Fabien Ferrage - Academia.edu (original) (raw)

Papers by Fabien Ferrage

Internal dynamics of proteins are usually characterized by the analysis of 15 N relaxation rates ... more Internal dynamics of proteins are usually characterized by the analysis of 15 N relaxation rates that reflect the motions of NH N vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C′C α vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders and . This amounts to "anchoring" the and operators to the N z term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C′C α vector appear more restricted than those of the NH N vector.

Methods in molecular biology (Clifton, N.J.), 2012

Nitrogen-15 relaxation is the most ubiquitous source of information about protein (backbone) dyna... more Nitrogen-15 relaxation is the most ubiquitous source of information about protein (backbone) dynamics used by NMR spectroscopists. It provides the general characteristics of hydrodynamics as well as internal motions on subnanosecond, micro- and millisecond timescales of a biomolecule. Here, we present a full protocol to perform and analyze a series of experiments to measure the (15)N longitudinal relaxation rate, the (15)N transverse relaxation rate under an echo train or a single echo, the (15)N-(1)H dipolar cross-relaxation rate, as well as the longitudinal and transverse cross-relaxation rates due to the cross-correlation of the nitrogen-15 chemical shift anisotropy and the dipolar coupling with the adjacent proton. These rates can be employed to carry out model-free analyses and can be used to quantify accurately the contribution of chemical exchange to transverse relaxation.

Accurate quantification of the 15 N-{ 1 H} steady-state NOE is central to current methods for the... more Accurate quantification of the 15 N-{ 1 H} steady-state NOE is central to current methods for the elucida- tion 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

Scientific Reports, 2015

Standard Magnetic Resonance magnets produce a single homogeneous field volume, where the analysis... more Standard Magnetic Resonance magnets produce a single homogeneous field volume, where the analysis is performed. Nonetheless, several modern applications could benefit from the generation of multiple homogeneous field volumes along the axis and inside the bore of the magnet. In this communication, we propose a straightforward method using a combination of ring structures of permanent magnets in order to cancel the gradient of the stray field in a series of distinct volumes. These concepts were demonstrated numerically on an experimentally measured magnetic field profile. We discuss advantages and limitations of our method and present the key steps required for an experimental validation.

Journal of The American Chemical Society, 2002

Citrate-capped gold nanoparticles as well as planar gold surfaces can be efficiently grafted with... more Citrate-capped gold nanoparticles as well as planar gold surfaces can be efficiently grafted with a covalently attached polymer monolayer a few nanometers thick, by simple contact of the metal surface with dilute aqueous solutions of hydrophilic polymers that are end-capped with disulfide moieties, as shown by UV/vis absorption, dynamic light scattering, and surface plasmon resonance studies. The hydrophilic polymer-coated gold colloids can be freeze-dried and stored as powders that can be subsequently dissolved to yield stable aqueous dispersions, even at very large concentrations. They allow for applying filtrations, gel permeation chromatography, or centrifugation. They do not suffer from undesirable nonspecific adsorption of proteins while allowing the diffusion of small species within the hydrogel surface coating. In addition, specific properties of the original hydrophilic polymers are retained such as a lower critical solution temperature. The latter feature could be useful to enhance optical responses of functionalized gold surfaces toward interaction with various substrates. (1) (a) Elghanian, R.; Storhoff, J. J.; Mucic, R. C.; Letsinger, R. L.; Mirkin, C. A.; Science 1997, 277, 1078-1081. (b) Bruchez, M., Jr.; Moronne, M.; Gin, P.; Weiss, S.; Alivisatos, P.

Journal of The American Chemical Society - J AM CHEM SOC, 2001

Pure organic molecules exhibiting a suitable concave rigid shape are expected to give porous glas... more Pure organic molecules exhibiting a suitable concave rigid shape are expected to give porous glasses in the solid state. Such a feature opens new opportunities to avoid crystallization and to improve molecular solubility in relation to the high internal energy of these solid phases. To quantitatively explore the latter strategy, a series of rigid tetrahedral conjugated molecules nC and the corresponding models nR have been synthesized. Related to the present purpose, several properties have been investigated using UV absorption, steady-state fluorescence emission, differential scanning calorimetry, 1 H NMR translational self-diffusion, magic angle spinning 13 C NMR, and multiple-beam interferometry experiments. The present tetrahedral crosses are up to 8 orders of magnitude more soluble than the corresponding model compounds after normalization to the same molecular length. In addition, they give concentrated monomeric solutions that can be used to cover surfaces with homogeneous films whose thickness goes down to the nanometer range. Such attractive features make cross-like molecular architectures promising for many applications.

The Journal of Physical Chemistry B, 2005

This paper reports on a novel procedure to tune the effective diffusion coefficient of a field-se... more This paper reports on a novel procedure to tune the effective diffusion coefficient of a field-sensitive reactant in the presence of a periodic external field. We investigate the motion of two negatively charged azo dyes interacting with alpha-cyclodextrin (alpha-CD) upon action of a periodic square wave electrical field. We show that the dyes exhibit an effective diffusion coefficient D(eff) that depends on the rate constants for dye complexation within alpha-CD, the period and the amplitude of the field. UV-vis absorption, gradient field (1)H NMR, and fluorescence correlation spectroscopy (FCS) after two photon excitation are used to evidence that D(eff) may be increased far beyond its intrinsic value when specific relations interpreted as a stochastic resonance are fulfilled. The present results may find useful applications in chemical kinetics as well as for molecular sorting.

Russian Chemical Bulletin, 2000

A biological approach to generating complex behaviors in chemistry is described. It is suggested ... more A biological approach to generating complex behaviors in chemistry is described. It is suggested theoretically that the assembly of “modules” composed of chemical reactions or molecular structures under appropriate external constraints can lead to features typical of the biological world like autocatalysis, kinetic proofreading, or oriented molecular motion. This approach may account for the primitive steps of molecular evolution and,