Ion-activated attractive patches as a mechanism for controlled protein interactions

Nonclassical nucleation pathways in protein crystallization

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.

Phase behavior and bulk structural properties of a microphase former with anisotropic competing interactions: A density functional theory study

Using classical density functional theory, we investigate systems exhibiting interactions where a short-range anisotropic attractive force competes with a long-range spherically symmetric repulsive force. The former is modelled within Wertheim's first-order perturbation theory for patchy particles, and the repulsive part is assumed to be a Yukawa potential which is taken into account via a mean-field approximation. From previous studies of systems with spherically symmetric competing interactions, it is well known that such systems can exhibit stable bulk cluster phases (microphase separation) provided that the repulsion is sufficiently weak compared to the attraction. For the present model system, we find rich phase diagrams including both reentrant clustering and liquid-gas binodals. In particular, the model predicts inhomogeneous bulk phases at extremely low packing fractions, which cannot be observed in systems with isotropic competing interactions.

What macromolecular crystallogenesis tells us - what is needed in the future

Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.

Can the propensity of protein crystallization be increased by using systematic screening with metals?

Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization.

Formation of Dendrimer Nanoassemblies by Oligomerization-Induced Liquid-Liquid Phase Separation

Dendrimers are hyperbranched macromolecules with applications in host-guest chemistry, self-assembly, nanocatalysis, and nanomedicine. We show that dendrimer-based globular nanoparticles are formed by using dendrimer oligomerization to isothermally induce liquid-liquid phase separation (LLPS). We first determined that LLPS of aqueous mixtures of the fourth-generation amino-functionalized poly(amido amine) dendrimer is observed by lowering temperature in the presence of sodium sulfate. In relation to LLPS, we experimentally characterized the effect of salt and dendrimer concentrations on the LLPS temperature and salt-dendrimer isothermal partitioning. Our results were theoretically examined using a two-parameter thermodynamic model. We then showed that the addition of a small amount of glutaraldehyde, which leads to the formation of soluble dendrimer oligomers by chemical cross-linking, increases the LLPS temperature. This implies that a dendrimer aqueous mixture, which is initially homogeneous at room temperature and exhibits LLPS only at relatively low temperatures, can exhibit LLPS at room temperature due to dendrimer oligomerization. The high dendrimer concentration inside the nanodroplets, produced from LLPS, accelerates dendrimer cross-linking, thereby yielding stable globular nanoparticles. These nanomaterials retain the host-guest properties of the initial dendrimers, indicating potential applications as nanocatalysts, extracting agents and drug carriers. Our work provides the basis for a new approach for obtaining dendrimer-based nanoassemblies by employing low-generation dendrimers as building blocks.

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.

Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules

Artistic representation of limited valance units consisting of a soft core (in blue) and a small number of flexible bonding patches (in orange).

Two-dimensional binary mixtures of patchy particles and spherical colloids

Using Monte Carlo simulation we study two dimensional mixtures of patchy and spherically symmetric particles. Such mixtures can be synthesized experimentally by covering colloids with appropriate types of DNA strands [L. Feng, et al., Adv. Mater., 2013, 25, 2779]. We focus on finding out the ordered structures that can be formed in such systems. The type of ordered phase strongly depends on the valency, size and binding energy of the patchy particles. If the patch size is small enough, i.e. it allows only one spherically symmetric particle to be bound, the ordered structure follows either a hexagonal or a tetragonal pattern depending on the valency of the patchy particles. Moreover, we find stable quasicrystals of dodecagonal symmetry. Additional structures can be obtained if the patches are larger and the binding energy is higher. Depending on the valency of the patchy particles we find either lanes or branched structures forming polygons of the spherically symmetric particles with few patchy particles inside. For pentavalent patchy particles we find stable quasicrystals of decagonal symmetry.

Strings and stripes formed by a protein system interacting via a single-patch attraction

The phase behavior of lactoferrin has been studied as a function of concentration at a pH and ionic strength where lactoferrin is known to interact effectively via a patch-patch attraction. In contrast to isotropic attractive potentials, the directional attraction gives rise to a different phase or solution behavior. At low concentrations, the protein dimerizes. As the concentration is increased, the protein self-assembles into elongated, stripe-like structures at intermediate protein concentrations, a behavior which has been predicted for the case of attractive one-patch colloids. The stripe phase is surprisingly difficult to detect using conventional techniques, i.e. small-angle X-ray scattering, since only a small fraction of the proteins participate in the stripes combined with sedimentation due to micron-sized entities. This is circumvented by monitoring the change in the overall protein concentration by static light scattering and the stripe formation can be followed. For visualization of the structures cryo-TEM is used.

