Novel approach to controlled protein crystallization through ligandation of yttrium cations

Electric field-induced control of protein crystal morphology

In a previous study (D. Ray, et al., J. Phys. Chem. Lett., 2024, 15, 8108-8113), we found that an alternating electric field considerably affects the location of the crystallization boundary and the liquid-liquid phase separation line as well as crystallization kinetics in lysozyme solutions containing sodium thiocyanate (NaSCN). The present study extends this work by investigating the influence of the same electric field on the microscopic appearance of lysozyme crystals as they form from a supersaturated solution. We observe a variety of distinct crystal morphologies, which we classify as single- and multi-arm crystals, flower-like crystal structures, whiskers, and sea-urchin crystals. Crystal morphologies exhibit significant variations with changes in protein and salt concentrations, and the electric field strongly alters the morphology-state diagram in the protein-versus-salt concentration plane. This alteration is likely due to the field effect on protein-protein interactions. We believe the effect is mediated by the field-enhanced adsorption of SCN- ions to the surface of lysozyme, ultimately driving the observed changes in crystallization behavior. These findings offer insights into how electric fields can be used to control crystal formation and morphology in protein systems.

Binding a C12-appended rhenium-(Bispyridine) carbonyl complex to β-Lactoglobulin: Effects of pH & cysteine modification on calyx affinity

Due to its commercial availability and well-defined structure, the interaction between bovine protein β-lactoglobulin (βLG) and a wide variety of non-native ligands - including transition metal complexes - has been explored, but its application as an artificial metalloenzyme scaffold is limited. This protein is hypothesized to transport fatty acids and other nutrients during juvenile development, and it binds hydrophobic ligands inside a binding pocket constructed upon an 8-stranded β-barrel, called the 'calyx'. Herein, we compare the binding behavior of two rhenium(anthracene-bispyridine) ('Anth-py2') tricarbonyl complexes, one with a 12‑carbon chain appended to the ligand scaffold ('C12Anth-py2') to βLG. We investigate (i) how calyx-binding specificity is affected by pH (which controls βLG structure at the entrance to the calyx) and (ii) modification of a free cysteine residue located in a putative second binding site of βLG (SMe-βLG). The binding affinities of [Re(C12Anth-py2)(CO)3(solv)]+ (ReC12) and [Re(Anth-py2)(CO)3(solv)]+ (ReCH) for βLG at pH 7.3 were similar at 36 ± 2 μM and 43 ± 1 μM, respectively. The KD of ReC12 decreased by ∼13 μM at pH 6.1 due to a well-known conformational change (Tanford transition) at the entrance to the calyx; the KD value was not significantly affected by Cys121 modification, indicating β-barrel calyx binding specificity. In contrast, ReCH experienced a decrease in KD in response to blocking the second binding (SMe-βLG), but was also unaffected by pH. The results show an increase in binding affinity and specificity as a result of targeted ligand design and utilization of native protein characteristics. The findings will inform and improve the design of future βLG-derived ArMs.

Effective patchiness from critical points of a coarse-grained protein model with explicit shape and charge anisotropy

Colloidal model systems are successful in rationalizing emergent phenomena like aggregation, rheology and phase behaviour of protein solutions. Colloidal theory in conjunction with isotropic interaction models is often employed to estimate the stability of such solutions. In particular, a universal criterion for the reduced second virial coefficient at the critical point is frequently invoked which is based on the behavior of short-range attractive fluids (Noro-Frenkel rule, ). However, if anisotropic models for the protein-protein interaction are considered, e.g. the Kern-Frenkel (KF) patchy particle model, the value of the criterion is shifted to lower values and explicitly depends on the number of patches. If an explicit shape anisotropy is considered, as e.g. in a coarse-grained protein model, the normalization of becomes ambiguous to some extent, as no unique exclusion volume can be defined anymore. Here, we investigate a low-resolution, coarse-grained model for the globular protein bovine serum albumin (BSA) and study effects of charge-anisotropy on the phase diagram (determined by simulations) at the isoelectric point. We present methods of assigning an "effective patchiness" to our protein model by comparing its critical properties to the KF model. We find that doubling the native charges increases the critical temperature Tc by ≈14% and that our BSA model can be compared to a 3 to 5 patch KF model. Finally, we argue that applying existing criteria from colloidal theory should be done with care, due to multiple, physically plausible ways of how to assign effective diameters to shape-anisotropic models.

Formation of Supplementary Metal-Binding Centers in Proteins under Stress Conditions

In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.

