Measurements of Protein-Protein Interactions by Size Exclusion Chromatography

A method is presented for determining second virial coefficients B_2 of protein solutions from retention time measurements in size exclusion chromatography (SEC). We determine B_2 by analyzing the concentration dependance of the chromatographic partition coefficient. We show the ability of this method to track the evolution of B_2 from positive to negative values in lysozyme and bovine serum albumin solutions. Our SEC results agree quantitatively with data obtained by light scattering.Comment: 18 pages including 1 table and 5 figure

Light scattering and phase behavior of Lysozyme-PEG mixtures

Measurements of liquid-liquid phase transition temperatures (cloud points) of mixtures of a protein (lysozyme) and a polymer, poly(ethylene glycol) (PEG) show that the addition of low molecular weight PEG stabilizes the mixture whereas high molecular weight PEG was destabilizing. We demonstrate that this behavior is inconsistent with an entropic depletion interaction between lysozyme and PEG and suggest that an energetic attraction between lysozyme and PEG is responsible. In order to independently characterize the lysozyme/PEG interactions, light scattering experiments on the same mixtures were performed to measure second and third virial coefficients. These measurements indicate that PEG induces repulsion between lysozyme molecules, contrary to the depletion prediction. Furthermore, it is shown that third virial terms must be included in the mixture's free energy in order to qualitatively capture our cloud point and light scattering data. The light scattering results were consistent with the cloud point measurements and indicate that attractions do exist between lysozyme and PEG.Comment: 5 pages, 2 figures, 1 tabl

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection

Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis). We show that these exhibit a stereotypical ‘phase transition’, whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have ‘memory’ of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture fine scale rules of interaction, which are primarily mediated by physical contact. Conversely, the Markovian self-propelled particle model captures the fine scale rules of interaction but fails to reproduce global dynamics. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects

Fraden,Measurements of protein-protein interactions by size exclusion chromatography,Biophys

ABSTRACT A method is presented for determining second virial coefficients (B 2) of protein solutions from retention time measurements in size exclusion chromatography. We determine B2 by analyzing the concentration dependence of the chromatographic partition coefficient. We show the ability of this method to track the evolution of B2 from positive to negative values in lysozyme and bovine serum albumin solutions. Our size exclusion chromatography results agree quantitatively with data obtained by light scattering

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Using optical microscopy, we have studied the phase behavior of mixtures of 12- to 22-bp-long nanoDNA oligomers. The mixtures are chosen such that only a fraction of the sample is composed of mutually complementary sequences, and hence the solutions are effectively mixtures of single-stranded and double-stranded (duplex) oligomers. When the concentrations are large enough, such mixtures phase-separate via the nucleation of duplex-rich liquid crystalline domains from an isotropic background rich in single strands. We find that the phase separation is approximately complete, thus corresponding to a spontaneous purification of duplexes from the single-strand oligos. We interpret this behavior as the combined result of the energy gain from the end-to-end stacking of duplexes and of depletion-type attractive interactions favoring the segregation of the more rigid duplexes from the flexible single strands. This form of spontaneous partitioning of complementary nDNA offers a route to purification of short duplex oligomers and, if in the presence of ligation, could provide a mode of positive feedback for the preferential synthesis of longer complementary oligomers, a mechanism of possible relevance in prebiotic environments