Biomedical subjects

D Vivarès

Publications and source records attributed to D Vivarès.

3 recordsLinked to original sources

PubMed2002

Interest of the normalized second virial coefficient and interaction potentials for crystallizing large macromolecules.

It has been shown for several years that the second virial coefficient, A(2), can be helpfully used to describe the thermodynamic behavior of biological macromolecules in solution prior to crystallization. The coefficient, which reflects either repulsive or attractive interactions between particles, can allow a rapid determination of crystallization conditions. Different biological systems, from 14 kDa to 4600 kDa, were studied by small angle X-ray scattering. With large macromolecules, the A(2) values were found at the low end of the crystallization slot described by George & Wilson [(1994) Acta Cryst. D50, 361-365]. This led us to investigate the physical meaning of the second virial coefficient and to propose the use of the dimensionless second virial coefficient independent of the molecular weight and the size of the particle, which only takes into account the interaction potential between macromolecules, to predict successful crystallization conditions for large macromolecules. With this normalized coefficient (a(2)), the effect of salt on small proteins becomes equivalent to the effect of PEG on large macromolecules in terms of interaction potentials.

Animals↗

PubMed2002

X-ray scattering studies of Aspergillus flavus urate oxidase: towards a better understanding of PEG effects on the crystallization of large proteins.

The determination of the three-dimensional structures of biological macromolecules by X-ray diffraction generally requires large good-quality crystals, which are often difficult to obtain as crystal nucleation and growth depend upon a great number of physicochemical parameters. In the future, the emergence of structural genomic projects will require new and rapid methods to determine crystallization conditions. Until now, the prediction of crystallization conditions has essentially been based on the knowledge of interparticular interactions in solutions inferred from studies on small soluble proteins in the presence of salts. The present study, by small-angle X-ray scattering, of urate oxidase from Aspergillus flavus, a homotetrameric enzyme of 128kDa, allowed the extension of the results to the crystallization of large proteins in the presence of polyethylene glycol (PEG). The protein crystallization, the nucleation rate and the different morphological crystal shapes obtained were correlated with the second virial coefficient (A(2)), which was found to be in a restricted range at the low end of the 'crystallization slot' proposed by George & Wilson [(1994). Acta Cryst. D50, 361--365].

Aspergillus flavus↗

PubMed2002

Catching the PEG-induced attractive interaction between proteins.

We present the experimental and theoretical background of a method to characterize the protein-protein attractive potential induced by one of the mostly used crystallizing agents in the protein-field, the poly(ethylene glycol) (PEG). This attractive interaction is commonly called, in colloid physics, the depletion interaction. Small-Angle X-ray Scattering experiments and numerical treatments based on liquid-state theories were performed on urate oxidase-PEG mixtures with two different PEGs (3350 Da and 8000 Da). A "two-component" approach was used in which the polymer-polymer, the protein-polymer and the protein-protein pair potentials were determined. The resulting effective protein-protein potential was characterized. This potential is the sum of the free-polymer protein-protein potential and of the PEG-induced depletion potential. The depletion potential was found to be hardly dependent upon the protein concentration but strongly function of the polymer size and concentration. Our results were also compared with two models, which give an analytic expression for the depletion potential.

Journal Article↗