1,721,233 research outputs found
Hard sphere hydrodynamics as reference state in velocity cross-correlation analysis of real systems
No full textThe ability of hard-sphere hydrodynamics to model translational motions in real systems is discussed. The possibility to split the excluded volume effect on mutual diffusion into thermodynamic and hydrodynamic contributions is established by using accurate experimental activity and mutual diffusion data. The combination of hard-sphere theory at the second order of volume fraction for mutual diffusion, intradiffusion, and thermodynamic properties allows calculation of velocity cross-correlation coefficients (VCC), herein proposed as new standard coefficients. The comparison of these new standards with real VCCs, corresponding to several aqueous solutions of conventional solutes and macromolecules, tests the applicability of this procedure. The new VCC analysis scales the excluded volume effect and allows more meaningful discussion about correlation of translational motion in solution, especially in the case of the cross-term solute-solvent VCCs in macromolecule-solvent mixtures. Possible extension to analytically quantity correlation between internal motions of biopolymers is briefly discussed
Membro editorial Board di "International Scholarly Research Notices" sezione Physical Chemistry
No full textDistinct diffusion in polymer-solvent mixtures
No full textThe specificity of interactions between pairs of molecules cannot be explicitly given by experimental transport coefficients such as intra- or mutual diffusion coefficients. But a microscopic interpretation of the transport properties exists, where distinct diffusion coefficients(DDCs) are related to preferential, correlated motion among distinct molecules. Since in general the DDCs do not play the role of an indicator for molecular self-association phenomena if not compared with some appropriate standard, here we propose DDCs of hard spheres at the second order of volume fraction as new standard coefficients. The analysis based on these novel DDCs is designed to study intermolecular interaction between macromolecule and solvent. Comparisons of the novel non-ideal with previous ideal reference states were done, and their combined use is shown to reinforce information conveyed by the usual velocity correlation analysis. The comparison of novel hard sphere standards with real DDCs, corresponding to an homologous chemical series of poly(ethylene glycol)-water mixtures, provides a look at this polymer-solvent mixture in a dilute and semi-dilute regime
Monitoring the preparation of protein derivative crystals via Raman-microscopy
No full textRaman microscopy is having increasing applications into molecular biology. Primary structure features can be analyzed, such as Se-Met labeled protein crystals to be used for MAD crystallography [1] or to check heavy metal incorporation in isomorphous derivative crystals. Secondary structure modification can be clearly identified according to relationships between amide band frequencies and Ramachandran angles [2]. Ligand binding [3] and protein dynamics/reactivity can also be efficiently followed.
The combined Raman and X-ray crystallography approach reinforces the interpretation of biophysical data. In particular, reactivity and dynamics of metal proteins have been investigated. This approach is particularly informative and well developed for hemoproteins [4, 5].
[1] A. Vergara, A. Merlino, E. Pizzo, G. D'Alessio, L. Mazzarella, Acta Cryst. D. (2008) D64, 167-171. [2] A. Merlino, F. Sica, A. Zagari, L. Mazzarella, A. Vergara, Biophys. Chem. (2008), 137, 24-27. [3] P. R. Carey, Ann. Rev. Phys. Chem. 2006, 57, 527-554. [4] L. Vitagliano, A. Vergara, G. Bonomi, A. Merlino, G. Smulevich, B. Howes, G. di Prisco, C. Verde, L. Mazzarella, J. Am. Chem. Soc. (2008) 130, 10527-10535. [5] A. Merlino, L. Vitagliano, B. Howes, C. Verde, G. di Prisco, G. Smulevich, F. Sica, A. Vergara, Biopolymers (2009), 91(12), 1117-1125.
PRIN is acknowledged for financial support.
Keywords: metal protein, ligand soaking, secondary structur
Applications of velocity cross-correlation integrals to study macromolecular solutions
No full textInteractions between pairs of molecules in solutions cannot be explicitly given by experimental transport coefficients such as intra- or mutual diffusion coefficients. But a microscopic interpretation of the transport properties exists, where velocity cross-correlation integrals (VCC) or distinct diffusion coefficients (DDC) are related to preferential, correlated motion among distinct molecules. Herein we review the ability of model systems to describe translation motions in real systems. Specifically, the comparison of new and old standards with a number of VCC and DDC corresponding to real systems proves the applicability of this procedure also to macromolecule-solvent mixtures
Use of Kirkwood–Buff Integrals for Extracting Distinct Diffusion Coeffi cients in Macromolecule–Solvent Mixtures
No full textThe possibility to extract velocity correlation quantities from fluctuation thermodynamic properties is explored in the case of macromolecule-solvent mixtures. Indeed, Kirkwood-Buff integrals, G_ij, together with self-diffusion and viscosity data can provide an approximation for distinct diffusion coefficients, DDC, D_ij^d. Herein, we calculate D_ij^d for binary PEG(2)-water(1) systems. These systems show positive values of D_22^d coefficients, indicating strong PEG-PEG interaction, and providing marker of water madiated PEG-PEG networks. The efficiency of several standard DDCs present in literature for D_ij^d analysis is compared, summarizing the usefulness of each one, depending on the non-ideality degre
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