Effective interactions and phase behavior of protein solutions in the presence of hexamine cobalt(III) chloride

It is well established that deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) exhibit a reentrant condensation (RC) phase behavior in the presence of the trivalent hexamine cobalt(III) cations (Hac) which can be important for their packing and folding. A similar behavior can be observed for negatively charged globular proteins in the presence of trivalent metal cations, such as Y3+ or La3+. This phase behavior is mainly driven by charge inversion upon an increasing salt concentration for a fixed protein concentration (cp). However, as Hac exhibits structural differences compared to other multivalent metal cations, with six ammonia ligands (NH3) covalently bonded to the central cobalt atom, it is not clear that Hac can induce a similar phase behavior for proteins. In this work, we systematically investigate whether negatively charged globular proteins β-lactoglobulin (BLG), bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) feature Hac-induced RC. Effective protein-protein interactions were investigated by small-angle X-ray scattering. The reduced second virial coefficient (B2/B2HS) was obtained as a function of salt concentration. The virial coefficient analysis performed confirms the reentrant interaction (RI) behavior for BLG without actually inducing RC, given the insufficient strengths of the interactions for the latter to occur. In contrast, the strength of attraction for BSA, HSA and OVA are too weak to show RC. Model free analysis of the inverse intensity [Formula: see text] also supports this finding. Looking at different q-range by employing static (SLS) and dynamic light scattering experiments, the presence of RI behavior can be confirmed. The results are further discussed in view of metal cation binding sites in nucleic acids (DNA and RNA), where Hac induced RC phase behavior.

Thermo-Resistive Phase Behavior of Trivalent Ion-Induced Microscopic Protein-Rich Phases: Correlating with Ion-Specific Protein Hydration

Proteins, in the presence of trivalent cations, exhibit intriguing phase behavior which is contrasting compared to mono- and divalent cations. At room temperature (RT), trivalent cations induce microscopic liquid-liquid phase separation (LLPS) in which a protein-rich phase coexists with a dilute phase. The critical solution temperature related phenomena in these complex fluids are well studied; however, such studies have mostly been restricted below the denaturation temperature (T_M) of the protein(s) involved. Here, we probe the phase behavior of bovine serum albumin (BSA) incubated at 70 °C (>T_M) in the presence of Na⁺, Mg²⁺, La³⁺, Y³⁺, and Ho³⁺ ions. BSA in the presence of mono- and bivalent ions forms an intense gel phase at 70 °C; however, the trivalent salts offer remarkable thermal resistivity and retain the fluid LLPS phase. We determine the microscopic phase behavior using differential interference contrast optical microscopy, which shows that the LLPS droplet structures in the M³⁺ ion-containing protein solutions prevail upon heating, whereas Mg²⁺ forms composed cross-linking gelation upon thermal incubation. We probe the interior environment of the protein aggregates by ps-resolved fluorescence anisotropy measurements using 8-anilino-1-naphthalenesulfonic acid (ANS) as an extrinsic fluorophore. It reveals that while the LLPS phase retains the rotational time constants upon heating, in the case of gelation, the immediate environment of ANS gets significantly perturbed. We investigate the explicit protein hydration at RT as well as at T > T_M using the ATR THz-FTIR (1.5-22.5 THz) spectroscopy technique and found that hydration shows strong ion specificity and correlates the phase transition behavior.

Nonspecific Binding of Adenosine Tripolyphosphate and Tripolyphosphate Modulates the Phase Behavior of Lysozyme

Adenosine tripolyphosphate (ATP) is a small polyvalent anion that has recently been shown to interact with proteins and have a major impact on assembly processes involved in biomolecular condensate formation and protein aggregation. However, the nature of non-specific protein-ATP interactions and their effects on protein solubility are largely unknown. Here, the binding of ATP to the globular model protein is characterized in detail using X-ray crystallography and nuclear magnetic resonance (NMR). Using NMR, we identified six ATP binding sites on the lysozyme surface, with one known high-affinity nucleic acid binding site and five non-specific previously unknown sites with millimolar affinities that also bind tripolyphosphate (TPP). ATP binding occurs primarily through the polyphosphate moiety, which was confirmed by the X-ray structure of the lysozyme-ATP complex. Importantly, ATP binds preferentially to arginine over lysine in non-specific binding sites. ATP and TPP have similar effects on solution-phase protein-protein interactions. At low salt concentrations, ion binding to lysozyme causes precipitation, while at higher salt concentrations, redissolution occurs. The addition of an equimolar concentration of magnesium to ATP does not alter ATP binding affinities but prevents lysozyme precipitation. These findings have important implications for both protein crystallization and cell biology. Crystallization occurs readily in ATP solutions outside the well-established crystallization window. In the context of cell biology, the findings suggest that ATP binds non-specifically to folded proteins in physiological conditions. Based on the nature of the binding sites identified by NMR, we propose several mechanisms for how ATP binding can prevent the aggregation of natively folded proteins.