Kinetics of liquid-liquid phase separation in protein solutions exhibiting LCST phase behavior studied by time-resolved USAXS and VSANS

We study the kinetics of the liquid-liquid phase separation (LLPS) and its arrest in protein solutions exhibiting a lower critical solution temperature (LCST) phase behavior using the combination of ultra-small angle X-ray scattering (USAXS) and very-small angle neutron scattering (VSANS). We employ a previously established model system consisting of bovine serum albumin (BSA) solutions with YCl₃. We follow the phase transition from sub-second to 10⁴ s upon an off-critical temperature jump. After a temperature jump, the USAXS profiles exhibit a peak that grows in intensity and shifts to lower q values with time. Below 45 °C, the characteristic length scale (ξ) obtained from this scattering peak increases with time with a power of about 1/3 for different sample compositions. This is in good agreement with the theoretical prediction for the intermediate stage of spinodal decomposition where the growth is driven by interface tension. Above 45 °C, ξ follows initially the 1/3 power law growth, then undergoes a significant slowdown, and an arrested state is reached below the denaturation temperature of the protein. This growth kinetics may indicate that the final composition of the protein-rich phase is located close to the high density branch of the LLPS binodal when a kinetically arrested state is reached.

Size effects of solvent molecules on the phase behavior and effective interaction of colloidal systems with the bridging attraction

There has been much recent research interest towards understanding the phase behavior of colloidal systems interacting with a bridging attraction, where the small solvent particles and large solute colloidal particles can be reversibly associated with each other. These systems show interesting phase behavior compared to the more widely studied depletion attraction systems. Here, we use Baxter's two-component sticky hard sphere model with a Percus-Yevick closure to solve the Ornstein-Zernike equation and study the size effect on colloidal systems with bridging attractions. The spinodal decomposition regions, percolation transition boundaries and binodal regions are systematically investigated as a function of the relative size of the small solvent and large solute particles as well as the attraction strength between the small and large particles. In the phase space determined by the concentrations of small and large particles, the spinodal and binodal regions form isolated islands. The locations and shapes of the spinodal and binodal regions sensitively depend on the relative size of the small and large particles and the attraction strength between them. The percolation region shrinks by decreasing the size ratio, while the binodal region slightly expands with the decrease of the size ratio. Our results are very important in understanding the phase behavior for a bridging attraction colloidal system, a model system that provides insight into oppositely charged colloidal systems, protein phase behavior, and colloidal gelation mechanisms.

Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding

Background

Human lactoferrin is an iron-binding protein of the innate immune system consisting of two connected lobes, each with a binding site located in a cleft. The clefts in each lobe undergo a hinge movement from open to close when Fe³⁺ is present in the solution and can be bound. The binding mechanism was assumed to relate on thermal domain fluctuations of the cleft domains prior to binding. We used Small Angle Neutron Scattering and Neutron Spin Echo Spectroscopy to determine the lactoferrin structure and domain dynamics in solution.

Results

When Fe³⁺ is present in solution interparticle interactions change from repulsive to attractive in conjunction with emerging metas aggregates, which are not observed without Fe³⁺. The protein form factor shows the expected change due to lobe closing if Fe³⁺ is present. The dominating motions of internal domain dynamics with relaxation times in the 30–50 ns range show strong bending and stretching modes with a steric suppressed torsion, but are almost independent of the cleft conformation. Thermally driven cleft closing motions of relevant amplitude are not observed if the cleft is open.

Conclusion

The Fe³⁺ binding mechanism is not related to thermal equilibrium fluctuations closing the cleft. A likely explanation may be that upon entering the cleft the iron ion first binds weakly which destabilizes and softens the hinge region and enables large fluctuations that then close the cleft resulting in the final formation of the stable iron binding site and, at the same time, stable closed conformation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13628-016-0032-3) contains supplementary material, which is available to authorized users.

