Effect of alcohols on aqueous lysozyme–lysozyme interactions from static light-scattering measurements

Structural and aggregation changes of silver carp myosin induced with alcohols: Effects of ethanol, 1,2-propanediol, and glycerol

This study investigated the effects of ethanol, 1,2-propanediol, and glycerol on the structure and aggregation behavior of silver carp (Hypophthalmichthys molitrix) myosin. All alcohols induced extensive alteration in the tertiary structure of myosin. Both ethanol and 1,2-propanediol further promoted an increase in the content of β-sheets in myosin and induced myosin aggregation. While glycerol had almost no impact on the secondary structure of myosin. Molecular dynamics simulations revealed that increasing the concentration of ethanol and 1,2-propanediol affected the overall structural changes in the myosin heavy chain (MHC), while glycerol exerted a more pronounced effect on the MHC tail when compared to the MHC head. Disruption of the hydration layers induced by ethanol and 1,2-propanediol contributed to local structural changes in myosin. Glycerol at a concentration of 20% induced the formation of a larger hydration layer around the MHC tail, which facilitated the stabilization of the protein structure.

Interactions in protein solutions close to liquid-liquid phase separation: ethanol reduces attractions via changes of the dielectric solution properties

Ethanol is a common protein crystallization agent, precipitant, and denaturant, but also alters the dielectric properties of solutions. While ethanol-induced unfolding is largely ascribed to its hydrophobic parts, its effect on protein phase separation and inter-protein interactions remains poorly understood. Here, the effects of ethanol and NaCl on the phase behavior and interactions of protein solutions are studied in terms of the metastable liquid-liquid phase separation (LLPS) and the second virial coefficient B₂ using lysozyme solutions. Determination of the phase diagrams shows that the cloud-point temperatures are reduced and raised by the addition of ethanol and salt, respectively. The observed trends can be explained using the extended law of corresponding states as changes of B₂. The results for B₂ agree quantitatively with those of static light scattering and small-angle X-ray scattering experiments. Furthermore, B₂ values calculated based on inter-protein interactions described by the Derjaguin-Landau-Verwey-Overbeek (DLVO) potential and considering the dielectric solution properties and electrostatic screening due to the ethanol and salt content quantitatively agree with the experimentally observed B₂ values.

Two different regimes in alcohol-induced coil-helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations

Inhomogeneous distribution of constituent molecules in a mixed solvent has been known to give remarkable effects on the solute, e.g., conformational changes of biomolecules in an alcohol-water mixture. We investigated the general effects of 2,2,2-trifluoroethanol (TFE) on proteins/peptides in a mixture of water and TFE using melittin as a model protein. Fluctuations and Kirkwood-Buff integrals (KBIs) in the TFE-H2O mixture, quantitative descriptions of inhomogeneity, were determined by small-angle X-ray scattering investigation and compared with those in the aqueous solutions of other alcohols. The concentration fluctuation for the mixtures ranks as methanol < ethanol ≪ TFE < tert-butanol < 1-propanol, indicating that the inhomogeneity of molecular distribution in the TFE-H2O mixture is unexpectedly comparable to those in the series of mono-ols. On the basis of the concentration dependence of KBIs between the TFE molecules, it was found that a strong attraction between the TFE molecules is not necessarily important to induce helix conformation, which is inconsistent with the previously proposed mechanism. To address this issue, by combining the KBIs and the helix contents reported by the experimental spectroscopic studies, we quantitatively evaluated the change in the preferential binding parameter of TFE to melittin attributed to the coil-helix transition. As a result, we found two different regimes on TFE-induced helix formation. In the dilute concentration region of TFE below ∼2 M, where the TFE molecules are not aggregated among themselves, the excess preferential binding of TFE to the helix occurs due to the direct interaction between them, namely independent of the solvent fluctuation. In the higher concentration region above ∼2 M, in addition to the former effect, the excess preferential binding is significantly enhanced by the solvent fluctuation. This scheme should be held as general cosolvent effects of TFE on proteins/peptides.