Trivalent cation-induced phase separation in proteins: ion specific contribution in hydration also counts

Multivalent (specifically trivalent) metal ions are known to induce microscopic phase separation (commonly termed as liquid-liquid phase separation (LLPS)) in negatively charged globular proteins even at ambient temperatures, the process being mostly driven by protein charge neutralization followed by aggregation. Recent simulation studies have revealed that such self-aggregation of proteins is entropy driven; however, it is associated with a solvation effect, which could as well be different from the usual notion of hydrophobic hydration. In this contribution we have experimentally probed the explicit change in hydration associated with ion-induced LLPS formation of a globular protein bovine serum albumin (BSA) at ambient temperature using FIR-THz FTIR spectroscopy (50-750 cm^-1; 1.5-22.5 THz). We have used ions of different charges: Na⁺, K⁺, Ca²⁺, Mg²⁺, La³⁺, Y³⁺, Ho³⁺ and Al³⁺. We found that all the trivalent ions induce LLPS; the formation of large aggregates has been evidenced from dynamic light scattering (DLS) measurements, but without perturbing the protein structure as confirmed from circular dichroism (CD) measurements. From the frequency dependent absorption coefficient (α(ν)) measurements in the THz frequency domain we estimate the various stretching/vibrational modes of water and we found that ions, forming LLPS, produce definite perturbation in the overall hydration, the extent of which is ion specific, invoking the definite role of hydrophilic (electrostatic) hydration of ions in the observed LLPS process.

Role of entropy in determining the phase behavior of protein solutions induced by multivalent ions

Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex hydration effects that result in a net entropy gain upon phase separation. To decipher the underlying molecular mechanism, we use all-atom molecular dynamics simulations along with the two-phase thermodynamic method for entropy calculation. Based on simulations of a single BSA protein in various salt solutions (NaCl, CaCl₂, MgCl₂, and YCl₃) at temperatures (T) ranging 283-323 K, we find that the cation-protein binding affinity increases with T, reflecting its thermodynamic driving force to be entropic in origin. We show that in the cation binding process, many tightly bound water molecules from the solvation shells of a cation and the protein are released to the bulk, resulting in entropy gain. To rationalize the LCST behavior, we calculate the ζ-potential that shows charge inversion of the protein for solutions containing multivalent ions. The ζ-potential increases with T. Performing simulations of two BSA proteins, we demonstrate that the protein-protein binding is mediated by multiple cation bridges and involves similar dehydration effects that cause a large entropy gain which more than compensates for rotational and translational entropy losses of the proteins. Thus, the LCST behavior is entropy-driven, but the associated solvation effects are markedly different from hydrophobic hydration. Our findings have direct implications for tuning the phase behavior of biological and soft-matter systems, e.g., protein condensation and crystallization.

Bulk phase behaviour vs interface adsorption: Effects of anions and isotopes on β-lactoglobulin (BLG) interactions

HYPOTHESIS

Protein adsorption is highly relevant in numerous applications ranging from food processing to medical implants. In this context, it is important to gain a deeper understanding of protein-protein and protein-surface interactions. Thus, the focus of this investigation is on the interplay of bulk properties and surface properties on protein adsorption. It was hypothesised that the type of solvent and ions in solution should significantly influence the protein's bulk and interface behaviour, which has been observed in literature and previous work for other net negatively charged, globular proteins such as bovine serum albumin (BSA).

EXPERIMENTS

The phase behaviour of β-lactoglobulin (BLG) with lanthanum chloride (LaCl₃) and iodide (LaI₃) in normal water H₂O(l) and heavy water (D₂O(l)) was established via optical microscopy and ultraviolet-visible spectroscopy. The formation of an adsorption layer and its properties such as thickness, density, structure, and hydration was investigated via neutron reflectivity, quartz-crystal microbalance with dissipation, and infra-red measurements.

FINDINGS

β-lactoglobulin does not show significant anion-induced or isotope-induced effects - neither in bulk nor at the solid-liquid interface, which deviates strongly from the behaviour of bovine serum albumin. We also provide a comprehensive discussion and comparison of protein-specific bulk and interface behaviour between bovine serum albumin and β-lactoglobulin dependent on anion, cation, solvent, and substrate properties. These findings pave the way for understanding the transition from adsorption to crystallisation.

