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Determining methyl sidechain conformations in a CS-ROSETTA model using methyl 1H-13C residual dipolar couplings.

Karamanos TK, Tugarinov V, Clore GM.

J Biomol NMR. 2020 Jan 16. doi: 10.1007/s10858-019-00294-w. [Epub ahead of print]


Probing transient excited states of the bacterial cell division regulator MinE by relaxation dispersion NMR spectroscopy.

Cai M, Huang Y, Shen Y, Li M, Mizuuchi M, Ghirlando R, Mizuuchi K, Clore GM.

Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25446-25455. doi: 10.1073/pnas.1915948116. Epub 2019 Nov 26.


XIPP: multi-dimensional NMR analysis software.

Garrett DS, Cai M, Clore GM.

J Biomol NMR. 2019 Nov 20. doi: 10.1007/s10858-019-00286-w. [Epub ahead of print]


Optimized NMR Experiments for the Isolation of I=1/2 Manifold Transitions in Methyl Groups of Proteins.

Tugarinov V, Karamanos TK, Ceccon A, Clore GM.

Chemphyschem. 2020 Jan 3;21(1):13-19. doi: 10.1002/cphc.201900959. Epub 2019 Dec 5.


A simple protocol for expression of isotope-labeled proteins in Escherichia coli grown in shaker flasks at high cell density.

Cai M, Huang Y, Craigie R, Clore GM.

J Biomol NMR. 2019 Dec;73(12):743-748. doi: 10.1007/s10858-019-00285-x. Epub 2019 Nov 1.


A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination.

Schwieters CD, Bermejo GA, Clore GM.

Protein Sci. 2020 Jan;29(1):100-110. doi: 10.1002/pro.3745. Epub 2019 Oct 27.


Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis.

Karamanos TK, Tugarinov V, Clore GM.

Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21529-21538. doi: 10.1073/pnas.1914999116. Epub 2019 Oct 7.


Exchange saturation transfer and associated NMR techniques for studies of protein interactions involving high-molecular-weight systems.

Tugarinov V, Clore GM.

J Biomol NMR. 2019 Sep;73(8-9):461-469. doi: 10.1007/s10858-019-00244-6. Epub 2019 Aug 12.


Spatial domain organization in the HIV-1 reverse transcriptase p66 homodimer precursor probed by double electron-electron resonance EPR.

Schmidt T, Schwieters CD, Clore GM.

Proc Natl Acad Sci U S A. 2019 Sep 3;116(36):17809-17816. doi: 10.1073/pnas.1911086116. Epub 2019 Aug 5.


Protein NMR: Boundless opportunities.

Bax A, Clore GM.

J Magn Reson. 2019 Sep;306:187-191. doi: 10.1016/j.jmr.2019.07.037. Epub 2019 Jul 9.


Inhibition of HIV Maturation via Selective Unfolding and Cross-Linking of Gag Polyprotein by a Mercaptobenzamide Acetylator.

Miller Jenkins LM, Paine EL, Deshmukh L, Nikolayevskiy H, Lyons GC, Scerba MT, George Rosenker K, Luecke HF, Louis JM, Chertova E, Gorelick RJ, Ott DE, Clore GM, Appella DH.

J Am Chem Soc. 2019 May 22;141(20):8327-8338. doi: 10.1021/jacs.9b02743. Epub 2019 May 13.


Probing initial transient oligomerization events facilitating Huntingtin fibril nucleation at atomic resolution by relaxation-based NMR.

Kotler SA, Tugarinov V, Schmidt T, Ceccon A, Libich DS, Ghirlando R, Schwieters CD, Clore GM.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3562-3571. doi: 10.1073/pnas.1821216116. Epub 2019 Feb 11.


TiO2 Nanoparticles Catalyze Oxidation of Huntingtin Exon 1-Derived Peptides Impeding Aggregation: A Quantitative NMR Study of Binding and Kinetics.

Ceccon A, Tugarinov V, Clore GM.

J Am Chem Soc. 2019 Jan 9;141(1):94-97. doi: 10.1021/jacs.8b11441. Epub 2018 Dec 26.


Probing the mechanism of inhibition of amyloid-β(1-42)-induced neurotoxicity by the chaperonin GroEL.

Wälti MA, Steiner J, Meng F, Chung HS, Louis JM, Ghirlando R, Tugarinov V, Nath A, Clore GM.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11924-E11932. doi: 10.1073/pnas.1817477115. Epub 2018 Dec 3.