Solvent-induced conformational tuning of lysozyme protein adlayers on silica surfaces: A QCM-D and LSPR study

There is broad interest in functionalizing solid surfaces with lysozyme, which is a widely studied antimicrobial protein. To date, most efforts have focused on developing more effective immobilization schemes to promote lysozyme attachment in fully aqueous conditions, while there remains an outstanding need to understand how tuning the solution-phase conformational stability of lysozyme proteins can modulate adsorption behavior and resulting adlayer properties. Inspired by the unique conformational behavior of lysozyme proteins in water-ethanol mixtures, we conducted quartz crystal microbalance-dissipation (QCM-D) and localized surface plasmon resonance (LSPR) measurements to systematically investigate the adsorption behavior of lysozyme proteins onto silica surfaces across a wide range of water-ethanol mixtures. Our findings revealed that lysozyme adsorption behavior strongly depended on the ethanol fraction in a non-monotonic fashion and this trend could be rationalized by taking into account how competing effects of water and ethanol solvation influence solution-phase protein size and conformational stability. Integrated analysis of the QCM-D and LSPR measurement trends enabled quantitative determination of the solvent mass within lysozyme adlayers, which tended to decrease at higher ethanol fractions and supported that the hydrodynamic properties of lysozyme adlayers are mainly influenced by the degree of protein conformational flexibility as opposed to solvation effects alone.

Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples

The addition of compounds to scavenge the radical species produced during biological small-angle X-ray scattering (BioSAXS) experiments is a common strategy to reduce the effects of radiation damage and produce better quality data. As almost half of the experiments leading to structures deposited in the SASBDB database used scavengers, finding potent scavengers would be advantageous for many experiments. Here, four compounds, three nucleosides and one nitrogenous base, are presented which can act as very effective radical-scavenging additives and increase the critical dose by up to 20 times without altering the stability or reducing the contrast of the tested protein solutions. The efficacy of these scavengers is higher than those commonly used in the field to date, as verified for lysozyme solutions at various concentrations from 7.0 to 0.5 mg ml^-1. The compounds are also very efficient at mitigating radiation damage to four proteins with molecular weights ranging from 7 to 240 kDa and pH values from 3 to 8, with the extreme case being catalase at 6.7 mg ml^-1, with a scavenging factor exceeding 100. These scavengers can therefore be instrumental in expanding BioSAXS to low-molecular-weight and low-concentration protein samples that were previously inaccessible owing to poor data quality. It is also demonstrated that an increase in the critical dose in standard BioSAXS experiments leads to an increment in the retrieved information, in particular at higher angles, and thus to higher resolution of the model.

Functional Molecular Network Analysis Enables Prediction of Response to Vedolizumab Therapy in Anti-TNF Refractory IBD Patients

BACKGROUND

We applied for the first time 2 label-free technologies, physiological intermolecular modulation spectroscopy (PIMS) and nematic protein organization technic (NPOT) in anti-tumor necrosis factor (TNF) refractory inflammatory bowel disease (IBD) patients to identify clinical responders to vedolizumab therapy and elucidate their underlying functional molecular network.

METHODS

PIMS analysis was performed in peripheral blood taken prior to the first vedolizumab application in 20 IBD patients (Crohn disease n = 13; ulcerative colitis n = 7) refractory to at least 1 previous anti-TNF agent therapy. Peripheral blood taken from clinical responders and nonresponders at week 14 of vedolizumab therapy were additionally subjected to NPOT analysis. Response to therapy was assessed by respective clinical disease activity scores (partial Mayo Score and Harvey-Bradshaw Index).

RESULTS

Clinical response to vedolizumab treatment was observed in 7 of 13 Crohn disease and 4 of 7 ulcerative colitis patients at week 14. Response to therapy was accurately predicted by PIMS blood analysis in 100% of ulcerative colitis and 77% of Crohn disease patients. Overall prediction of clinical response with PIMS blood analysis was achieved with a 89% positive predictive value and a 82% negative predictive value. NPOT analysis revealed the heightened expression of the proteins ITGB7, ITGAV, ITG3, PF4, and ASGH in the peripheral blood of vedolizumab responders compared to nonresponders.

CONCLUSIONS

PIMS analysis of the blood of anti-TNF refractory IBD patients was able to stratify responders to vedolizumab therapy with high accuracy and specificity. NPOT technology could decipher underling molecular networks in the blood of responders, enabling subsequent personalized therapeutic approaches in IBD.

Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform

The second virial coefficient, B₂, measures a protein solution's deviation from ideal behavior. It is widely used to predict or explain solubility, crystallization condition, aggregation propensity, and critical temperature for liquid-liquid phase separation. B₂ is determined by the interaction energy between two protein molecules and, specifically, by the integration of the Mayer f-function in the relative configurational space (translation and rotation) of the two molecules. Simple theoretical models, such as one attributed to Derjaguin, Landau, Verwey, and Overbeek (DLVO), can fit the dependence of B₂ on salt concentrations. However, model parameters derived often are physically unrealistic and hardly transferable from protein to protein. Previous B₂ calculations incorporating atomistic details were done with limited sampling in the configurational space, due to enormous computational cost. Our FMAP method, based on fast Fourier transform, can considerably accelerate such calculations, and here we adapt it to calculate B₂ values for proteins represented at the atomic level in implicit solvent. After tuning of a single parameter in the energy function, FMAPB2 predicts well the B₂ values for lysozyme and other proteins over wide ranges of solvent conditions (salt concentration, pH, and temperature). The method is available as a web server at http://pipe.rcc.fsu.edu/fmapb2 .

Redesigning food protein formulations with empirical phase diagrams: A case study on glycerol-poor and glycerol-free formulations

Redesigning existing food protein formulations is necessary in situations where food authorities propose dose adjustments or removal of currently employed additives. Redesigning formulations involves evaluating substitute additives to obtain similar long-term physical stability as the original formulation. Such formulation screening experiments benefit from comprehensive data visualization, understanding the effects of substitute additives on long-term physical stability, and identification of short-term optimization targets. This work employs empirical phase diagrams to reach these benefits by combining multidimensional long-term protein physical stability data with short-term empirical protein properties. A case study was performed where multidimensional protein phase diagrams (1152 formulations) allowed for identification of stabilizing effects as a result of pH, methionine, sugars, salt, and minimized glycerol content. Corresponding empirical protein property diagrams (144 formulations) resulted in the identification of normalized surface tension as a short-term empirical protein property to reach long-term physical stability presumably similar to the original product, namely via preferential hydration. Additionally, changes in pH and salt were identified as environmental optimization targets to reach stability via repulsive electrostatic forces. This case study shows the applicability of the empirical phase diagram method to rationally perform formulation redesign screenings, while simultaneously expanding knowledge on protein long-term physical stability.

Quantifying the protein-protein association rate in polymer solutions: crowding-induced diffusion and energy modifications

A theoretical framework is developed to study protein-protein association in polymer solutions under diffusion-limited conditions. Starting from the basal association rate, two fundamental aspects concerning macromolecular crowding are particularly taken into account. One is the effect of microviscosity on protein diffusion. The length-scale dependent relations of translational and rotational diffusion coefficients are incorporated. Another is relevant to the crowding-induced effective interaction between the pair of proteins. The resultant energy modifications to the basal association rate are properly introduced, following an instructive classification with increasing crowder size: repulsive interaction dominant, repulsive and attractive interactions competitive, and attractive interaction prevailing. With specific energy modification terms, we are able to investigate the deviations of the association rate from the Stokes-Einstein (SE) behavior (i.e., the linear relationship with respect to the reciprocal of macroviscosity) in a quantitative manner. Our theory is applied to study the association of TEM1-β-lactamase (TEM) and the β-lactamase inhibitor protein (BLIP) in polyethylene glycol (PEG) solutions, with varying concentration and polymerization. We explicitly evaluate the relative association rate constant as a function of the solution macroviscosity. The theoretical results demonstrate very good agreement with the experimental data. Moreover, the complicated non-trivial deviations, either positive (slower than SE) or negative (faster than SE), are systematically rationalized. The precise role of energy modifications and the microviscosity effect on diffusion, in particular on rotational diffusion, are clearly unraveled.

Second Virial Coefficient As Determined from Protein Phase Behavior

We quantitatively link the macroscopic phase behavior of protein solutions to protein-protein interactions based on a coarse-grained colloidal approach. We exploit the extended law of corresponding states and apply the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory in order to infer the second virial coefficient b₂, an integral measure of the interaction potential, from the phase behavior, namely, cloud-point temperature (CPT) measurements under conditions favoring protein crystallization. This determination of b₂ yields values that quantitatively agree with the results of static light scattering (SLS) experiments. The strength of the attractions is quantified in terms of an effective Hamaker constant, which accounts for van der Waals attractions as well as non-DLVO forces, such as hydration and hydrophobic interactions. Our approach based on simple lab experiments to determine the CPT in combination with the DLVO theory is expected to facilitate further biophysical research on protein-protein interactions in complex solution environments.

