Vincent Dahirel

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

Cellular immune control of HIV is mediated, in part, by induction of single amino acid mutations that reduce viral fitness, but compensatory mutations limit this effect. Here, we sought to determine if higher order constraints on viral evolution exist, because some coordinately linked combinations of mutations may hurt viability. Immune targeting of multiple sites in such a multidimensionally conserved region might render the virus particularly vulnerable, because viable escape pathways would be greatly restricted. We analyzed available HIV sequences using a method from physics to reveal distinct groups of amino acids whose mutations are collectively coordinated (“HIV sectors”). From the standpoint of mutations at individual sites, one such group in Gag is as conserved as other collectively coevolving groups of sites in Gag. However, it exhibits higher order conservation indicating constraints on the viability of viral strains with multiple mutations. Mapping amino acids from this group onto protein structures shows that combined mutations likely destabilize multiprotein structural interactions critical for viral function. Persons who durably control HIV without medications preferentially target the sector in Gag predicted to be most vulnerable. By sequencing circulating viruses from these individuals, we find that individual mutations occur with similar frequency in this sector as in other targeted Gag sectors. However, multiple mutations within this sector are very rare, indicating previously unrecognized multidimensional constraints on HIV evolution. Targeting such regions with higher order evolutionary constraints provides a novel approach to immunogen design for a vaccine against HIV and other rapidly mutating viruses.

Nonspecific DNA-protein interaction: why proteins can diffuse along DNA.

Recent single molecule experiments have reported that DNA binding proteins (DNA-BPs) can diffuse along DNA. This suggests that interactions between proteins and DNA play a role during the target search even far from their specific site on DNA. Here we show by means of Monte Carlo simulations and analytical calculations that there is a counterintuitive repulsion between the two oppositely charged macromolecules at a nanometer range. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the DNA-protein interaction free energy has a minimum at a finite surface-to-surface separation, in which proteins can easily slide. When a protein encounters its target, the free energy barrier is completely counterbalanced by the H-bond interaction, thus enabling the sequence recognition.

Toward the description of electrostatic interactions between globular proteins: Potential of mean force in the primitive model

Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern. Contrarily to Poisson-Boltzmann predictions, attractive, and repulsive direct forces between proteins are not screened similarly. Moreover, it has been shown that the relative orientations of the charge patterns strongly influence salt-mediated interactions. More precisely, for short distances between the proteins, ions enhance the difference of the effective forces between (i) like-charged and oppositely charged proteins, (ii) attractive and repulsive relative orientations of the proteins, which may affect the selectivity of protein/protein recognition. Finally, such results observed with the simplest models are applied to a more elaborate one to demonstrate their generality.

What can be learnt from the comparison of multiscale brownian dynamics simulations, nuclear magnetic resonance and light scattering experiments on charged micelles?

We investigate the dynamical behavior of charged micelles with a novel multiscale Brownian Dynamics simulation and two different experimental methods, Pulsed field Gradient Nuclear Magnetic Resonance, which gives access to self-diffusion coefficients, and Dynamic Light Scattering, which provides mutual diffusion coefficients. The simulation method is a very efficient multiscale procedure which relies on a separated treatment of micelle–microions interactions and micelle–micelle interactions. From this unique combination of methodologies, the size and the charge of the micelles could be fitted. This is the first time a simulation including both electrostatic and hydrodynamic interactions between all the solutes (nanoparticles and microions) is directly compared to experiments in order to characterize nanoparticles. The size, the bare charge and the effective charge we deduce from this study are thus much more reliable than those obtain from more approximative analytical theories. We could therefore reassess quantitatively the evolution of the micelle charateristics with the concentration in added salt.

Ion-mediated interactions between charged and neutral nanoparticles

Monte-Carlo simulations are used to study the ion-mediated effective interaction between weakly charged and highly charged nanoparticles in an implicit solvent. Three models of nanoparticles are successively studied, from crude charged hard spheres to dipolar and non-spherical nanoparticles. The analysis of the effective potential revealed that in an electrolyte solution, even a neutral nanoparticle feels an important repulsive force in the presence of a charged nanoparticle, with a typical range similar to the Debye length. When the two nanoparticles carry charges of opposite sign, we have shown that this repulsion can reverse the effect of the direct attractive electrostatic potential at short distances. This also yields the change of sign of the effective potential as a function of the relative orientations of two anisotropic nanoparticles. Moreover, we found that the 3-body terms of the effective potentials can overcome the 2-body terms, which is not observed in the case of symmetrically charged nanoparticles.

