P. Calmettes

How random is a highly denatured protein

There has been renewed interest in determining the physicochemical properties of denatured states of proteins. In many denatured states there is evidence for the existence of nonrandom configurational distributions. Here we examine the small-angle neutron scattering profile of yeast phosphoglycerate kinase in the native state and in highly denaturing conditions. We show that the denatured protein scattering profile can be interpreted using a model developed for synthetic polymers in which the chain behaves as a random coil in a good solvent, i.e. with excluded volume interactions. The implications of this result for our appreciation of the protein folding process are discussed.

Picosecond Dynamical Changes on Denaturation of Yeast Phosphoglycerate Kinase Revealed by Quasielastic Neutron Scattering

Quasielastic neutron scattering experiments performed on yeast phosphoglycerate kinase in the native form and denatured in 1.5 M guanidinium chloride reveal a change in the fast (picosecond time scale) diffusive internal dynamics of the protein. The momentum and energy transfer dependences of the scattering for both states are fitted by an analytical model in which, on the experimentally accessible picosecond time scale and angstrom length scale, the dynamics of a fraction of the nonexchangeable hydrogens in the protein is described as a superposition of vibrations with uniform diffusion in a sphere, the rest of the hydrogens undergoing only vibrational motion. The fraction diffusing changes, from ≈60% in the native protein to ≈82% in the denatured protein. The radius of the sphere also changes slightly, from ≈1.8 Å in the native protein to ≈2.2 Å in the denatured protein. Possible implications of these results for the general protein folding problem are discussed. Proteins 28:380–387, 1997

Molecular solvent model for a cryptate solution in acetonitrile: A hypernetted chain study

Hypernetted chain calculations are reported for pure liquid acetonitrile and for a 0.39 M acetonitrile solution of cryptate K+ 222, ClO−4. The obtained molecular correlations between solvent and solute particles are discussed in detail. It is found that the acetonitrile correlations are very similar in the pure liquid and in the solution. The solvation geometries around the cations and the anions are surprisingly unsymmetric and hence far from the picture which chemists currently use to describe ionic solvation. The theoretical results are compared to available wide‐angle neutron scattering data for the pure liquid and to small‐angle neutron scattering data for the cryptate solution. To our knowledge, this is the first integral equation study of molecular correlations in a real nonaqueous electrolyte solution.

Repulsive interparticle interactions in a denatured protein solution revealed by small angle neutron scattering

In order to investigate the effect of concentration in biological processes such as protein folding, small angle neutron scattering measurements were used to determine the second virial coefficient of solutions of both native and strongly denatured phosphoglycerate kinase and the radius of gyration of the protein at zero concentration. The value of the second virial coefficient is a good probe of the non‐ideality of a solution. The present results show that the unfolding of the protein leads to a drastic change in the repulsive intermolecular interactions. We conclude that these interactions are due mainly to the behaviour of the denatured polypeptide chain as an excluded volume polymer.

Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory.

Small-angle neutron scattering profiles are presented from phosphoglycerate kinase, in the native form and strongly denatured in 4 M guanidinium chloride (GdnHCl) solution. The data are interpreted using a model in which the excess scattering density associated with the protein is represented as a finite freely jointed chain of spheres. The similarity of the model-derived scattering function to experiment increases asymptotically with the number of spheres. The improvement of the fit obtained with more than approximately 200 spheres (i.e., two residues per sphere) is insignificant. The effects of finite size of the scattering units and of scattering length variation along the polypeptide chain are examined. Improved agreement with experiment is obtained when these effects are taken into account. A method for rapid calculation of the scattering profile of a full, all-atom configuration is examined. It is found that a representation of the chain containing two scattering units per residue, placed at the backbone and side-chain scattering length centroids, reproduces the full, all-atom profile to within 2%.

Structure of nonaqueous electrolyte solutions by small‐angle neutron scattering, hypernetted chain, and Brownian dynamics

Small‐angle neutron scattering from solutions of n‐tetrapentylammonium bromide in deuterated acetonitrile was studied at room temperature for concentrations between 0.17 and 1.01 M. The hypernetted chain (HNC) integral equation with solvent‐averaged pair potentials was used to describe both the scattering spectra and the osmotic coefficient of the nondeuterated solutions. It is shown that the so‐called Friedman–Gurney potential can be replaced by a simple soft sphere potential in order to reproduce the scattering data. The results give a new insight into the structure and the distribution of ions. Within statistical uncertainties Brownian dynamics simulations for the same pair potentials lead to correlation functions similar to those given by HNC.

Dynamics and spatial correlations of tetrapentylammonium ions in acetonitrile

Quasielastic neutron scattering (QENS) spectra were measured for a 0.43 M solution of n‐tetrapentylammonium bromide in deuterated acetonitrile at 25 °C, 5 °C, and −15 °C. Values of the translational diffusion coefficient of the cations were inferred from these data using a simple model of translation and rotation. These values are significantly higher than the ones obtained by nuclear magnetic resonance (NMR) spin–echo measurements. The difference can be explained by the different time scales covered by QENS and NMR. QENS shows essentially the contribution of a second order electrophoretic effect to the diffusion coefficient whereas NMR encompasses both electrophoretic and relaxation effects. Consequently, the combination of both techniques allows the two effects to be separated. The relaxation contribution to the diffusion coefficient was calculated by brownian dynamics simulation and compared to the experimental results. The solvent‐averaged ion pair potentials used for this computation were simultaneou...

Small-angle neutron scattering from heavy water in the vicinity of the critical point

Small-angle neutron scattering spectra from supercritical heavy water were recorded along a near-critical isochore at temperatures between (Tc,exp+1.63 K) and (Tc,exp+22.02 K), Tc,exp being the experimental critical temperature. At low values of the wave number transfer q, the scattered intensity shows a pronounced increase due to the divergence of density fluctuations at the critical point. In the studied q range, from 0.07 to 0.36 A−1, all the spectra can be accurately described by the Fisher–Langer correlation function provided that a multiplicative additional term describing short-range correlations between water molecules is taken into account. The value found for the amplitude of the critical correlation length is ξ0=(1.36±0.06) A, in fair agreement with the value predicted by the two-scale hypothesis.

Small hydrophobic organic ions in aqueous solutions

Small‐angle neutron scattering experiments were performed at 25 °C on solutions of tetraphenylphosphonium chloride and sodium tetraphenylborate in deuterated water and in deuterated dimethylformamide. The results show a strong attraction between either the organic cations or the organic anions when the salts are dissolved in water. On the contrary, in the organic solvent the attraction between the equally charged organic ions is found to be very weak. This is the first structural evidence of hydrophobic association of small organic ions in water.

Dynamics of liquid acetonitrile at high frequencies

Quasielastic neutron scattering spectra were measured for pure acetonitrile at 25 °C. In the framework of a simple model of translation and rotation, it was found that the short‐time self‐diffusion coefficient of liquid acetonitrile is similar to the long‐time one measured by NMR. As far as the rotational motion is concerned, the characteristic time was found to be close to the typical value of the molecule spinning motion. The complete inelastic and quasielastic spectra may be further used to check the results of molecular dynamics simulations of acetonitrile.