Thermomyces lanuginosus lipase-catalyzed synthesis of natural flavor esters in a continuous flow microreactor

Enzymatic catalysis is considered to be among the most environmental friendly processes for the synthesis of fine chemicals. In this study, lipase from Thermomyces lanuginosus (Lecitase Ultra™) was used to catalyze the synthesis of flavor esters, i.e., methyl butanoate and methyl benzoate by esterification of the acids with methanol in a microfluidic system. Maximum reaction rates of 195 and 115 mM min⁻¹ corresponding to catalytic efficiencies (k_cat/K_M) of 0.30 and 0.24 min⁻¹ mM⁻¹ as well as yield conversion of 54 and 41 % were observed in methyl butanoate and methyl benzoate synthesis, respectively. Catalytic turnover (k_cat) was higher for methyl butanoate synthesis. Rate of synthesis and yield decreased with increasing flow rates. For both esters, increase in microfluidic flow rate resulted in increased advective transport over molecular diffusion and reaction rate, thus lower conversion. In microfluidic synthesis using T. lanuginosus lipase, the following reaction conditions were 40 °C, flow rate 0.1 mL min⁻¹, and 123 U g⁻¹ enzyme loading found to be the optimum operating limits. The work demonstrated the application of enzyme(s) in a microreactor system for the synthesis of industrially important esters.

Proteins in binary solvents

Proteins in living organisms exist in complex aqueous solutions or embedded in membranes. In solution, proteins are surrounded by a tightly bound hydration layer, which is more ordered and less mobile than bulk water. As a consequence, water plays a major role in controlling protein structure stability, conformational flexibility, dynamics, and functionality, but it also appears that protein surface regulates the structuring of the surrounding water. The presence of cosolvents can modify the hydration layer characteristics and then the whole protein structural and dynamical properties. Because cytoplasm or biological liquids are complex solutions, the knowledge of the solvation shell characteristics in mixed solvents should be considered as a crucial step in describing biological processes at molecular level. This review reports on recent studies on the structural and thermodynamic properties of model proteins dissolved in binary solvent mixtures by small-angle neutron scattering (SANS) and differential scanning microcalorimetry (DSC) techniques. We will show that contrast variation SANS experiments allow to acquire a direct knowledge of both protein structure and protein solvation shell (in terms of low-resolution shape and solvent/cosolvent composition), while DSC experiments provide information on all the relevant thermodynamic properties. We will focus on two main points. First, an extended description of the thermodynamic model used to define the equilibria between water and cosolvent molecules in the protein solvation shell will be presented. Second, the determination of the peculiar characteristics of the protein solvation layer, which will be illustrated by considering different systems. As a conclusion, we will show that the investigation of structure and thermodynamics of proteins in binary aqueous mixtures is an important way to understand the role of hydration in protein stability and activity.

Effects of methanol on lipases: molecular, kinetic and process issues in the production of biodiesel

The biotechnological production of biodiesel is based on transesterification/esterification reactions between a source of fatty acids and a short-chain alcohol, usually methanol, catalysed by enzymes belonging to the class known as lipases. Several lipases used in industrial processes, although stable in the presence of other organic solvents, are inactivated by methanol at or below the concentration optimal for biodiesel production, making it necessary to use stepwise methanol feeding or pre-treatment of the enzyme. In this review article we focus on what is currently know about methanol inactivation of lipases, a phenomenon which is not common to all lipase enzymes, with the goal of improving the biocatalytic process. We suggest that different mechanisms can lead to inactivation of different lipases, in particular substrate inhibition and protein unfolding. Attempts to improve the performances of methanol sensitive lipases by mutagenesis as well as process engineering approaches are also summarized.

Physiological intermolecular modification spectroscopy for the prediction of response to anti-tumor necrosis factor therapy in patients with inflammatory bowel diseases

BACKGROUND/AIMS

Anti-tumor necrosis factor (TNF) antibodies have clinical efficiency only in a subgroup of patients with inflammatory bowel diseases (IBD). Prediction of clinical response is a critical clinical problem. Physiological intermolecular modification spectroscopy (PIMS) is a label-free technology performed in physiological conditions. PIMS enables real-time monitoring of dynamic molecular resonance of entire proteins and macromolecules of an individual. The aim of this study was to explore the capacity of PIMS to discriminate IBD patients regarding response to anti-TNF treatment.

