pubmed PDF Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1995) The impact of direct refinement against proton chemical shifts in protein structure determination by NMR. J. Magn. Reson. Series B 107, 293-297. pubmed PDF Frank, M.K., Clore, G.M. & Gronenborn, A.M. (1995) Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of Streptococcal protein G. Protein Science 4, 2605-2615. pubmed PDF Balagurumoorthy, P., Sakamoto, K., Lewis, M.S., Zambrano, N., Clore, G.M., Gronenborn, A.M., Appella, E. & Harrington, R.E. (1995) Four p53 DNA binding domains bind natural p53 response elements and bend the DNA. Proc. Natl. Acad. Sci. U.S.A. 92, 8591-8585. pubmed PDF Qin, J., Clore, G.M. & Gronenborn, A.M. (1996) Ionization equilibria for the side chain carboxyl groups in oxidized and reduced human thioredoxin and in the complex with its target peptide from the transcription factor NFkB. Biochemistry 35, 7-13. pubmed PDF Pedone, P.V., Ghirlando, R., Clore, G.M., Gronenborn, A.M., Felsenfeld, G. & Omichinski, J.G. (1996) The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high affinity DNA binding. Proc. Natl. Acad. Sci. U.S.A. 93, 2822-2826. pubmed PDF Pedone, P.V., Omichinski, J.G., Nony, P., Trainor, C., Gronenborn, A.M., Clore, G.M. & Felsenfeld, G. (1997) The N-terminal fingers of cGATA-2 and cGATA-3 are independent sequence-specific DNA binding domains. EMBO J. 16, 2874-2882. pubmed PDF Clore, G.M. & Gronenborn, A.M. (1997) NMR structures of proteins and protein complexes beyond 20,000 Mr.Nature Struct. Biol. 4, 849-853 (1997), pubmed. Cai, M., Huang, Y., Zheng, R., Wei, S.-Q., Ghirlando, R., Lee, M.S., Craigie, R., Gronenborn, A.M. & Clore, G.M. (1998) Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration. Nature Struct. Biol. 5, 903-909. pubmed PDF Garrett, D.S., Seok, Y.-J., Peterkofsky, A., Gronenborn, A.M. & Clore, G.M. (1999) Solution structure of the 40,000 Mr phosphoryl transfer complex between Enzyme I and HPr. Nature Struct. Biol. 6, 166-173. pubmed PDF Yang, F., Bewley, C.A., Louis, J.M., Gustafson, K.R., Boyd, M.R., Gronenborn, A.M., Clore, G.M. & Wlodawer, A. (1999) Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping. J. Mol. Biol. 288, 403-412. pubmed PDF Clore, G.M., Starich, M.R., Bewley, C.A., Cai, M. & Kuszewski, J. (1999) Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints. J. Am. Chem. Soc. 121, 6513-6514. PDF Yu, B., Blaber, M., Gronenborn, A.M., Clore, G.M. & Caspar, D.L.D. (1999) Disordered water within a hydrophobic cavity visualized by X-ray crystallography. Proc. Natl. Acad. Sci. U.S.A. 96, 103-108. pubmed PDF Huang, K., Louis, J.M., Donaldson, L., Lim, F,-L., Sharrocks, A.D. & Clore, G.M. (2000) Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors. EMBO J. 19, 2615-2628. pubmed PDF Kuszewski, J. & Clore, G.M. (2000) Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force. J. Magn. Reson. 146, 249-254. pubmed PDF Kontaxis, G., Clore, G.M. & Bax, A. (2000) Evaluation of cross-relaxation effects and measurement of one-bond couplings in proteins with short transverse relaxation times. J. Magn. Reson. 143, 184-196. pubmed PDF Wang, G., Louis, J.M., Sondej, M., Seok, Y.-J., Peterkofsky, A. & Clore, G.M. (2000) Solution structure of the phosphoryl transfer complex between the signal transducing protein HPr and IIAGlucose of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system. EMBO J. 19, 5635-5649. pubmed PDF Louis, J.M., Weber, I.T., Tözser, J., Clore, G.M. & Gronenborn, A.M. (2000) HIV-1 protease: maturation, enzyme specificity and drug resistance. Adv. Pharmacol. 49, 111-146. pubmed PDF Schwieters, C.D. & Clore, G.M. (2001) The VMD-XPLOR visualization package for NMR structure refinement. J. Magn. Reson.149, 239-244. pubmed PDF Murphy, E.C., Zhurkin, V.B., Louis, J.M., Cornilescu, G. and Clore, G.M. (2001) Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occuring point mutation. J. Mol. Biol. 312, 481-499. pubmed PDF Louis, J.M., Bewley, C.A. & Clore, G.M. (2001) Design and properties of NCCG-gp41, a chimeric gp41 molecule with nanomolar HIV-fusion inhibitory activity. J. Biol. Chem. 276, 29485-29489. pubmed PDF Bewley, C.A., Louis, J.M., Ghirlando, R. & Clore, G.M. (2002) Design of a novel peptide inhibitor of HIV fusion that disrupts the internal trimeric coiled-coil of gp41. J. Biol. Chem. 277, 14238-14245. pubmed PDF Braddock, D.T., Baber, J.L., Levens, D. & Clore, G.M. (2002) Molecular basis of sequence specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA. EMBO J. 21, 3476-3485. pubmed PDF Supplementary Clore, G.M. & Schwieters, C.D. (2003) Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1HN/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics. J. Am. Chem. Soc. 125, 2902-2912. pubmed PDF Clore, G.M. & Kuszewski, J. (2003) Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation. J. Am. Chem. Soc. 125, 1518-1525. pubmed PDF Cai, M., Williams, D.C., Wang, G., Lee, B.R., Peterkofsky, A. & Clore, G.M. (2003) Solution structure of the phosphoryl transfer complex between the signal transducing protein IIAGlucose and the cytoplasmic domain of the glucose transporter IICBGlucose of the Escherichia coli glucose phosphotransferase system. J. Biol. Chem. 278, 25191-25206. pubmed PDF Iwahara, J., Anderson, D.E., Murphy, E.C. & Clore, G.M. (2003) EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancement. J. Am. Chem. Soc. 125, 6634-6635. pubmed PDF Supplementary Information Williams, D.C., Cai, M. & Clore, G.M. (2004) Molecular basis for synergistic activation by Oct1 and Sox2 revealed from the solution structure of the 42 kDa Oct1·Sox2·Hoxb1-DNA ternary transcription factor complex. J. Biol. Chem. 279, 1449-1457. pubmed PDF Schulz, D.M., Ihling, C., Clore, G.M. & Sinz, A. (2004) Mapping the topology and determination of a low resolution three-dimensional structure of the calmodulin-mellitin complex by chemical cross-linking and high resolution FTICR mass spectrometry. Biochemistry 43, 4703-4715. 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 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. (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 Coordinates for N=8 ensemble Iwahara, J. & Clore, G.M. (2006) Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy. J. Am. Chem. Soc. 128, 404-405. pubmed PDF Supplementary Information 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 Coordinates for N=4 ensemble 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 Iwahara, J., Jung, Y.-S., & Clore, G.M. (2007) Heteronuclear NMR spectroscopy for lysine NH3 groups in proteins: unique effect of water-exchange on 15N transverse relaxation. J. Am. Chem. Soc. 129, 2971-2980. 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. 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 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 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 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 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 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
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