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Philippe Pelupessy

Publications and source records attributed to Philippe Pelupessy.

11 recordsLinked to original sources
PubMed2006

Measuring fast hydrogen exchange rates by NMR spectroscopy.

We introduce a method to measure hydrogen exchange rates based on the observation of the coherence of a neighboring spin S such as (15)N that has a scalar coupling J(IS) to the exchanging proton I. The decay of S(x) coherence under a Carr-Purcell-Meiboom-Gill (CPMG) multiple echo train is recorded in the presence and absence of proton decoupling. This method allows one to extract proton exchange rates up to 10(5)s(-1). We could extend the pH range for the study of the indole proton in tryptophan, allowing the determination of the exchange constants of the cationic, zwitterionic, and anionic forms of tryptophan.

Algorithms↗
PubMed2006

Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts.

We propose a strategy based on the combination of experimental NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlated relaxation rates and chemical shift analysis for the determination of Psi torsion angles in proteins. The method allows the determination of a dihedral angle that is not easily accessible by nuclear magnetic resonance (NMR). The measurement of dihedral angle restraints can be used for structure calculation, which is known to improve the quality of NMR structures. The method is of particular interest in the case of large proteins, for which spectral assignment of the nuclear Overhauser effect spectra, and therefore straightforward structural determination, is out of reach. One advantage of the method is that it is reasonably simple to implement, and could be used in association with other methods aiming at obtaining structural information on complex systems, such as residual dipolar coupling measurements. An illustrative example is analyzed in the case of the 30-kDa protein 6-phosphogluconolactonase.

Animals↗
PubMed2006

Protein backbone dynamics through 13C'-13Calpha cross-relaxation in NMR spectroscopy.

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(alpha) vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2N(z)() and 2N(z)(). 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(alpha) vector appear more restricted than those of the NH(N) vector.

Nuclear Magnetic Resonance, Biomolecular↗
PubMed2005

Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy.

The principal components and orientations of the chemical shift anisotropy (CSA) tensors of the carbonyl (C'), nitrogen (N), and amide proton (H(N)) nuclei of 64 distinct amide bonds in human ubiquitin have been determined in isotropic solution by a set of 14 complementary auto- and cross-correlated relaxation rates involving the CSA interactions of the nuclei of interest and several dipole-dipole (DD) interactions. The CSA parameters thus obtained depend to some degree on the models used for local motions. Three cases have been considered: restricted isotropic diffusion, three-dimensional Gaussian axial fluctuations (3D-GAF), and independent out-of-plane motions of the NH(N) vectors with respect to the peptide planes.

Amides↗
PubMed2005

Anisotropic local motions and location of amide protons in proteins.

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.

Amides↗
PubMed2003

Adiabatic single scan two-dimensional NMR spectrocopy.

New excitation schemes, based on the use adiabatic pulses, for single scan two-dimensional NMR experiments (Frydman et al., Proc. Nat. Acad. Sci. 2002, 99, 15 858-15 862) are introduced. The advantages are discussed. Applications in homo- and heteronuclear experiments are presented.

Journal Article↗
PubMed2003

Symmetrical reconversion: measuring cross-correlation rates with enhanced accuracy.

A new strategy has been developed to measure cross-correlation rates with much enhanced accuracy. The method relies on the use of four complementary experiments. Errors due to pulse miscalibration and to uncontrolled attenuation factors associated with relaxation are cancelled out. Problems due to violations of the secular approximation are greatly alleviated. The method has been applied to the measurement of N/NH (CSA/DD) cross-correlated relaxation rates in human ubiquitin.

Anisotropy↗
PubMed2003

Correlated motions of successive amide N-H bonds in proteins.

New nuclear magnetic resonance (NMR) methods are described for the measurement of cross-correlation rates of zero- and double-quantum coherences involving two nitrogen nuclei belonging to successive amino acids in proteins and peptides. Rates due to the concerted fluctuations of two NH(N) dipole-dipole interactions and to the correlated modulations of two nitrogen chemical shift anisotropies have been obtained in a sample of doubly labeled Ubiquitin. Ambiguities in the determination of dihedral angles can be lifted by comparison of different rates. By defining a heuristic order parameter, experimental rates can be compared with those expected for a rigid molecule. The cross-correlation order parameter that can be derived from a model-free approach can be separated into structural and dynamic contributions.

Amides↗
PubMed2003

Cross-correlation between a carbonyl C' chemical shift anisotropy and a long-range dipolar C'HA coupling in proteins using symmetrical reconversion.

A new sequence is described to measure the cross-correlation rates between the chemical shift anisotropy of the carbonyl carbon-13 nucleus and the dipole-dipole interaction between this carbonyl and the alpha-proton in proteins. The sequence is based on the symmetrical reconversion principle and is insensitive to experimental errors and to violations of the secular approximation. The cross-correlation rate depends on the backbone angle psi. The advantages and limitations of the sequence are discussed.

Anisotropy↗
PubMed2002

Measurement of long-range cross-correlation rates using a combination of single- and multiple-quantum NMR spectroscopy in one experiment.

A method is described to determine long-range cross-correlations between the modulations of an anisotropic chemical shift (e.g., of a C' carbonyl carbon in a protein) and the fluctuations of a weak long-range dipolar interaction (e.g., in cross-correlation between the same C' carbonyl and the H(N) proton of the neighboring amide group). Such long-range correlations are difficult to measure because the corresponding long-range scalar couplings are so small that Redfield's secular approximation is often violated. The method, which combines features of single- and double-quantum NMR spectroscopy, allows one to cancel the effects of dominant short-range dipolar interactions (e.g., between the CSA of the amide nitrogen N and the dipolar coupling to its attached proton H(N)) and is designed so that the secular approximation is rescued even if the scalar coupling between the long-range dipolar coupling partners is very small. The cross-correlation rates thus determined in ubiquitin cover a wide range because of local motions and variations of the CSA tensors.

Anisotropy↗