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1. Are zinc-finger domains of protein kinase C dynamic structures that unfold by lipid or redox activation?

Author

Ulrich Hämmerling, Claudia M. Cremers, Valerie Vinogradov, David Cowburn, Feng Zhao, Marianne Ilbert, Beatrice Hoyos, Ursula Jakob, Rebeca Acín-Pérez, Ranjani Varadan, Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Bioénergétique et Ingénierie des Protéines (BIP ), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Protein Folding, Physiology, Recombinant Fusion Proteins, Clinical Biochemistry, chemistry.chemical_element, Zinc, Mitochondrion, Biochemistry, Redox, 03 medical and health sciences, Mice, 0302 clinical medicine, Heat shock protein, Phorbol Esters, Animals, News & Views, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Protein kinase C, Germ-Line Mutation, Heat-Shock Proteins, Protein Kinase C, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, General Environmental Science, Zinc finger, 0303 health sciences, Chemistry, Escherichia coli Proteins, Cytochromes c, Zinc Fingers, Cell Biology, Cell biology, Mitochondria, Rats, Second messenger system, General Earth and Planetary Sciences, Protein folding, Oxidation-Reduction, 030217 neurology & neurosurgery, Molecular Chaperones
Abstract

Protein kinase C (PKC) is activated by lipid second messengers or redox action, raising the question whether these activation modes involve the same or alternate mechanisms. Here we show that both lipid activators and oxidation target the zinc-finger domains of PKC, suggesting a unifying activation mechanism. We found that lipid agonist-binding or redox action leads to zinc release and disassembly of zinc fingers, thus triggering large-scale unfolding that underlies conversion to the active enzyme. These results suggest that PKC zinc fingers, originally considered purely structural devices, are in fact redox-sensitive flexible hinges, whose conformation is controlled both by redox conditions and lipid agonists. Antioxid. Redox Signal. 14, 757–766.

Published
2011

2. Nuclear spin relaxation in isotropic and anisotropic media

Author

Matthew P. Nicholas, Ertan Eryilmaz, Fabien Ferrage, David Cowburn, Ranajeet Ghose, Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), New York Structural Biology Center (NYSBC), Columbia University [New York]-Wadsworth Center, New York State Department of Health [Albany]-New York State Department of Health [Albany]-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-City University of New York [New York] (CUNY)-Rockefeller University [New York]-Memorial Sloane Kettering Cancer Center [New York]-Icahn School of Medicine at Mount Sinai [New York] (MSSM)- Albert Einstein College of Medicine [New York]-Weill Medical College of Cornell University [New York], Department of Chemistry [Michigan], The City College of New York (CCNY), City University of New York [New York] (CUNY)-City University of New York [New York] (CUNY), Graduate Center of the City University of New York, NY 10016, City University of New York [New York] (CUNY), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)

Subjects
Physics, Nuclear and High Energy Physics, Stochastic Processes, Magnetic Resonance Spectroscopy, Condensed matter physics, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Isotropy, Rotational diffusion, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, Biochemistry, Article, 0104 chemical sciences, Analytical Chemistry, Solid-state nuclear magnetic resonance, 0103 physical sciences, Spin echo, Relaxation (physics), Anisotropy, 010306 general physics, Spectroscopy, Magnetic dipole–dipole interaction, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2010

3. Accurate sampling of high-frequency motions in proteins by steady-state (15)N-{(1)H} nuclear Overhauser effect measurements in the presence of cross-correlated relaxation

Author

Fabien Ferrage, Ranajeet Ghose, David Cowburn, Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), New York Structural Biology Center (NYSBC), Columbia University [New York]-Wadsworth Center, New York State Department of Health [Albany]-New York State Department of Health [Albany]-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-City University of New York [New York] (CUNY)-Rockefeller University [New York]-Memorial Sloane Kettering Cancer Center [New York]-Icahn School of Medicine at Mount Sinai [New York] (MSSM)- Albert Einstein College of Medicine [New York]-Weill Medical College of Cornell University [New York], Department of Chemistry [Michigan], The City College of New York (CCNY), City University of New York [New York] (CUNY)-City University of New York [New York] (CUNY), Graduate Center of the City University of New York, NY 10016, City University of New York [New York] (CUNY), École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Steady state (electronics), Magnetic Resonance Spectroscopy, Nuclear Overhauser effect, 010402 general chemistry, 01 natural sciences, Biochemistry, Molecular physics, Catalysis, Article, 03 medical and health sciences, Colloid and Surface Chemistry, Nuclear magnetic resonance, Sampling (signal processing), 030304 developmental biology, 0303 health sciences, Nitrogen Isotopes, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Relaxation (NMR), Proteins, Reproducibility of Results, General Chemistry, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, Dipole, Protons
Abstract

International audience; The steady-state {(1)H}-(15)N NOE experiment is used in most common NMR analyses of backbone dynamics to accurately ascertain the effects of the fast dynamic modes. We demonstrate here that, in its most common implementation, this experiment generates an incorrect steady state in the presence of CSA/dipole cross-correlated relaxation leading to large errors in the characterization of these high-frequency modes. This affects both the quantitative and qualitative interpretation of (15)N backbone relaxation in dynamic terms. We demonstrate further that minor changes in the experimental implementation effectively remove these errors and allow a more accurate interpretation of protein backbone dynamics.