Decorated networks of native proteins: nanomaterials with tunable mesoscopic domain size

Natural and artificial proteins with designer properties and functionalities offer unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit this potential we need to design the system such that assembly results in desired architecture forms while avoiding denaturation and therefore retaining protein functionality. Here we address this challenge with a model system of fluorescent proteins. By manipulating self-assembly using techniques inspired by soft matter where interactions between the components are controlled to yield the desired structure, we have developed a methodology to assemble networks of proteins of one species which we can decorate with another, whose coverage we can tune. Consequently, the interfaces between domains of each component can also be tuned, with potential applications for example in energy - or electron - transfer. Our model system of eGFP and mCherry with tuneable interactions reveals control over domain sizes in the resulting networks.

Solvent effect for an effective attraction between like-charged macroions immersed in an electrolyte solution: The intensification mechanism of the effective attraction caused by the translational motion of solvent particles

The effective interaction between macroanions immersed in an electrolyte solution was calculated using an integral equation theory of liquids to study the solvent granularity effect on the effective attraction mediated by cations. Explicit and implicit solvent models were examined. The effective attraction for the explicit solvent model was found to be stronger than that for the implicit solvent model. This solvent effect was remarkably enhanced only when the effective attraction between macroanions was strong; this means that the solvent effect is not a usual excluded volume effect. The intensification mechanism of the attraction by the solvent granularity is analyzed in the present study, and an indirect mechanism is proposed.

Bulk Phase Behavior vs Interface Adsorption: Specific Multivalent Cation and Anion Effects on BSA Interactions

Proteins are ubiquitous and play a critical role in many areas from living organisms to protein microchips. In humans, serum albumin has a prominent role in the foreign body response since it is the first protein which will interact with, e.g., an implant or stent. In this study, we focused on the influence of salts (i.e., different cations (Y³⁺, La³⁺) and anions (Cl^-, I^-) on bovine serum albumin (BSA) in terms of its bulk behavior as well as the role of charges for protein adsorption at the solid-liquid interface in order to understand and control the underlying molecular mechanisms and interactions. This is part of our group's effort to gain a deeper understanding of protein-protein and protein-surface interactions in the presence of multivalent ions. In the bulk, we established two new phase diagrams and found not only multivalent cation-triggered phase transitions, but also a dependence of the protein behavior on the type of anion. The attractive interactions between proteins were observed to increase from Cl^- < NO₃^- < I^-, resulting in iodide preventing re-entrant condensation and promoting liquid-liquid phase separation in bulk. Using ellipsometry and a quartz-crystal microbalance with dissipation (QCM-D), we obtained insight into the growth of the protein adsorption layer. Importantly, we found that phase transitions at the substrate can be triggered by certain interface properties, whether they exist in the bulk solution or not. Through the use of a hydrophilic, negatively charged surface (native silica), the direct binding of anions to the interface was prevented. Interestingly, this led to re-entrant adsorption even in the absence of re-entrant condensation in bulk. However, the overall amount of adsorbed protein was enhanced through stronger attractive protein-protein interactions in the presence of iodide salts. These findings illustrate how carefully chosen surface properties and salts can directly steer the binding of anions and cations, which guide protein behavior, thus paving the way for specific/triggered protein-protein, protein-salt, and protein-surface interactions.

Multivalent ions and biomolecules: Attempting a comprehensive perspective

Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.

Unification of lower and upper critical solution temperature phase behavior of globular protein solutions in the presence of multivalent cations

In globular protein systems, upper critical solution temperature (UCST) behavior is common, but lower critical solution temperature (LCST) phase transitions are rare. In addition, the temperature sensitivity of such systems is usually difficult to tune. Here we demonstrate that the charge state of globular proteins in aqueous solutions can alter their temperature-dependent phase behavior. We show a universal way to tune the effective protein interactions and induce both UCST and LCST-type transitions in the system using trivalent salts. We provide a phase diagram identifying LCST and UCST regimes as a function of protein and salt concentrations. We further propose a model based on an entropy-driven cation binding mechanism to explain the experimental observations.

Model for Counterion Binding and Charge Reversal on Protein Surfaces

The structural stability and solubility of proteins in liquid therapeutic formulations is important, especially since new generations of therapeutics are designed for efficacy before consideration of stability. We introduce an electrostatic binding model to measure the net charge of proteins with bound ions in solution. The electrostatic potential on a protein surface is used to separately group together acidic and basic amino acids into patches, which are then iteratively bound with oppositely charged counterions. This model is aimed toward formulation chemists for initial screening of a range of conditions prior to lab-work. Computed results compare well with experimental zeta potential measurements from the literature covering a range of solution conditions. Importantly, the binding model reproduces the charge reversal phenomenon that is observed with polyvalent ion binding to proteins and its dependence on ion charge and concentration. Intriguingly, protein sequence can be used to give similarly good agreement with experiment as protein structure, interpreted as resulting from the close proximity of charged side chains on a protein surface. Further, application of the model to human proteins suggests that polyanion binding and overcharging, including charge reversal for cationic proteins, is a general feature. These results add to evidence that addition of polyanions to protein formulations could be a general mechanism for modulating solution stability.