Ion-mediated interactions in suspensions of oppositely charged nanoparticles

The structure of oppositely charged spherical nanoparticles (polyions), dispersed in ionic solutions with continuous solvent (primitive model), is investigated by Monte Carlo (MC) simulations, within explicit and implicit microion representations, over a range of polyion valences and densities, and microion concentrations. Systems with explicit microions are explored by semigrand canonical MC simulations, and allow density-dependent effective polyion pair potentials v(alphabeta) (eff)(r) to be extracted from measured partial pair distribution functions. Implicit microion MC simulations are based on pair potentials of mean force v(alphabeta) ((2))(r) computed by explicit microion simulations of two charged polyions, in the low density limit. In the vicinity of the liquid-gas separation expected for oppositely charged polyions, the implicit microion representation leads to an instability against density fluctuations for polyion valences mid R:Zmid R: significantly below those at which the instability sets in within the exact explicit microion representation. Far from this instability region, the v(alphabeta) ((2))(r) are found to be fairly close to but consistently more repulsive than the effective pair potentials v(alphabeta) (eff)(r). This is corroborated by additional calculations of three-body forces between polyion triplets, which are repulsive when one polyion is of opposite charge to the other two. The explicit microion MC data were exploited to determine the ratio of salt concentrations c and c(o) within the dispersion and the reservoir (Donnan effect). c/c(o) is found to first increase before finally decreasing as a function of the polyion packing fraction.

Effective charges of micellar species obtained from Brownian dynamics simulations and from an analytical transport theory

We focus here on the effective charge of ionic micelles in aqueous solutions. First, we show that this quantity may be obtained by using an analytical transport theory based on the continuous solvent model to fit the experimental electrical conductivity of micellar solutions. In particular, we demonstrate the robustness of the fitting procedure on the example of real aqueous solutions of n-dodecyltrimethylammonium bromide and n-tetradecyltrimethylammonium chloride. Moreover, the approximate theoretical results are validated by a comparison to numerical simulations of Brownian dynamics. On the other hand, we propose to investigate the condensation properties of counterions on the micellar species by using Brownian dynamics. For that purpose, we have performed simulations of aqueous solutions that contain micellar species carrying their structural charge and the adequate number of counterions. We obtain a qualitative agreement between the fitted effective charges and the ones obtained by computing the mean number of bound counterions from numerical simulations.

Influence of the volume fraction on the electrokinetic properties of maghemite nanoparticles in suspension

We used several complementary experimental and theoretical tools to characterise the charge properties of well-defined maghemite nanoparticles in solution as a function of the volume fraction. The radius of the nanoparticles is equal to 6 nm. The structural charge was measured from chemical titration and was found high enough to expect some counterions to be electrostatically attracted to the surface, decreasing the apparent charge of the nanoparticle. Direct-current conductivity measurements were interpreted by an analytical transport theory to deduce the value of this apparent charge, denoted here by ‘dynamic effective charge’. This dynamic effective charge is found to decrease strongly with the volume fraction. In contrast, the ‘static’ effective charge, defined thanks to the Bjerrum criterion and computed from Monte Carlo simulations turns out to be almost independent of the volume fraction. In the range of Debye screening length and volume fraction investigated here, double layers around nanoparticles actually interact with each other. This strong interaction between nanocolloidal maghemite particles is probably responsible for the experimental dependence of the electrokinetic properties with the volume fraction.

Two-scale Brownian dynamics of suspensions of charged nanoparticles including electrostatic and hydrodynamic interactions.

We propose here a multiscale strategy based on continuous solvent Brownian dynamics (BD) simulations to study the dynamical properties of aqueous suspensions of charged nanoparticles. We extend our previous coarse-graining strategy [V. Dahirel et al., J. Chem. Phys. 126, 114108 (2007)] to account for hydrodynamic interactions between solute particles. Within this new procedure, two BD simulations are performed: (1) The first one investigates the time scales of the counterions and coions (the microions) with only one nanoparticle in the simulation box but explicit microions, (ii) the second one investigates the larger time scale of the nanoparticles with numerous nanoparticles in the simulation box but implicit microions. We show how individual and collective transport coefficients can be computed from this two-scale procedure. To ensure the validity of our procedure, we compute the transport coefficients of a 10-1 model electrolyte in aqueous solution with a 1-1 added salt. We do a systematic comparison between the results obtained within the new procedure and those obtained with explicit BD simulations of the complete system containing several nanoparticles and explicit microions. The agreement between the two methods is found to be excellent: Even if the new procedure is much faster than explicit simulations, it allows us to compute transport coefficients with a good precision. Moreover, one step of our procedure also allows us to compute the individual transport coefficients relative to the microions (self-diffusion coefficients and electrophoretic mobility).

Coarse-graining in suspensions of charged nanoparticles*

A coarse-grain description of nanocolloidal suspensions in the presence of an added salt is presented here. It enables us to simulate trajectories of the nanoparticles from effective functions that depend on average densities of salt ions. In practice, the ion-averaged effective potential is used as input of a Brownian dynamics (BD) simulation. This potential may be derived by various methods, ranging from purely analytical to fully numerical ones. For the description of dynamical properties, this simulation also requires an effective diffusion coefficient that must be calculated or experimentally determined, and that accounts for the effects of microions on the mobility of the nanoparticles. The different versions of our coarse-graining procedure are applied to the case of a maghemite suspension, for which an explicit description of all ions would be very time-consuming.