METHODS

Protein extracts of peripheral blood mononuclear cells (PBMC) from 30 outpatients diagnosed with ulcerative colitis (UC) or Crohn's disease (CD) and treated with infliximab were subjected to PIMS analysis in a blinded transversal study. Total protein from each patient's PBMCs was challenged with infliximab. Dynamic changes in macromolecular interaction were registered while the temperature rose from -37 to 37°C. Individual macromolecular volume and molecular elasticity were determined for each patient.

RESULTS

Clinical data revealed that 67% of UC and 79% of CD patients responded to infliximab therapy during the 3-month study period based on their respective clinical activity score. These results confirm that PIMS data predicted response to anti-TNF therapy with an accuracy of 96%.

CONCLUSION

PIMS stratified IBD patients into two groups, responders and nonresponders, which correlated with the clinical efficacy of anti-TNF therapy. PIMS seems to be a powerful technology to adapt IBD treatment to the individual patient. Further studies with PIMS might enable to predict clinical response to biological treatment in IBD patients before the therapy is initiated.

Effects of environmental factors on MSP21-25 aggregation indicate the roles of hydrophobic and electrostatic interactions in the aggregation process

Merozoite surface protein 2 (MSP2), one of the most abundant proteins on the merozoite surface of Plasmodium falciparum, is recognized to be important for the parasite's invasion into the host cell and is thus a promising malaria vaccine candidate. However, mediated mainly by its conserved N-terminal 25 residues (MSP21-25), MSP2 readily forms amyloid fibril-like aggregates under physiological conditions in vitro, which impairs its potential as a vaccine component. In addition, there is evidence that MSP2 exists in aggregated forms on the merozoite surface in vivo. To elucidate the aggregation mechanism of MSP21-25 and thereby understand the behavior of MSP2 in vivo and find ways to avoid the aggregation of relevant vaccine in vitro, we investigated the effects of agitation, pH, salts, 1-anilinonaphthalene-8-sulfonic acid (ANS), trimethylamine N-oxide dihydrate (TMAO), urea, and sub-micellar sodium dodecyl sulfate (SDS) on the aggregation kinetics of MSP21-25 using thioflavin T (ThT) fluorescence. The results showed that MSP21-25 aggregation was accelerated by agitation, while repressed by acidic pHs. The salts promoted the aggregation in an anion nature-dependent pattern. Hydrophobic surface-binding agent ANS and detergent urea repressed MSP21-25 aggregation, in contrast to hydrophobic interaction strengthener TMAO, which enhanced the aggregation. Notably, sub-micellar SDS, contrary to its micellar form, promoted MSP21-25 aggregation significantly. Our data indicated that hydrophobic interactions are the predominant driving force of the nucleation of MSP21-25 aggregation, while the elongation is controlled mainly by electrostatic interactions. A kinetic model of MSP21-25 aggregation and its implication were also discussed.

Octupolar approximation for the excluded volume of axially symmetric convex bodies

We propose a simply computable formula for the excluded volume of convex, axially symmetric bodies, based on the classical Brunn-Minkoski theory for convex bodies, which is briefly outlined in an Appendix written in a modern mathematical language. This formula is applied to cones and spherocones, which are regularized cones; a shape-reconstruction algorithm is able to generate the region in space inaccessible to them and to compute their excluded volume, which is found to be in good agreement with our approximate analytical formula. Finally, for spherocones with an appropriately tuned amplitude, we predict the occurrence of a relative deep minimum of the excluded volume in a configuration lying between the parallel alignment (where the excluded volume is maximum) and the antiparallel alignment (where the excluded volume is minimum).

Thermodynamic versus conformational metastability in fibril-forming lysozyme solutions

The role of intermolecular interaction in fibril-forming protein solutions and its relation with molecular conformation is a crucial aspect for the control and inhibition of amyloid structures. Here, we study the fibril formation and the protein-protein interactions of lysozyme at acidic pH and low ionic strength. The amyloid formation occurs after a long lag time and is preceded by the formation of oligomers, which seems to be off-pathway with respect to fibrillation. By measuring the osmotic isothermal compressibility and the collective diffusion coefficient of lysozyme in solution, we observe that the monomeric solution is kept in a thermodynamically metastable state by strong electrostatic repulsion, even in denaturing conditions. The measured repulsive interaction between monomers is satisfactorily accounted for by classical polyelectrolyte theory. Further, we observe a slow conformational change involving both secondary and tertiary structure, which drives the proteins toward a more hydrophobic conformation. Denatured proteins are driven out of metastability through conformational substates, which are kinetically populated and experience a lower activation energy for fibril formation. Thus, our results highlight the role of electrostatic repulsion, which hinders the aggregation of partially denatured proteins and operates as a gatekeeper favoring the association of those monomers whose conformation is capable of forming amyloid structure.