Specific Ion Effects of Trivalent Cations on the Structure and Charging State of β-Lactoglobulin Adsorption Layers

The properties of proteins at interfaces are important to many processes as well as in soft matter materials such as aqueous foam. Particularly, the protein interfacial behavior is strongly linked to different factors like the solution pH or the presence of electrolytes. Here, the nature of the electrolyte ions can significantly modify the interfacial properties of proteins. Therefore, molecular level studies on interfacial structures and charging states are needed. In this work, we addressed the effects of Y³⁺ and Nd³⁺ cations on the adsorption of the whey protein β-lactoglobulin (BLG) at air-water interfaces as the function of electrolyte concentration. Both cations caused very similar but dramatic changes at the interface and in the bulk solution. Here, measurements of the electrophoretic mobility and with vibrational sum-frequency generation (SFG) spectroscopy were applied and consistently showed a reversal of the BLG net charge at remarkably low ion concentrations of 30 (bulk) and 40 (interface) μM of Y³⁺ or Nd³⁺ for a BLG concentration of 15 μM. SFG spectra of carboxylate stretching vibrations from Asp or Glu residues of interfacial BLG showed significant changes in the resonance frequency, which we associate to specific and efficient binding of Y³⁺ or Nd³⁺ ions to the proteins carboxylate groups. Characteristic reentrant condensation for BLG moieties with bound trivalent ions was found in a broad concentration range around the point of zero net charge. The highest colloidal stability of BLG was found for ion concentrations <20 μM and >50 μM. Investigations on macroscopic foams from BLG solutions revealed the existence of structure-property relations between the interfacial charging state and the foam stability. In fact, a minimum in foam stability at 20 μM ion concentration was found when the interfacial net charge was negligible. At this concentration, we propose that the persistent BLG molecules and weakly charged BLG aggregates drive foam stability, while outside the bulk reentrant zone the electrostatic disjoining pressure inside foam lamellae dominates foam stability. Our results provide new information on the charge reversal at the liquid-gas interface of protein/ion dispersions. Therefore, we see our findings as an important step in the clarification of reentrant condensation effects at interfaces and their relevance to foam stability.

Phase-Separation Kinetics in Protein-Salt Mixtures with Compositionally Tuned Interactions

Liquid-liquid phase separation (LLPS) in protein systems is relevant for many phenomena, from protein condensation diseases to subcellular organization to possible pathways toward protein crystallization. Understanding and controlling LLPS in proteins is therefore highly relevant for various areas of (biological) soft matter research. Solutions of the protein bovine serum albumin (BSA) have been shown to have a lower critical solution temperature-LLPS (LCST-LLPS) induceable by multivalent salts. Importantly, the nature of the multivalent cation used influences the LCST-LLPS in such systems. Here, we present a systematic ultrasmall-angle X-ray scattering investigation of the kinetics of LCST-LLPS of BSA in the presence of different mixtures of HoCl₃ and LaCl₃, resulting in different effective interprotein attraction strengths. We monitor the characteristic length scales ξ( t, T_fin) after inducing LLPS by subjecting the respective systems to temperature jumps in their liquid-liquid coexistence regions. With increasing interprotein attraction and increasing T_fin, we observe an increasing deviation from the growth law of ξ ∼ t^1/3 and an increased trend toward arrest. We thus establish a multidimensional method to tune phase transitions in our systems. Our findings help shed light on general questions regarding LLPS and the tunability of its kinetics in both proteins and colloidal systems.

Controlling Phase Separation of Lysozyme with Polyvalent Anions

The ability of polyvalent anions to influence protein-protein interactions and protein net charge was investigated through solubility and turbidity experiments, determination of osmotic second virial coefficients ( B₂₂), and ζ-potential values for lysozyme solutions.  B₂₂ values showed that all anions reduce protein-protein repulsion between positively charged lysozyme molecules, and those anions with higher net valencies are more effective. The polyvalent anions pyrophosphate and tripolyphosphate were observed to induce protein reentrant condensation, which has been previously observed with negatively charged proteins in the presence of trivalent cations. Reentrant condensation is a phenomenon in which low concentrations of polyvalent ions induce protein precipitation, but further increasing polyvalent ion concentration causes the protein precipitate to resolubilize. Interestingly, citrate does not induce lysozyme reentrant condensation despite having a similar charge, size, and shape to pyrophosphate. We observe qualitative differences in protein behavior when compared against negatively charged proteins in solutions of trivalent cations. The polyphosphate ions induce a much stronger protein-protein attraction, which correlates with the occurrence of a liquid-gel transition that replaces the liquid-liquid transition observed with trivalent cations. The results indicate that solutions of polyphosphate ions provide a model system for exploring the link between the protein-phase diagram and model interaction potentials and also highlight the importance that ion-specific effects can have on protein solubility.

