Structural and Biophysical Characterization of Staphylococcus Aureus SaMazF Shows Conservation of Functional Dynamics

The Staphylococcus aureus genome contains three toxin-antitoxin modules, including one mazEF module, SamazEF. Using an on-column separation protocol we are able to obtain large amounts of wild-type SaMazF toxin. The protein is well-folded and highly resistant against thermal unfolding but aggregates at elevated temperatures. Crystallographic and nuclear magnetic resonance (NMR) solution studies show a well-defined dimer. Differences in structure and dynamics between the X-ray and NMR structural ensembles are found in three loop regions, two of which undergo motions that are of functional relevance. The same segments also show functionally relevant dynamics in the distantly related CcdB family despite divergence of function. NMR chemical shift mapping and analysis of residue conservation in the MazF family suggests a conserved mode for the inhibition of MazF by MazE

Nucleation of protein crystals – a nanoscopic perspective

International audienc

Mineral Growth beyond the Limits of Impurity Poisoning

International audienc

Mineral Growth beyond the Limits of Impurity Poisoning

More often than not, minerals formed in nature are grown at low supersaturation and from sources that are impure with respect to the crystals' main building blocks. Quite paradoxically, these conditions are in conflict with the established crystal growth theories that focus on the interplay between the crystal interface and impurities that are present in the growth medium. These theories predict a kinetic dead zone for the cases where low purity is combined with weak driving forces. Hints toward reconciling this apparent disparity have been given by the observation that a specific class of steps, so-called macrosteps, can circumvent the debilitating kinetic effects of impurities in ways that up until now are poorly understood. In this contribution, we examine the mechanism of crystal growth by means of kinetic Monte Carlo simulation at conditions close to impurity-induced kinetic arrest. In agreement with previous reports, we show that as a result of impurity binding to the crystal surface, steps spontaneously group into bunches and later condense into macrosteps. A kinetic analysis demonstrates that these macrosteps are able to evade crystal growth cessation under conditions where single steps are firmly pinned. We identify the mechanism of interstep cooperativity which leads to cessation evasion by macrosteps and demonstrate that it applies to a range of supersaturation and impurity concentration values. On the basis of these findings, we present a model that explains how minerals can grow from mother liquor solutions that would otherwise seem to be nonconducive to crystal growth.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Mesoscopic Impurities Expose a Nucleation-Limited Regime of Crystal Growth

Nanoscale self-assembly is naturally subject to impediments at the nanoscale. The recently developed ability to follow processes at the molecular level forces us to resolve older, coarse-grained concepts in terms of their molecular mechanisms. In this Letter, we highlight one such example. We present evidence based on experimental and simulation data that one of the cornerstones of crystal growth theory, the Cabrera-Vermilyea model of step advancement in the presence of impurities, is based on incomplete physics. We demonstrate that the piercing of an impurity fence by elementary steps is not solely determined by the Gibbs-Thomson effect, as assumed by Cabrera-Vermilyea. Our data show that for conditions leading up to growth cessation, step retardation is dominated by the formation of critically sized fluctuations. The growth recovery of steps is counter to what is typically assumed, not instantaneous. Our observations on mesoscopic impurities for lysozyme expose a nucleation-dominated regime of growth that has not been hitherto considered, where the system alternates between zero and near-pure velocity. The time spent by the system in arrest is the nucleation induction time required for the step to amass a supercritical fluctuation that pierces the impurity fence.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

On the Self-Purification Cascade during Crystal Growth from Solution

We report on the failure of the Cabrera–Vermilyea (CV) step pinning model to reproduce the elementary step kinetics for the case of tetragonal lysozyme crystals growing from contaminated solutions. We measured the supersaturation dependency of the step velocity using confocal microscopy for three different commercially available lysozyme batches with varying levels of impurity content, that is, Seikagaku, Fluka, and Sigma. Strong nonlinear dependencies are obtained in the high to intermediate supersaturation range and near-linear dependencies at lower driving forces. The clear absence of a dead zone for the Fluka and Seikagaku data is in direct contradiction to the CV model. As such, we developed a time-dependent impurity model based on Bliznakov kinetics assuming Langmuir adsorption. Admissible fits are obtained for Fluka and Seikagaku lysozyme corroborating the self-purification interpretation due to the diminishing terrace exposure times at higher supersaturation levels. The steeper recovery toward pure kinetics for Sigma lysozyme than predicted by Langmuir adsorption prompted us to expand the model to allow for impurity–impurity interaction. The resultant kinetic model, which assumes a Kisliuk-like mode of impurity adsorption, did yield acceptable fits with Sigma step kinetics. This Bliznakov–Kisliuk model also predicts clustering of impurity molecules on the surface, which is corroborated by our in situ experimental atomic force microscopy observations

Nucleation of glucose isomerase protein crystals in a nonclassical disguise: The role of crystalline precursors

International audienceProtein crystallization is an astounding feat of nature. Even though proteins are large, anisotropic molecules with complex, heterogeneous surfaces, they can spontaneously group into two- and three-dimensional arrays with high precision. And yet, the biggest hurdle in this assembly process, the formation of a nucleus, is still poorly understood. In recent years, the two-step nucleation model has emerged as the consensus on the subject, but it still awaits extensive experimental verification. Here, we set out to reconstruct the nucleation pathway of the candidate protein glucose isomerase (GI), for which there have been indications that it may follow a two-step nucleation pathway under certain conditions. We find that the precursor phase present during the early stages of the reaction process is nanoscopic crystallites that have lattice symmetry equivalent to the mature crystals found at the end of a crystallization experiment. Our observations underscore the need for experimental data at a lattice-resolving resolution on other proteins so that a general picture of protein crystal nucleation can be formed

Observing classical nucleation theory at work by monitoring phase transitions with molecular precision

It is widely accepted that many phase transitions do not follow nucleation pathways as envisaged by the classical nucleation theory. Many substances can traverse intermediate states before arriving at the stable phase. The apparent ubiquity of multi-step nucleation has made the inverse question relevant: does multistep nucleation always dominate single-step pathways? Here we provide an explicit example of the classical nucleation mechanism for a system known to exhibit the characteristics of multi-step nucleation. Molecular resolution atomic force microscopy imaging of the two-dimensional nucleation of the protein glucose isomerase demonstrates that the interior of subcritical clusters is in the same state as the crystalline bulk phase. Our data show that despite having all the characteristics typically associated with rich phase behaviour, glucose isomerase 2D crystals are formed classically. These observations illustrate the resurfacing importance of the classical nucleation theory by re-validating some of the key assumptions that have been recently questioned.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Step Crowding Effects Dampen the Stochasticity of Crystal Growth Kinetics

Crystals grow by laying down new layers of material which can either correspond in size to the height of one unit cell (elementary steps) or multiple unit cells (macrosteps). Surprisingly, experiments have shown that macrosteps can grow under conditions of low supersaturation and high impurity density such that elementary step growth is completely arrested. We use atomistic simulations to show that this is due to two effects: the fact that the additional layers bias fluctuations in the position of the bottom layer towards growth and by a transition, as step height increases, from a 2D to a 3D nucleation mechanism. © 2016 American Physical Society.SCOPUS: ar.jinfo:eu-repo/semantics/publishe