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Geoffrey Bodenhausen

Publications and source records attributed to Geoffrey Bodenhausen.

At least 37 records · Page 2Linked to original sources
PubMed2005

Effects of protein-pheromone complexation on correlated chemical shift modulations.

Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{C'N} and DQC{C'N}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand).

Amino Acids↗
PubMed2005

Determination of 13C CSA tensors: extension of the model-independent approach to an RNA kissing complex undergoing anisotropic rotational diffusion in solution.

Chemical shift anisotropy (CSA) tensor parameters have been determined for the protonated carbons of the purine bases in an RNA kissing complex in solution by extending the model-independent approach [Fushman, D., Cowburn, D. (1998) J. Am. Chem. Soc. 120, 7109-7110]. A strategy for determining CSA tensor parameters of heteronuclei in isolated X-H two-spin systems (X = 13C or 15N) in molecules undergoing anisotropic rotational diffusion is presented. The original method relies on the fact that the ratio kappa2=R2 auto/R2 cross of the transverse auto- and cross-correlated relaxation rates involving the X CSA and the X-H dipolar interaction is independent of parameters related to molecular motion, provided rotational diffusion is isotropic. However, if the overall motion is anisotropic kappa2 depends on the anisotropy D(parallel)/D (perpendicular) of rotational diffusion. In this paper, the field dependence of both kappa2 and its longitudinal counterpart kappa1=R1 auto/R1 cross are determined. For anisotropic rotational diffusion, our calculations show that the average kappa(av) = 1/2 (kappa1+kappa2), of the ratios is largely independent of the anisotropy parameter D(parallel)/D (perpendicular). The field dependence of the average ratio kappa(av) may thus be utilized to determine CSA tensor parameters by a generalized model-independent approach in the case of molecules with an overall motion described by an axially symmetric rotational diffusion tensor.

Anisotropy↗
PubMed2004

Multiple refocusing in NMR spectroscopy: compensation of pulse imperfections by scalar couplings.

When applying multiple refocusing pulses to characterize the cross-correlated relaxation of heteronuclear multiple quantum coherence 2NxHx in biomolecules, the unavoidable effects of pulse imperfections are compensated by the scalar couplings between nitrogen atoms and protons. The experiment, which is useful as a tool for studying slow internal dynamics of biomolecules, greatly benefits from this compensation. The underlying effect is a manifestation of an interchange between three noncommuting components of the density operator. One perturbing Hamiltonian is counteracted by another, which leads to a nearly complete suppression of the perturbation. The effect proves to be an example of a hitherto unknown phenomenon in NMR spectroscopy.

Journal Article↗
PubMed2004

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein.

In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.

Amino Acid Sequence↗
PubMed2004

Evidence for slow motion in proteins by multiple refocusing of heteronuclear nitrogen/proton multiple quantum coherences in NMR.

A novel NMR method characterizes slow motions in proteins by multiple refocusing of double- and zero-quantum coherences of amide protons and nitrogen-15 nuclei. If both nuclei experience changes in their isotropic chemical shifts because of internal motions on slow time scales (mus - ms), this leads to a difference in the relaxation rates of double- and zero-quantum coherences. This is due to CSM/CSM (chemical shift modulation) cross-correlation effects that are related to the well-known chemical exchange contribution Rex to the decay rate R2 = 1/T2 of nitrogen-15 nuclei. The CSM/CSM contributions can be distinguished from other mechanisms through their dependence on the repetition rate of a Carr-Purcell-Meiboom-Gill (CPMG) multiple refocusing sequence. In ubiquitin, motional processes can be identified that could hitherto not be observed by conventional CPMG nitrogen-15 NMR.

Anisotropy↗
PubMed2004

Frequency-switched single-transition cross-polarization: a tool for selective experiments in biomolecular NMR.

Frequency-switched single-transition cross-polarization (FS-ST-CP) provides a versatile tool for selective coherence transfer in heteronuclear NMR of biomolecules such as proteins and nucleic acids. This type of coherence transfer is spin-state-selective and can therefore benefit from the extension of the life-times of selected coherences due to partial cancellation of interfering relaxation mechanisms. The limits of the selectivity of the transfer are discussed by theory and illustrated by experiment. The methods are particularly efficient to obtain quantitative structural and dynamic information for selected residues in medium-sized nitrogen-15 or carbon-13 labeled macromolecules.

Carbon Isotopes↗
PubMed2004

Triple quantum decoherence under multiple refocusing: slow correlated chemical shift modulations of C' and N nuclei in proteins.