Reentrant Phase Behavior in Protein Solutions Induced by Multivalent Salts: Strong Effect of Anions Cl- Versus NO3

In this work, the effects of the two anions Cl^- and NO₃^- on the phase behavior of bovine serum albumin (BSA) in solution with trivalent salts are compared systematically. In the presence of trivalent metal salts, negatively charged proteins such as BSA in solution undergo a reentrant condensation (RC) phase behavior, which has been established for several proteins with chlorides of trivalent salts. Here, we show that replacing Cl^- by NO₃^- leads to a marked change in the phase behavior. The effect is investigated for the two different cations Y³⁺ and La³⁺. The salts are thus YCl₃, Y(NO₃)₃, LaCl₃, and La(NO₃)₃. The experimental phase behavior shows that while the chloride salts induce both liquid-liquid phase separation (LLPS) and RC, the nitrate salts also induce LLPS, but RC becomes partial with La(NO₃)₃ and disappears with Y(NO₃)₃. The observed phase behavior is rationalized by effective protein-protein interactions which are characterized using small-angle X-ray scattering. The results based on the reduced second virial coefficients B₂/ B₂^HS and 1/ I( q → 0) demonstrate that the NO₃^- salts induce a stronger attraction than the Cl^- salts. Overall, the effective attraction, the width of the condensed regime in the RC phase diagram, and the nature of LLPS follow the order LaCl₃ < YCl₃ < La(NO₃)₃ < Y(NO₃)₃. Despite the decisive role of cations in RC phase behavior, isothermal titration calorimetry measurements indicate that replacing anions does not significantly influence the cation binding to proteins. The experimental results observed are discussed based on an "enhanced Hofmeister effect" including electrostatic and hydrophobic interactions between protein-cation complexes.

Tuning phase transitions of aqueous protein solutions by multivalent cations

In the presence of trivalent cations, negatively charged globular proteins show a rich phase behaviour including reentrant condensation, crystallisation, clustering and lower critical solution temperature metastable liquid-liquid phase separation (LCST-LLPS). Here, we present a systematic study on how different multivalent cations can be employed to tune the interactions and the associated phase behaviour of proteins. We focus our investigations on the protein bovine serum albumin (BSA) in the presence of HoCl3, LaCl3 and YCl3. Using UV-Vis spectroscopy and small-angle X-ray scattering (SAXS), we find that the interprotein attraction induced by Ho3+ is very strong, while the one induced by La3+ is comparatively weak when comparing the data to BSA-Y3+ systems based on our previous work. Using zeta potential and isothermal titration calorimetry (ITC) measurements, we establish different binding affinities of cations to BSA with Ho3+ having the highest one. We propose that a combination of different cation features such as radius, polarisability and in particular hydration effects determine the protein-protein interaction induced by these cations. Our findings imply that subtle differences in cation properties can be a sensitive tool to fine-tune protein-protein interactions and phase behaviour in solution.

Two time scales for self and collective diffusion near the critical point in a simple patchy model for proteins with floating bonds

Using dynamic Monte Carlo and Brownian dynamics, we investigate a floating bond model in which particles can bind through mobile bonds. The maximum number of bonds (here fixed to 4) can be tuned by appropriately choosing the repulsive, nonadditive interactions among bonds and particles. We compute the static and dynamic structure factor (intermediate scattering function) in the vicinity of the gas-liquid critical point. The static structure exhibits a weak tetrahedral network character. The intermediate scattering function shows a temporal decay deviating from a single exponential, which can be described by a double exponential decay where the two time scales differ approximately by one order of magnitude. This time scale separation is robust over a range of wave numbers. The analysis of clusters in real space indicates the formation of noncompact clusters and shows a considerable stretch in the instantaneous size distribution when approaching the critical point. The average time evolution of the largest subcluster of given initial clusters with 10 or more particles also shows a double exponential decay. The observation of two time scales in the intermediate scattering function at low packing fractions is consistent with similar findings in globular protein solutions with trivalent metal ions that act as bonds between proteins.