Published
2009

4. On the measurement of 15N–{1H} nuclear Overhauser effects

Author

Ranajeet Ghose, Andrea Piserchio, Fabien Ferrage, David Cowburn, New York Structural Biology Center (NYSBC), Columbia University [New York]-Wadsworth Center, New York State Department of Health [Albany]-New York State Department of Health [Albany]-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-City University of New York [New York] (CUNY)-Rockefeller University [New York]-Memorial Sloane Kettering Cancer Center [New York]-Icahn School of Medicine at Mount Sinai [New York] (MSSM)- Albert Einstein College of Medicine [New York]-Weill Medical College of Cornell University [New York], Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Department of Chemistry [Michigan], The City College of New York (CCNY), City University of New York [New York] (CUNY)-City University of New York [New York] (CUNY), Graduate Center of the City University of New York, NY 10016, City University of New York [New York] (CUNY), Perron, Nicolas, Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), University at Albany - Department of Chemistry, State University of New York (SUNY), Ferrage, Fabien, École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Nuclear and High Energy Physics, Thermodynamic equilibrium, Biophysics, Analytical chemistry, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Scale (descriptive set theory), Nuclear Overhauser effect, 010402 general chemistry, 01 natural sciences, Biochemistry, Measure (mathematics), Article, [PHYS.PHYS.PHYS-CHEM-PH] Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 03 medical and health sciences, Magnetization, Humans, Computer Simulation, Statistical physics, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Spin-½, 0303 health sciences, Nitrogen Isotopes, Chemistry, Ubiquitin, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Protein dynamics, Relaxation (NMR), Condensed Matter Physics, [CHIM.ORGA] Chemical Sciences/Organic chemistry, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Hydrogen
Abstract

Accurate quantification of the 15N–{1H} steady-state NOE is central to current methods for the elucidation of protein backbone dynamics on the fast, sub-nanosecond time scale. This experiment is highly susceptible to systematic errors arising from multiple sources. The nature of these errors and their effects on the determined NOE ratio is evaluated by a detailed analysis of the spin dynamics during the pair of experiments used to measure this ratio and possible improvements suggested. The experiment that includes 1H irradiation, is analyzed in the framework of Average Liouvillian Theory and a modified saturation scheme that generates a stable steady-state and eliminates the need to completely saturate 1H nuclei is presented. The largest source of error, however, in 1H-dilute systems at ultra-high fields is found to be an overestimation of the steady-state NOE value as a consequence of the incomplete equilibration of the magnetization in the so-called “reference experiment”. The use of very long relaxation delays is usually an effective, but time consuming, solution. Here, we introduce an alternative reference experiment, designed for larger, deuterated systems, that uses the fastest relaxing component of the longitudinal magnetization as a closer approximation to the equilibrium state for shorter relaxation delays. The utility of the modified approach is illustrated through simulations on realistic spin systems over a wide range of time scales and experimentally verified using a perdeuterated sample of human ubiquitin.

Published
2008

5. Joint Composite-Rotation Adiabatic-Sweep Isotope Filtration

Author

Arthur G. Palmer, David Cowburn, Elizabeth R. Valentine, Francesca Massi, Fabien Ferrage, Department of Biochemistry and Molecular Biophysics (DBMB), Columbia University [New York], Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), New York Structural Biology Center (NYSBC), Columbia University [New York]-Wadsworth Center, New York State Department of Health [Albany]-New York State Department of Health [Albany]-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-City University of New York [New York] (CUNY)-Rockefeller University [New York]-Memorial Sloane Kettering Cancer Center [New York]-Icahn School of Medicine at Mount Sinai [New York] (MSSM)- Albert Einstein College of Medicine [New York]-Weill Medical College of Cornell University [New York], École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Ferrage, Fabien

Subjects
Magnetic Resonance Spectroscopy, Analytical chemistry, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 010402 general chemistry, 01 natural sciences, Biochemistry, Molecular physics, Article, [PHYS.PHYS.PHYS-CHEM-PH] Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 03 medical and health sciences, symbols.namesake, Adiabatic process, Spectroscopy, 030304 developmental biology, 0303 health sciences, Carbon Isotopes, Isotope, Spins, Nitrogen Isotopes, Chemistry, Proteins, Reproducibility of Results, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Heteronuclear molecule, Isotopes of carbon, symbols, RNA, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Hamiltonian (quantum mechanics), Two-dimensional nuclear magnetic resonance spectroscopy
Abstract

Joint composite-rotation adiabatic-sweep isotope filter are derived by combining the composite-rotation [A. C. Stuart, K. A. Borzilleri, J. M. Withka, and A. G. Palmer, J. Am. Chem. Soc. 121, 5346–5347 (1999)] and adiabatic-sweep [C. Zwahlen, P. Legault, S. J. F. Vincent, J. Greenblatt, R. Konrat, and L. E. Kay, J. Am. Chem. Soc. 119, 6711–6721 (1997); Ē. Kupče and R. Freeman, J. Magn. Reson. 127, 36–48 (1997)] approaches. The joint isotope filters have improved broadband filtration performance, even for extreme values of the one-bond 1H-13C scalar coupling constants in proteins and RNA molecules. An average Hamiltonian analysis is used to describe evolution of the heteronuclear scalar coupling interaction during the adiabatic sweeps within the isotope filter sequences. The new isotope filter elements permit improved selective detection of NMR resonance signals originating from 1H spins attached to an unlabeled natural abundance component of a complex in which other components are labeled with 13C and 15N isotopes.

Published
2007

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