93 research outputs found
Discrete charge patterns, Coulomb correlations and interactions in protein solutions
The effective Coulomb interaction between globular proteins is calculated as
a function of monovalent salt concentration , by explicit Molecular
Dynamics simulations of pairs of model proteins in the presence of microscopic
co and counterions. For discrete charge patterns of monovalent sites on the
surface, the resulting osmotic virial coefficient is found to be a
strikingly non-monotonic function of . The non-monotonicity follows from a
subtle Coulomb correlation effect which is completely missed by conventional
non-linear Poisson-Boltzmann theory and explains various experimental findings.Comment: 4 twocolumn pages with 4 figure
Shape-Dependent Thermodynamics and Non-Local Hydrodynamics in a Non-Gibbsian Steady-State of a Drift-Diffusion System
Shape-dependent thermodynamics and non-local hydrodynamics are argued to
occur in dissipative steady states of driven diffusive systems. These
predictions are confirmed by numerical simulations. Unlike power-law
correlations, these phenomena cannot be explained by a hypothesis of
``criticality''. Instead, they require the effective Hamiltonian of the system
to contain very long-range potentials, making the invariant probability
measures formally ``non-Gibbsian''.Comment: 4 pages, Latex Version 2.09, 1 Postscript figur
Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions
The osmotic virial coefficient of globular protein solutions is
calculated as a function of added salt concentration at fixed pH by computer
simulations of the ``primitive model''. The salt and counter-ions as well as a
discrete charge pattern on the protein surface are explicitly incorporated. For
parameters roughly corresponding to lysozyme, we find that first
decreases with added salt concentration up to a threshold concentration, then
increases to a maximum, and then decreases again upon further raising the ionic
strength. Our studies demonstrate that the existence of a discrete charge
pattern on the protein surface profoundly influences the effective interactions
and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek
(DLVO) theory fail for large ionic strength. The observed non-monotonicity of
is compared to experiments. Implications for protein crystallization are
discussed.Comment: 43 pages, including 17 figure
Adsorption of mono- and multivalent cat- and anions on DNA molecules
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose
nucleic acid (DNA) molecule from a salt solution is investigated by computer
simulation. The ions are modelled as charged hard spheres, the DNA molecule as
a point charge pattern following the double-helical phosphate strands. The
geometrical shape of the DNA molecules is modelled on different levels ranging
from a simple cylindrical shape to structured models which include the major
and minor grooves between the phosphate strands. The densities of the ions
adsorbed on the phosphate strands, in the major and in the minor grooves are
calculated. First, we find that the adsorption pattern on the DNA surface
depends strongly on its geometrical shape: counterions adsorb preferentially
along the phosphate strands for a cylindrical model shape, but in the minor
groove for a geometrically structured model. Second, we find that an addition
of monovalent salt ions results in an increase of the charge density in the
minor groove while the total charge density of ions adsorbed in the major
groove stays unchanged. The adsorbed ion densities are highly structured along
the minor groove while they are almost smeared along the major groove.
Furthermore, for a fixed amount of added salt, the major groove cationic charge
is independent on the counterion valency. For increasing salt concentration the
major groove is neutralized while the total charge adsorbed in the minor groove
is constant. DNA overcharging is detected for multivalent salt. Simulations for
a larger ion radii, which mimic the effect of the ion hydration, indicate an
increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure
Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors
A set of physicochemical properties describing a protein of known structure is employed for a calibrative approach to protein solubility. Common hydrodynamic and electrophoretic properties routinely measured in the bio-analytical laboratory such as zeta potential, dipole moment, the second osmotic virial coefficient are first estimated in silico as a function a pH and solution ionic strength starting with the protein crystal structure. The utility of these descriptors in understanding the solubility of a series of ribonuclease Sa mutants is investigated. A simple two parameter model was trained using solubility data of the wild type protein measured at a restricted number of solution pHs. Solubility estimates of the mutants demonstrate that zeta potential and dipole moment may be used to rationalize solubility trends over a wide pH range. Additionally a calibrative model based on the protein’s second osmotic virial coefficient, B22 was developed. A modified DVLO type potential along with a simplified representation of the protein allowed for efficient computation of the second viral coefficient. The standard error of prediction for both models was on the order of 0.3 log S units. These results are very encouraging and demonstrate that these models may be trained with a small number of samples and employed extrapolatively for estimating mutant solubilities
A General Approach for Predicting the Filtration of Soft and Permeable Colloids: The Milk Example
Membrane filtration operations (ultra-, microfiltration) are now extensively used for concentrating or separating an ever-growing variety of colloidal dispersions. However, the phenomena that determine the efficiency of these operations are not yet fully understood. This is especially the case when dealing with colloids that are soft, deformable, and permeable. In this paper, we propose a methodology for building a model that is able to predict the performance (flux, concentration profiles) of the filtration of such objects in relation with the operating conditions. This is done by focusing on the case of milk filtration, all experiments being performed with dispersions of milk casein micelles, which are sort of ″natural″ colloidal microgels. Using this example, we develop the general idea that a filtration model can always be built for a given colloidal dispersion as long as this dispersion has been characterized in terms of osmotic pressure Π and hydraulic permeability k. For soft and permeable colloids, the major issue is that the permeability k cannot be assessed in a trivial way like in the case for hard-sphere colloids. To get around this difficulty, we follow two distinct approaches to actually measure k: a direct approach, involving osmotic stress experiments, and a reverse-calculation approach, that consists of estimating k through well-controlled filtration experiments. The resulting filtration model is then validated against experimental measurements obtained from combined milk filtration/SAXS experiments. We also give precise examples of how the model can be used, as well as a brief discussion on the possible universality of the approach presented here
A unifying model for concentration polarization, gel-layer formation and particle deposition in cross-flow membrane filtration of colloidal suspensions
Everything you always wanted to know about SDPD⋆ (⋆but were afraid to ask)
An overview of the smoothed dissipative particle dynamics (SDPD) method is presented in a format that tries to quickly answer questions that often arise among users and newcomers. It is hoped that the status of SDPD is clarified as a mesoscopic particle model and its potentials and limitations are highlighted, as compared with other methods
Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility
- …