Effective potential between negatively charged patches on acidic proteins immersed in various electrolyte solutions

Effective interactions between O-sized anions in various electrolyte solutions were calculated by using the integral equation theory with some simple models. The results indicated that only multivalent cations mediated a strong effective attraction between O-sized anions at a certain concentration. The effective interaction turned from repulsive to attractive as the electrolyte concentration increased, and the effective attraction decreased when more electrolyte was added. Moreover, the effective interactions between O-sized anions in the electrolyte solution did not present a long repulsive tail, although the effective attraction caused by the divalent cations appeared. By contrast, the effective attraction mediated by monovalent cations and the reentrant behavior did not appear and the effective interaction was basically repulsive. These behaviors agree with the experimental results for reentrant condensation of acidic proteins in various electrolyte solutions. The calculated results suggest that the dissociated carboxylic acidic groups on the proteins form attractive patches between proteins under certain concentration conditions.

Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands

The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.

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.

The potential of hexatungstotellurate(VI) to induce a significant entropic gain during protein crystallization

The limiting factor in protein crystallography is still the production of high-quality crystals. In this regard, the authors have recently introduced hexatungstotellurate(VI) (TEW) as a new crystallization additive, which proved to be successful within the liquid-liquid phase separation (LLPS) zone. Presented here are comparative crystal structure analyses revealing that protein-TEW binding not only induces and stabilizes crystal contacts, but also exhibits a significant impact on the solvent-driven crystallization entropy, which is the driving force for the crystallization process. Upon the formation of TEW-mediated protein-protein contacts, the release of water molecules from the hydration shells of both molecules, i.e. TEW and the protein, causes a reduced solvent-accessible surface area, leading to a significant gain in solvent entropy. Based on the crystal structures of aurone synthase (in the presence and absence of TEW), insights have also been provided into the formation of a metastable LLPS, which is caused by the formation of protein clusters, representing an ideal starting point in protein crystallization. The results strongly encourage the classification of TEW as a valuable crystallization additive.

An Anionic Surfactant on an Anionic Substrate: Monovalent Cation Binding

Neutron reflectometry has been used to study the adsorption of the anionic surfactant bis(2-ethylhexyl) sulfosuccinate cesium salt on the anionic surface of mica. Evidence of significant adsorption is reported. The adsorption is reversible and changes little with pH. This unexpected adsorption behavior of an anionic molecule on an anionic surface is discussed in terms of recent models for surfactant adsorption such as cation bridging, where adsorption has been reported with the divalent ion calcium but not previously observed with monovalent ions.

Steering patchy particles using multivalent electrolytes

Proteins and many recently designed colloids can be regarded as patchy particles where directional interactions strongly influence and govern assembly behavior. Using explicit ion implicit solvent Metropolis Monte Carlo simulations, we investigate spherical model particles, carrying both charge and electric patches, in dilute aqueous 1 : 1, 1 : 3, and 3 : 1 electrolyte solutions. Striking differences in pair interaction free energies and orientational correlations are induced by three different salts which are discussed and rationalized in terms of ion-binding to surface groups, ion-ion correlations, and double layer forces. These findings suggest a general strategy where directional, intermolecular interactions can be invoked and tuned via small amounts of a carefully chosen electrolyte.

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.

Anomalous Protein-Protein Interactions in Multivalent Salt Solution

The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.

A survey of the different roles of polyoxometalates in their interaction with amino acids, peptides and proteins

This perspective provides a comprehensive description of the different roles of POMs in their interaction with relevant biological molecules.

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.

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.

The MORPHEUS II protein crystallization screen

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

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.

Ion-specific control of the self-assembly dynamics of a nanostructured protein lattice

Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca(2+). These diagrams revealed a localized region of optimum yield of nanosheets at intermediate Ca(2+) concentration. Replacement of Mg(2+) or Ba(2+) for Ca(2+) indicates that Ca(2+) acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca(2+) bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. Our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.

Real-time observation of nonclassical protein crystallization kinetics

We present a real-time study of protein crystallization of bovine β-lactoglobulin in the presence of CdCl(2) using small-angle X-ray scattering and optical microscopy. From observing the crystallization kinetics, we propose the following multistep crystallization mechanism that is consistent with our data. In the first step, an intermediate phase is formed, followed by the nucleation of crystals within the intermediate phase. During this period, the number of crystals increases with time, but the crystal growth is slowed down by the surrounding dense intermediate phase due to the low mobility. In the next step, the intermediate phase is consumed by nucleation and slow growth, and the crystals are exposed to the dilute phase. In this stage, the number of crystals becomes nearly constant, whereas the crystals grow rapidly due to access to the free protein molecules in the dilute phase. 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 metastable intermediate phase in this process.

