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

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

Growth from Solutions: Kink dynamics, Stoichiometry, Face Kinetics and stability in turbulent flow

1. Kink dynamics. The first segment of a polygomized dislocation spiral step measured by AFM demonstrates up to 60% scattering in the critical length l*- the length when the segment starts to propagate. On orthorhombic lysozyme, this length is shorter than that the observed interkink distance. Step energy from the critical segment length based on the Gibbs-Thomson law (GTL), l* = 20(omega)alpha/(Delta)mu is several times larger than the energy from 2D nucleation rate. Here o is tine building block specific voiume, a is the step riser specific free energy, Delta(mu) is the crystallization driving force. These new data support our earlier assumption that the classical Frenkel, Burton -Cabrera-Frank concept of the abundant kink supply by fluctuations is not applicable for strongly polygonized steps. Step rate measurements on brushite confirms that statement. This is the1D nucleation of kinks that control step propagation. The GTL is valid only if l* <Dk/vk, the diffusion path of a kink that has diffusivity Dk and average growth velocity vk. This is equivalent to supersaturations sigma less than approx. alpha/2l*, where alpha is the building block size. For lysozyme, sigma much less than (1%). Conventionally used interstep distance generated by screw dislocation, 19(omega)alpha/Delta(mu) should be replaced by the very different real one, approx.4l*. 2. Stoichiometry. Kink, and thus step and face rates of a non-Kossel complex molecular monocomponent or any binary, AB, lattice was found theoretically to be proportional to 1/(zeta(sup 1/2) + zeta(sup - 1/2)), where zeta = [B]/[A] is the stoichiometry ratio in solution. The velocities reach maxima at zeta = 1. AFM studies of step rates on CaOxalate monohydrate (kidney stones) from aqueous solution was found to obey the law mentioned above. Generalization for more complex lattice will be discussed. 3. Turbulence. In agreement with theory, high precision in-situ laser interferometry of the (101) KDP crystal face shows step bunching if solution flows parallel to the step flow. The bunch height increases with the distance the bunch travels, i.e. with the face size. However, when the flow rate, u, increases, at u greater than approx. 1 m / s , the average step bunch height decreases as 1/u. The pheonomenon is attributed to the turbulent rather than laminar viscous boundary layer where diffusivity Dt = 0.5u(sub tau),y, i.e. increases linearly with the distance y from the solid face. Friction velocity, u(sub tau) approx. u(sup 7/8). Dramatically larger rate of the mass/heat transport within the turbulent, as compared to the laminar, viscous layer will be discussed

Step Bunching: Influence of Impurities and Solution Flow

Step bunching results in striations even at relatively early stages of its development and in inclusions of mother liquor at the later stages. Therefore, eliminating step bunching is crucial for high crystal perfection. At least 5 major effects causing and influencing step bunching are known: (1) Basic morphological instability of stepped interfaces. It is caused by concentration gradient in the solution normal to the face and by the redistribution of solute tangentially to the interface which redistribution enhances occasional perturbations in step density due to various types of noise; (2) Aggravation of the above basic instability by solution flowing tangentially to the face in the same directions as the steps or stabilization of equidistant step train if these flows are antiparallel; (3) Enhanced bunching at supersaturation where step velocity v increases with relative supersaturation s much faster than linear. This v(s) dependence is believed to be associated with impurities. The impurities of which adsorption time is comparable with the time needed to deposit one lattice layer may also be responsible for bunching; (4) Very intensive solution flow stabilizes growing interface even at parallel solution and step flows; (5) Macrosteps were observed to nucleate at crystal corners and edges. Numerical simulation, assuming step-step interactions via surface diffusion also show that step bunching may be induced by random step nucleation at the facet edge and by discontinuity in the step density (a ridge) somewhere in the middle of a face. The corresponding bunching patterns produce the ones observed in experiment. The nature of step bunching generated at the corners and edges and by dislocation step sources, as well as the also relative importance and interrelations between mechanisms 1-5 is not clear, both from experimental and theoretical standpoints. Furthermore, several laws controlling the evolution of existing step bunches have been suggested, though unambiguous conclusions are still missing. Addressing these issues is the major goal of the present project. The theory addressing the above problem, experimental methods, several figures which include: (1) the spatial wave numbers at which the system is neutrally stable as a function of growth velocity for linear kinetics and supersaturation for nonlinear kinetics; (2) a schematic of the experiment of lysozyme crystal growing under conditions of natural convection; (3) fluctuations in time, t, of the normal growth rate, R(t), vicinal slope, p(t) and Fourier Spectra of R(t), discussions and conclusions are presented