A new experiment allows the identification of residues that feature slow conformational exchange in macromolecules. Rotations about dihedral angles that are slower than the global correlation time tau(c) cause a modulation of the isotropic chemical shifts of the nuclei. If these fluctuations are correlated they induce a differential line broadening between three-spin single-quantum and triple-quantum coherences involving three nuclei such as the carbonyl C', the neighbouring amide nitrogen N and the amide proton H(N) belonging to a pair of consecutive amino acids. A cross-correlated relaxation rate R (CS/CS)(C'N) can be determined that corresponds to the sum of the isotropic and anisotropic contributions to the chemical shift modulations of the carbonyl carbon and nitrogen nuclei. Only the isotropic contributions depend on the pulse repetition rate of a multiple-refocusing sequence. An attenuation of the relaxation rate with increasing pulse repetition rate can therefore be attributed to slow motions. The asparagine N25 residue of ubiquitin, located in the first alpha-helix, is shown to feature significant slow conformational exchange.

Algorithms↗
PubMed2004

Evidence of slow motions by cross-correlated chemical shift modulation in deuterated and protonated proteins.

Cross-correlated fluctuations of isotropic chemical shifts can provide evidence for slow motions in biomolecules. Slow side-chain dynamics have been investigated in (15)N and (13)C enriched ubiquitin by monitoring the relaxation of C(alpha)-C(beta) two-spin coherences (Frueh et al., 2001). This method, which had hitherto been demonstrated only for protonated ubiquitin, has now been applied to both protonated and deuterated proteins. Deuteration reduces the dipole-dipole contributions to the DD/DD cross-correlation, thus facilitating the observation of subtle effects due to cross-correlation of the fluctuations of the isotropic (13)C chemical shifts. The decays of double- and zero-quantum coherences are significantly slower in the deuterated protein than in the protonated sample. Slow motions are found both in loops and in secondary structure elements.

Anisotropy↗
PubMed2003

Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method.

The translational diffusion coefficient of an integral membrane protein/surfactant complex has been measured using a novel pulsed field gradient NMR method. In this new approach, the information about the localization of the molecules is temporarily stored in the form of longitudinal magnetization of isotopes with long spin-lattice relaxation times. This allows one to increase the duration of the diffusion interval by about 1 order of magnitude. Unlike standard proton NMR methods using pulsed field gradients and stimulated echoes, the new method can be applied to macromolecular assemblies with diffusion coefficients well below 10(-10) m(2) s(-1), corresponding to masses in excess of 25 kDa in aqueous solution at room temperature. The method was illustrated by application to a water-soluble complex of tOmpA, the hydrophobic transmembrane domain of bacterial outer membrane protein A, with the detergent octyl-tetraoxyethylene (C(8)E(4); overall mass of complex approximately 45 kDa). The diffusion coefficient was found to be D = (4.99 +/- 0.07) x 10(-11) m(2) s(-1), consistent with measurements by size exclusion chromatography and by ultracentrifugation. The method has also been applied to a solution of recombinant human tRNA(3)(Lys), which has a molecular mass of 24 kDa, and the diffusion coefficient D = (1.05 +/- 0.015) x 10(-10) m(2) s(-1).

Bacterial Outer Membrane Proteins↗
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

Transferred cross-relaxation and cross-correlation in NMR: effects of intermediate exchange on the determination of the conformation of bound ligands.

Exchange transferred effects in solution-state NMR experiments allow one to determine the conformation of ligands that are weakly bound to macromolecules. Exchange-transferred nuclear Overhauser effect spectroscopy ('TR-NOESY') provides information about internuclear distances in a ligand in the bound state. Recently the possibility of obtaining dihedral angle information from a ligand in the bound state by exchange-transferred cross-correlation spectroscopy ('TR-CCSY') has been reported. In both cases the analysis of the signal amplitudes is usually based on the assumption that rapid exchange occurs between the free and bound forms of the ligand. In this paper we show that the fast exchange condition is not easily attained for observing exchange-transferred cross-correlation effects even in systems where exchange-transferred NOE can be observed. Extensive simulations based on analytical expressions for signal intensities corresponding to fast, intermediate, and slow chemical exchange have been carried out on a test system to determine the exchange regimes in which the fast exchange condition can be fulfilled for successfully implementing TR-NOESY and TR-CCSY.

Algorithms↗
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

Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation.

The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RNA.

Base Sequence↗
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↗