No Arabic abstract
We study by Small Angle Neutron Scattering (SANS) the structure of Hyaluronan -Lysozyme complexes. Hyaluronan (HA) is a polysaccharide of 9 nm intrinsic persistence length that bears one negative charge per disaccharide monomer (Mmol = 401.3 g/mol); two molecular weights, Mw = 6000 and 500 000 Da were used. The pH was adjusted at 4.7 and 7.4 so that lysozyme has a global charge of +10 and + 8 respectively. The lysozyme concentration was varied from 3 to 40 g/L, at constant HA concentration (10 g/L). At low protein concentration, samples are monophasic and SANS experiments reveal only fluctuations of concentration although, at high protein concentration, clusters are observed by SANS in the dense phase of the diphasic samples. In between, close to the onset of the phase separation, a distinct original scattering is observed. It is characteristic of a rod-like shape, which could characterize single complexes involving one or a few polymer chains. For the large molecular weight (500 000) the rodlike rigid domains extend to much larger length scale than the persistence length of the HA chain alone in solution and the range of the SANS investigation. They can be described as a necklace of proteins attached along a backbone of diameter one or a few HA chains. For the short chains (Mw ~ 6000), the rod length of the complexes is close to the chain contour length (~ 15 nm).
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble of reactive pathways, exponentially reducing the cost of simulating thermally activated transitions. The algorithm also yields a rigorous stochastic estimate of the reaction coordinate. After illustrating this approach on a simple toy model, we successfully validate it against the results of ultra-long plain MD protein folding simulations for a fast folding protein (Fip35), which were performed on the Anton supercomputer. Using our algorithm, computing a folding trajectory for this protein requires only 1000 core hours, a computational load which could be even carried out on a desktop workstation.
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be determined from the same set of X-ray data. We demonstrate here how barriers of activation can be determined solely from five-dimensional crystallography [5]. Directly linking molecular structures with barriers of activation between them allows for gaining insight into the structural nature of the barrier. We analyze comprehensive time series of crystal-lographic data at 14 different temperature settings and determine entropy and enthalpy contributions to the barriers of activation. 100 years after the discovery of X-ray scattering, we advance X-ray structure determination to a new frontier, the determination of energy landscapes.
We describe a model of cytoskeletal mechanics based on the force-induced conformational change of protein cross-links in a stressed polymer network. Slow deformation of simulated networks containing cross-links that undergo repeated, serial domain unfolding leads to an unusual state--with many cross-links accumulating near the critical force for further unfolding. Thermal activation of these links gives rise to power-law rheology resembling the previously unexplained mechanical response of living cells. Moreover, we hypothesize that such protein cross-links function as biochemical mechano-sensors of cytoskeletal deformation.
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this melting transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.