Inhibition of protein crystallization by evolutionary negative design

In this perspective we address the question: why are proteins seemingly so hard to crystallize? We suggest that this is because of evolutionary negative design, i.e. proteins have evolved not to crystallize, because crystallization, as with any type of protein aggregation, compromises the viability of the cell. There is much evidence in the literature that supports this hypothesis, including the effect of mutations on the crystallizability of a protein, the correlations found in the properties of crystal contacts in bioinformatics databases, and the positive use of protein crystallization by bacteria and viruses.Comment: 5 page

The solute-rich mesoscopic precursors of crystal nuclei of olanzapine solid forms

Olanzapine (OZPN) is a BCS class II drug used to treat schizophrenia (bipolar disorder). OZPN exhibits rich solid-state diversity. To date, 60 distinct forms have been identified, including 3 polymorphs (I, II, III), 52 crystalline solvates, 3 dihydrates (DB, DD, DE), a disordered higher hydrate, plus an amorphous form. Atomic Force Microscopy (AFM) results suggest that the nucleation of OZPN DD on the surface of OZPN I in water may follow a non-classical mechanisms that includes formation of solute-rich mesoscopic clusters [1]. Since the solubility of OZPN I in water is very low, the kinetics of transformation are difficult to monitor. To increase the solubility of OZPN I, we added different ratios of a co-solvent, ethanol. AFM observations revealed that clusters similar to those seen in purely aqueous environments are present on the surface of OZPN:EtOH:H2O crystals in contact with both supersaturated and undersaturated EtOH/H2O solutions. To establish the mechanism of cluster formation, we monitored the dependence of the cluster size and volume fraction on time, OZPN concentration, and co-solvent concentration using Brownian Microscopy (BM). The characteristics of the cluster population were correlated with the standard enthalpy, entropy and free energy of crystallization obtained from temperature dependence of the solubility of OZPN:EtOH:H2O crystals. We verified, using small angle x-ray scattering, that the crystal form was preserved at all solvent compositions. We observed that the cluster radius was constant, at R ≈ 37 nm, in all solvent compositions tested and at all times. The volume of the cluster population φ mapped the non-monotonic dependence of the crystallization enthalpy on the EtOH content, indicating that φ is determined by the thermodynamics of the solute-solvent interactions. The decoupled behaviour of R suggests that, in contrast to φ, the cluster size is kinetically determined. These conclusions comply with the prediction of a model of mesoscopic solvent rich clusters, based on formation of transient solute oligomers in the solutions [3]. These are the first observations of solute-rich clusters in solutions of pharmaceutically active compounds and of their role in the nucleation of crystals and the transformations between crystal forms. The suggested cluster formation mechanism may point to means to control these behaviours that are crucial for the properties of pharmaceutical preparations.  References:[1] M. Warzecha, R. Guo, R. M. Bhardwaj, S. M. Reutzel-Edens, S. L. Price, D. Lamprou and A. J. Florence, In preparation 2017.[2] Gebauer, D., Kellermeier, M., Gale, J. D., Bergström, L. & Cölfen, H. Pre-nucleation clusters as solute precursors in crystallisation. Chem. Soc. Rev. 2014, 43, 2348 [3] Vekilov, P. G. The two-step mechanism of nucleation of crystals in solution. Nanoscale, 2010, 2, 2346

Early Onset of Kinetic Roughening due to a Finite Step Width in Hematin Crystallization

The structure of the interface of a growing crystal with its nutrient phase largely determines the growth dynamics. We demonstrate that hematin crystals, crucial for the survival of malaria parasites, transition from faceted to rough growth interfaces at increasing thermodynamic supersaturation Δμ. Contrary to theoretical predictions and previous observations, this transition occurs at moderate values of Δμ. Moreover, surface roughness varies nonmonotonically with Δμ, and the rate constant for rough growth is slower than that resulting from nucleation and spreading of layers. We attribute these unexpected behaviors to the dynamics of step growth dominated by surface diffusion and the loss of identity of nuclei separated by less than the step width w. We put forth a general criterion for the onset of kinetic roughening using w as a critical length scale.National Institutes of Health (U.S.) (Grant 1R21AI126215-01)National Science Foundation (U.S.) (Grant DMR-1710354)United States. National Aeronautics and Space Administration (Grant NNX14AD68G)United States. National Aeronautics and Space Administration (Grant NNX14AE79G)Robert A. Welch Foundation (Grant E-1794