The low-density/high-density liquid phase transition for model globular proteins

The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and finite temperature classical Density Functional Theory calculations. We use a parametrized potential that can vary smoothly from the standard Lennard-Jones interaction characteristic of simple fluids, to the ten Wolde-Frenkel model for the effective interaction of globular proteins in solution. We find that the large excluded volume characteristic of large macromolecules such as proteins is the dominant effect in determining the liquid-vapor surface tension and nucleation properties. The variation of the range of the potential only appears important in the case of small excluded volumes such as for simple fluids. The DFT calculations are then used to study homogeneous nucleation of the high-density phase from the low-density phase including the nucleation barriers, nucleation pathways and the rate. It is found that the nucleation barriers are typically only a few $k_{B}T$ and that the nucleation rates substantially higher than would be predicted by Classical Nucleation Theory.Comment: To appear in Langmui

Quantitative plane-resolved crystal growth and dissolution kinetics by coupling in situ optical microscopy and diffusion models : the case of salicylic acid in aqueous solution

The growth and dissolution kinetics of salicylic acid crystals are investigated in situ by focusing on individual microscale crystals. From a combination of optical microscopy and finite element method (FEM) modeling, it was possible to obtain a detailed quantitative picture of dissolution and growth dynamics for individual crystal faces. The approach uses real-time in situ growth and dissolution data (crystal size and shape as a function of time) to parametrize a FEM model incorporating surface kinetics and bulk to surface diffusion, from which concentration distributions and fluxes are obtained directly. It was found that the (001) face showed strong mass transport (diffusion) controlled behavior with an average surface concentration close to the solubility value during growth and dissolution over a wide range of bulk saturation levels. The (1̅10) and (110) faces exhibited mixed mass transport/surface controlled behavior, but with a strong diffusive component. As crystals became relatively large, they tended to exhibit peculiar hollow structures in the end (001) face, observed by interferometry and optical microscopy. Such features have been reported in a number of crystals, but there has not been a satisfactory explanation for their origin. The mass transport simulations indicate that there is a large difference in flux across the crystal surface, with high values at the edge of the (001) face compared to the center, and this flux has to be redistributed across the (001) surface. As the crystal grows, the redistribution process evidently can not be maintained so that the edges grow at the expense of the center, ultimately creating high index internal structures. At later times, we postulate that these high energy faces, starved of material from solution, dissolve and the extra flux of salicylic acid causes the voids to close

Controlling crystallization and its absence: Proteins, colloids and patchy models

The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and technological importance. Much can be learnt from the exquisite control that biological systems exert over the behaviour of proteins, where protein crystallization and aggregation are generally suppressed, but where in particular instances complex crystalline assemblies can be formed that have a functional purpose. We also explore the insights that can be obtained from computational modelling, focussing on the subtle interplay between the interparticle interactions, the preferred local order and the resulting crystallization kinetics. In particular, we highlight the role played by ``frustration'', where there is an incompatibility between the preferred local order and the global crystalline order, using examples from atomic glass formers and model anisotropic particles.Comment: 11 pages, 7 figure

Role of water in Protein Aggregation and Amyloid Polymorphism

A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and simulation studies have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked. In this Account, we provide a perspective on how interactions with water affect folding landscapes of A$\beta$ monomers, A$\beta_{16-22}$ oligomer formation, and protofilament formation in a Sup35 peptide. Simulations show that the formation of aggregation-prone structures (N$^*$) similar to the structure in the fibril requires overcoming high desolvation barrier. The mechanism of protofilament formation in a polar Sup35 peptide fragment illustrates that water dramatically slows down self-assembly. Release of water trapped in the pores as water wires creates protofilament with a dry interface. Similarly, one of the main driving force for addition of a solvated monomer to a preformed fibril is the entropy gain of released water. We conclude by postulating that two-step model for protein crystallization must also hold for higher order amyloid structure formation starting from N$^*$. Multiple N$^*$ structures with varying water content results in a number of distinct water-laden polymorphic structures. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow down fibril growth rates in hydrophilic sequences.Comment: 27 pages, 4 figures; Accounts of Chemical Research, 201