Hen egg-white lysozyme crystallisation: protein stacking and structure stability enhanced by a Tellurium(VI)-centred polyoxotungstate

As synchrotron radiation becomes more intense, detectors become faster and structure-solving software becomes more elaborate, obtaining single crystals suitable for data collection is now the bottleneck in macromolecular crystallography. Hence, there is a need for novel and advanced crystallisation agents with the ability to crystallise proteins that are otherwise challenging. Here, an Anderson-Evans-type polyoxometalate (POM), specifically Na6 [TeW6 O24 ]⋅22 H2 O (TEW), is employed as a crystallisation additive. Its effects on protein crystallisation are demonstrated with hen egg-white lysozyme (HEWL), which co-crystallises with TEW in the vicinity (or within) the liquid-liquid phase separation (LLPS) region. The X-ray structure (PDB ID: 4PHI) determination revealed that TEW molecules are part of the crystal lattice, thus demonstrating specific binding to HEWL with electrostatic interactions and hydrogen bonds. The negatively charged TEW polyoxotungstate binds to sites with a positive electrostatic potential located between two (or more) symmetry-related protein chains. Thus, TEW facilitates the formation of protein-protein interfaces of otherwise repulsive surfaces, and thereby the realisation of a stable crystal lattice. In addition to retaining the isomorphicity of the protein structure, the anomalous scattering of the POMs was used for macromolecular phasing. The results suggest that hexatungstotellurate(VI) has great potential as a crystallisation additive to promote both protein crystallisation and structure elucidation.

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

The understanding of protein interactions to control phase and nucleation behavior of protein solutions is an important challenge for soft matter, biological and medical research. Here, we present ion bridges of multivalent cations between proteins as an ion-activated mechanism for patchy interaction that is directly supported by experimental findings in protein crystals. A deep understanding of experimentally observed phenomena in protein solutions--including charge reversal, reentrant condensation, metastable liquid-liquid phase separation, cluster formation and different pathways of crystallization--is gained by an analytic model that directly displays parameter dependencies and physical connections. The direct connection between experiment and theory provides a conceptual framework for future experimental, computational and theoretical research on topics such as rational design of phase behavior and crystallization pathways on the basis of the statistical physics of patchy particles.

Protein cluster formation in aqueous solution in the presence of multivalent metal ions--a light scattering study

The formation of protein clusters as precursors for crystallization and phase separation is of fundamental and practical interest in protein science. Using multivalent ions, the strengths of both long-range Coulomb repulsion and short-range attraction can be tuned in protein solutions, representing a well-controlled model system to study static and dynamic properties of clustering during the transition from a charge-stabilized to an aggregate regime. Here, we study compressibility, diffusion, and size of solutes by means of static (SLS) and dynamic light scattering (DLS) in solutions of bovine serum albumin (BSA) and YCl3. For this and comparable systems, an increasing screening and ultimately inversion of the protein surface charge induce a rich phase behavior including reentrant condensation, liquid-liquid phase separation and crystallization, which puts the cluster formation in the context of precursor formation and nucleation of liquid and crystalline phases. We find that, approaching the turbid aggregate regime with increasing salt concentration cs, the diffusion coefficients decrease and the scattered intensity increases by orders of magnitude, evidencing increasing correlation lengths likely associated with clustering. The combination of static and dynamic observations suggests the formation of BSA clusters with a size on the order of 100 nm. The global thermodynamic state seems to be stable over at least several hours. Surprisingly, results on collective diffusion and inverse compressibility from different protein concentrations can be rescaled into master curves as a function of cs/c*, where c* is the critical salt concentration of the transition to the turbid aggregate regime.

Reentrant condensation, liquid–liquid phase separation and crystallization in protein solutions induced by multivalent metal ions

We briefly summarize the recent progress in tuning protein interactions as well as phase behavior in protein solutions using multivalent metal ions. We focus on the influence of control parameters and the mechanism of reentrant condensation, the metastable liquid–liquid phase separation and classical vs. non-classical pathways of protein crystallization.

Cation bridging studied by specular neutron reflection

The binding of an anionic surfactant onto an anionic surface by addition of divalent ions is reported based on experimental data from specular neutron reflection (NR) and attenuated total internal reflection IR spectroscopy (ATR-IR). Similar measurements using monovalent ions (sodium) do not show any evidence of such adsorption, even though the amount of surfactant can be much higher. This data is interpreted in terms of the so-called bridging mechanism of ion binding.