Morphological Instability of Steps During Crystal Growth from Solution Flow

It is shown that step moving to meet solution flow can be unstable against lateral perturbations. The instability of long-wavelength perturbations occurs at values of the solution flow intensity less than some critical value depending on the step velocity. At given intensity of the solution flow, the instability comes at the step velocity exceeding a critical velocity. Decay of short-wavelength fluctuations is conditioned by the line tension of the step. The step moving along the solution flow is laterally stable at all values of the step velocity and the intensity of the solution flow. The overlapping diffusion field of the neighbour steps suppresses the lateral instability but it gives an instability of the step train against doubling of the period, i.e. neighbouring steps are attracted. The equidistant train moving to meet the solution flow is stable against the period variations.Comment: 22 pages, REVTEX (will be appeared in Journal of Crystal Growth

Study on Nucleation Kinetics of Lysozyme Crystallization

The nucleation kinetics of hen egg-white lysozyme crystallization was investigated using a hot stage cooling crystallizer and a microscope to monitor the solution crystallization process in real time. Images of crystals were continuously recorded under varied precipitant and protein concentrations. The nucleation rate was found to be higher at higher precipitant concentration, and increase monotonically with protein concentration if the precipitant concentration was held constant. Attempt was made to interpret the experimental data using classical nucleation theory. It was found that the model predictions are lower than the experimental values at low supersaturations but agree well with experimental data at high supersaturations. The trends in the experimental data suggest that two nucleation mechanisms might co-exist: heterogeneous nucleation seeming to be the dominant at low supersaturation while at higher supersaturation homogeneous nucleation seeming to play the major role

Anisotropy of the Coulomb Interaction between Folded Proteins: Consequences for Mesoscopic Aggregation of Lysozyme

AbstractToward quantitative description of protein aggregation, we develop a computationally efficient method to evaluate the potential of mean force between two folded protein molecules that allows for complete sampling of their mutual orientation. Our model is valid at moderate ionic strengths and accounts for the actual charge distribution on the surface of the molecules, the dielectric discontinuity at the protein-solvent interface, and the possibility of protonation or deprotonation of surface residues induced by the electric field due to the other protein molecule. We apply the model to the protein lysozyme, whose solutions exhibit both mesoscopic clusters of protein-rich liquid and liquid-liquid separation; the former requires that protein form complexes with typical lifetimes of approximately milliseconds. We find the electrostatic repulsion is typically lower than the prediction of the Derjaguin-Landau-Verwey-Overbeek theory. The Coulomb interaction in the lowest-energy docking configuration is nonrepulsive, despite the high positive charge on the molecules. Typical docking configurations barely involve protonation or deprotonation of surface residues. The obtained potential of mean force between folded lysozyme molecules is consistent with the location of the liquid-liquid coexistence, but produces dimers that are too short-lived for clusters to exist, suggesting lysozyme undergoes conformational changes during cluster formation

Design rules for the self-assembly of a protein crystal

Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most protein crystals are open structures stabilized by anisotropic interactions. Here, we use theory and simulation to show that assembly of one such structure is not predicted by the second virial coefficient or enhanced by the critical point. Instead, good assembly requires that the thermodynamic driving force be on the order of the thermal energy and that interactions be made as nonspecific as possible without promoting liquid-vapor phase separation.Comment: 5 pages, 4 figure

Phase diagram of model anisotropic particles with octahedral symmetry

We computed the phase diagram for a system of model anisotropic particles with six attractive patches in an octahedral arrangement. We chose to study this model for a relatively narrow value of the patch width where the lowest-energy configuration of the system is a simple cubic crystal. At this value of the patch width, there is no stable vapour-liquid phase separation, and there are three other crystalline phases in addition to the simple cubic crystal that is most stable at low pressure. Firstly, at moderate pressures, it is more favourable to form a body-centred cubic crystal, which can be viewed as two interpenetrating, and almost non-interacting, simple cubic lattices.Secondly, at high pressures and low temperatures, an orientationally ordered face-centred cubic structure becomes favourable. Finally, at high temperatures a face-centred cubic plastic crystal is the most stable solid phase.Comment: 12 pages,10 figure