Decorrelating Kinetic and Relaxation Parameters in Exchange Saturation Transfer NMR: A Case Study of N-Terminal Huntingtin Peptides Binding to Unilamellar Lipid Vesicles.

Ceccon A, Clore GM, Tugarinov V.

J Phys Chem B. 2018 Dec 13;122(49):11271-11278. doi: 10.1021/acs.jpcb.8b07112. Epub 2018 Sep 12.


Extensive Sampling of the Cavity of the GroEL Nanomachine by Protein Substrates Probed by Paramagnetic Relaxation Enhancement.

Wälti MA, Libich DS, Clore GM.

J Phys Chem Lett. 2018 Jun 21;9(12):3368-3371. doi: 10.1021/acs.jpclett.8b01586. Epub 2018 Jun 7.


Interaction of Huntingtin Exon-1 Peptides with Lipid-Based Micellar Nanoparticles Probed by Solution NMR and Q-Band Pulsed EPR.

Ceccon A, Schmidt T, Tugarinov V, Kotler SA, Schwieters CD, Clore GM.

J Am Chem Soc. 2018 May 23;140(20):6199-6202. doi: 10.1021/jacs.8b02619. Epub 2018 May 14.


Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy.

Deshmukh L, Tugarinov V, Appella DH, Clore GM.

Angew Chem Int Ed Engl. 2018 Mar 1;57(10):2687-2691. doi: 10.1002/anie.201713172. Epub 2018 Feb 2.


Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR.

Deshmukh L, Tugarinov V, Louis JM, Clore GM.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9855-E9862. doi: 10.1073/pnas.1716098114. Epub 2017 Oct 30.


Chaperonin GroEL accelerates protofibril formation and decorates fibrils of the Het-s prion protein.

Wälti MA, Schmidt T, Murray DT, Wang H, Hinshaw JE, Clore GM.

Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9104-9109. doi: 10.1073/pnas.1711645114. Epub 2017 Aug 7.


Xplor-NIH for molecular structure determination from NMR and other data sources.

Schwieters CD, Bermejo GA, Clore GM.

Protein Sci. 2018 Jan;27(1):26-40. doi: 10.1002/pro.3248. Epub 2017 Sep 18.


Probing the Binding Modes of a Multidomain Protein to Lipid-based Nanoparticles by Relaxation-based NMR.

Ceccon A, Tugarinov V, Boughton AJ, Fushman D, Clore GM.

J Phys Chem Lett. 2017 Jun 1;8(11):2535-2540. doi: 10.1021/acs.jpclett.7b01019. Epub 2017 May 24.


Confinement and Stabilization of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin GroEL Demonstrated by Relaxation-Based NMR.

Libich DS, Tugarinov V, Ghirlando R, Clore GM.

Biochemistry. 2017 Feb 21;56(7):903-906. doi: 10.1021/acs.biochem.6b01237. Epub 2017 Feb 8.


Long Distance Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR Spectroscopy.

Schmidt T, Wälti MA, Baber JL, Hustedt EJ, Clore GM.

Angew Chem Int Ed Engl. 2016 Dec 19;55(51):15905-15909. doi: 10.1002/anie.201609617. Epub 2016 Nov 17.


A simple and robust protocol for high-yield expression of perdeuterated proteins in Escherichia coli grown in shaker flasks.

Cai M, Huang Y, Yang R, Craigie R, Clore GM.

J Biomol NMR. 2016 Oct;66(2):85-91. Epub 2016 Oct 5.


Transient HIV-1 Gag-protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations.

Deshmukh L, Louis JM, Ghirlando R, Clore GM.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12456-12461. Epub 2016 Oct 17.


Quantitative Resolution of Monomer-Dimer Populations by Inversion Modulated DEER EPR Spectroscopy.

Schmidt T, Ghirlando R, Baber J, Clore GM.

Chemphyschem. 2016 Oct 5;17(19):2987-2991. doi: 10.1002/cphc.201600726. Epub 2016 Aug 2.


Global Dynamics and Exchange Kinetics of a Protein on the Surface of Nanoparticles Revealed by Relaxation-Based Solution NMR Spectroscopy.

Ceccon A, Tugarinov V, Bax A, Clore GM.

J Am Chem Soc. 2016 May 11;138(18):5789-92. doi: 10.1021/jacs.6b02654. Epub 2016 Apr 27.


Improving NMR Structures of RNA.

Bermejo GA, Clore GM, Schwieters CD.