Gelation transitions of colloidal systems with bridging attractions

Gelation transitions in a colloidal system, where there is a strong reversible attraction between small, soft microgels and large, hard spheres, are systematically investigated. Different from widely studied depletion attraction systems that are also two-component systems, the strong attraction between small solvent and large solute particles introduces bridging attractions between large solute particles. We conclusively demonstrate that the formation of physical gels at the intermediate volume fraction of our bridging attraction system follows more closely with the percolation line that is in stark contrast to what is observed in depletion attraction systems, where the gelation transition is related with the frustrated spinodal separation, not a purely kinetic phenomenon. Our results introduce a different way to control gelation transitions in spherical colloidal systems, and imply that people need to be prudent when generalizing the physical picture of the gelation transitions obtained from systems with different origins of effective attraction as the solvent molecule may play important roles.

Cation-Induced Hydration Effects Cause Lower Critical Solution Temperature Behavior in Protein Solutions

The phase behavior of protein solutions is important for numerous phenomena in biology and soft matter. We report a lower critical solution temperature (LCST) phase behavior of aqueous solutions of a globular protein induced by multivalent metal ions around physiological temperatures. The LCST behavior manifests itself via a liquid-liquid phase separation of the protein-salt solution upon heating. Isothermal titration calorimetry and zeta-potential measurements indicate that here cation-protein binding is an endothermic, entropy-driven process. We offer a mechanistic explanation of the LCST. First, cations bind to protein surface groups driven by entropy changes of hydration water. Second, the bound cations bridge to other protein molecules, inducing an entropy-driven attraction causing the LCST. Our findings have general implications for condensation, LCST, and hydration behavior of (bio)polymer solutions as well as the understanding of biological effects of (heavy) metal ions and their hydration.

Temperature (de)activated patchy colloidal particles

We present a new model of patchy particles in which the interaction sites can be activated or deactivated by varying the temperature of the system. We study the thermodynamics of the system by means of Wertheim's first order perturbation theory, and use Flory-Stockmayer theory of polymerization to analyse the percolation threshold. We find a very rich phase behaviour including lower critical points and reentrant percolation.

Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution

The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs = 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.

Anisotropic protein-protein interactions due to ion binding

Self-association of proteins is strongly affected by long-range electrostatic interactions caused by equilibrium adsorption of small ions such as protons and multivalent metals. By affecting the molecular net charge, solution pH is thus a widely used parameter to tune stability and phase behavior of proteins. We here review recent studies where the charge distribution is perturbed not only by protons, but also by other binding ions, leading to a rich and inherently anisotropic charge distribution. Focus is on coarse grained simulation techniques, coupled to experiments of protein-protein interaction at varying salt and pH conditions. Finally, and with future bio-colloidal models in mind, we discuss the validity of coarse graining charge anisotropy using electric multipoles.

On the question of two-step nucleation in protein crystallization

We report a real-time study on protein crystallization in the presence of multivalent salts using small angle X-ray scattering (SAXS) and optical microscopy, focusing particularly on the nucleation mechanism as well as on the role of the metastable intermediate phase (MIP). Using bovine beta-lactoglobulin as a model system in the presence of the divalent salt CdCl2, we have monitored the early stage of crystallization kinetics which demonstrates a two-step nucleation mechanism: protein aggregates form a MIP, which is followed by the nucleation of crystals within the MIP. Here we focus on characterizing and tuning the structure of the MIP using salt and the related effects on the two-step nucleation kinetics. The results suggest that increasing the salt concentration near the transition zone pseudo-c** enhances the energy barrier for both MIPs and crystal nucleation, leading to slow growth. The structural evolution of the MIP and its effect on subsequent nucleation is discussed based on the growth kinetics. The observed kinetics can be well described, using a rate-equation model based on a clear physical two-step picture. This real-time study not only provides evidence for a two-step nucleation process for protein crystallization, but also elucidates the role and the structural signature of the MIPs in the nonclassical process of protein crystallization.

How fluorescent labelling alters the solution behaviour of proteins

The impact of adding a fluorescent dye to a protein is examined using protein phase diagrams and numerical simulations. The addition of the dye is the equivalent of adding a large attractive patch to the surface of the protein, which results in significant changes to the protein solution behaviour.