Structure. 2016 May 3;24(5):806-815. doi: 10.1016/j.str.2016.03.007. Epub 2016 Apr 7.


Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.

Deshmukh L, Schwieters CD, Grishaev A, Clore GM.

Chemphyschem. 2016 Jun 3;17(11):1548-52. doi: 10.1002/cphc.201600212. Epub 2016 Mar 16.


Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

Venditti V, Egner TK, Clore GM.

Chem Rev. 2016 Jun 8;116(11):6305-22. doi: 10.1021/acs.chemrev.5b00592. Epub 2016 Jan 7. Review.


Reply to Marchenko et al.: Flux analysis of GroEL-assisted protein folding/unfolding.

Libich DS, Tugarinov V, Clore GM.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):E6833-4. doi: 10.1073/pnas.1520474112. Epub 2015 Nov 24. No abstract available.


The C34 Peptide Fusion Inhibitor Binds to the Six-Helix Bundle Core Domain of HIV-1 gp41 by Displacement of the C-Terminal Helical Repeat Region.

Louis JM, Baber JL, Clore GM.

Biochemistry. 2015 Nov 17;54(45):6796-805. doi: 10.1021/acs.biochem.5b01021. Epub 2015 Nov 9.


Practical Aspects of Paramagnetic Relaxation Enhancement in Biological Macromolecules.

Clore GM.

Methods Enzymol. 2015;564:485-97. doi: 10.1016/bs.mie.2015.06.032. Epub 2015 Jul 2. Review.


The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy.

Tugarinov V, Libich DS, Meyer V, Roche J, Clore GM.

Angew Chem Int Ed Engl. 2015 Sep 14;54(38):11157-61. doi: 10.1002/anie.201505416.


Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering.

Venditti V, Schwieters CD, Grishaev A, Clore GM.

Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11565-70. doi: 10.1073/pnas.1515366112. Epub 2015 Aug 24.


Mutations Proximal to Sites of Autoproteolysis and the α-Helix That Co-evolve under Drug Pressure Modulate the Autoprocessing and Vitality of HIV-1 Protease.

Louis JM, Deshmukh L, Sayer JM, Aniana A, Clore GM.

Biochemistry. 2015 Sep 8;54(35):5414-24. doi: 10.1021/acs.biochem.5b00759. Epub 2015 Aug 21.


Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR.

Libich DS, Tugarinov V, Clore GM.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8817-23. doi: 10.1073/pnas.1510083112. Epub 2015 Jun 29.


Dependence of distance distributions derived from double electron-electron resonance pulsed EPR spectroscopy on pulse-sequence time.

Baber JL, Louis JM, Clore GM.

Angew Chem Int Ed Engl. 2015 Apr 27;54(18):5336-9. doi: 10.1002/anie.201500640. Epub 2015 Mar 10.


Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy.

Deshmukh L, Ghirlando R, Clore GM.

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3374-9. doi: 10.1073/pnas.1501985112. Epub 2015 Feb 23.


Visualizing transient dark states by NMR spectroscopy.

Anthis NJ, Clore GM.

Q Rev Biophys. 2015 Feb;48(1):35-116. doi: 10.1017/S0033583514000122.


Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I.

Venditti V, Tugarinov V, Schwieters CD, Grishaev A, Clore GM.

Nat Commun. 2015 Jan 12;6:5960. doi: 10.1038/ncomms6960.


Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid β protofibril interactions using ¹³C(methyl)-DEST and lifetime line broadening.

Fawzi NL, Libich DS, Ying J, Tugarinov V, Clore GM.

Angew Chem Int Ed Engl. 2014 Sep 22;53(39):10345-9. doi: 10.1002/anie.201405180. Epub 2014 Aug 11.


Using small angle solution scattering data in Xplor-NIH structure calculations.

Schwieters CD, Clore GM.

Prog Nucl Magn Reson Spectrosc. 2014 Jul;80:1-11. doi: 10.1016/j.pnmrs.2014.03.001. Epub 2014 Apr 3. Review.


Encounter complexes and dimensionality reduction in protein-protein association.

Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S.

Elife. 2014 Apr 8;3:e01370. doi: 10.7554/eLife.01370.


Investigation of the structure and dynamics of the capsid-spacer peptide 1-nucleocapsid fragment of the HIV-1 gag polyprotein by solution NMR spectroscopy.

Deshmukh L, Ghirlando R, Clore GM.

Angew Chem Int Ed Engl. 2014 Jan 20;53(4):1025-8. doi: 10.1002/anie.201309127. Epub 2013 Dec 11.

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