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: theory and experiments

Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluid-solid transition and the gas-liquid coexistence curve (binodal) shift to lower temperatures and the gap between them increases. The experimentally observed trends are consistent with our theoretical predictions based on the thermodynamic perturbation theory and the Derjaguin-Landau-Verwey-Overbeek model for the lysozyme-lysozyme pair interactions. The values of the parameters describing the interactions, namely the refractive indices, dielectric constants, Hamaker constant and cut-off length, are extracted from literature or are experimentally determined by independent experiments, including static light scattering, to determine the second virial coefficient. We observe that both, glycerol and DMSO, render the potential more repulsive, while sodium chloride reduces the repulsion.

Mechanistic insights into protein precipitation by alcohol

Ethanol is used to precipitate proteins during various processes, including purification and crystallization. To elucidate the mechanism of protein precipitation by alcohol, we have investigated the solubility and structural changes of protein over a wide range of alcohol concentrations. Conformation of hen egg-white lysozyme was changed from native to α-helical rich structure in the presence of ethanol at concentrations above 60%. The solubility of lysozyme was reduced with increasing ethanol concentration, although gel formation at ethanol concentrations between 60% and 75% prevented accurate solubility measurements. SH-modified lysozyme showed largely unfolded structure in water and α-helical structure in the presence of ethanol. More importantly, solubility of the chemically modified lysozyme molecules decreased with increasing ethanol concentration. There is no indication of increased solubility upon unfolding of the lysozyme molecules by ethanol, indicating that any favorable interaction of ethanol with the hydrophobic side chains, if indeed occuring, is offset by the unfavorable interaction of ethanol with the hydrophilic side chains and peptide bonds.

Reexamining protein-protein and protein-solvent interactions from Kirkwood-Buff analysis of light scattering in multi-component solutions

The classic analysis of Rayleigh light scattering (LS) is re-examined for multi-component protein solutions, within the context of Kirkwood-Buff (KB) theory as well as a more generalized canonical treatment. Significant differences arise when traditional treatments that approximate constant pressure and neglect concentration fluctuations in one or more (co)solvent/co-solute species are compared with more rigorous treatments at constant volume and with all species free to fluctuate. For dilute solutions, it is shown that LS can be used to rigorously and unambiguously obtain values for the osmotic second virial coefficient (B(22)), in contrast with recent arguments regarding protein interactions deduced from LS experiments. For more concentrated solutions, it is shown that conventional analysis over(under)-estimates the magnitude of B(22) for significantly repulsive(attractive) conditions, and that protein-protein KB integrals (G(22)) are the more relevant quantity obtainable from LS. Published data for α-chymotrypsinogen A and a series of monoclonal antibodies at different pH and salt concentrations are re-analyzed using traditional and new treatments. The results illustrate that while traditional analysis may be sufficient if one is interested in only the sign of B(22) or G(22), the quantitative values can be significantly in error. A simple approach is illustrated for determining whether protein concentration (c(2)) is sufficiently dilute for B(22) to apply, and for correcting B(22) values from traditional LS regression at higher c(2) values. The apparent molecular weight M(2, app) obtained from LS is shown to generally not be equal to the true molecular weight, with the differences arising from a combination of protein-solute and protein-cosolute interactions that may, in principle, also be determined from LS.

Existence of metastable intermediate lysozyme conformation highlights the role of alcohols in altering protein stability

Alcohols have a manifold effect on the conformational and thermodynamic stability of native proteins. Here, we study the effect of moderate concentrations of trifluoroethanol (TFE) on the thermal stability of hen egg-white lysozyme (HEWL), by far-UV circular dichroism and by steady-state and time-resolved photoluminescence of intrinsic tryptophans. Our results highlight that TFE affects lysozyme stability by preferential solvation of the protein molecule. Furthermore, we discovered the existence at 20% TFE of an equilibrium partially folded state of lysozyme, intermediate between the native and the unfolded state. A three-state model is therefore used to interpolate the thermal denaturation data. Our analysis explains how the stabilization of the intermediate conformation enhances the entropic contribution to unfolding, and thus decreases the unfolding temperature, while, at the same time, TFE enhances the conformational stability of the native fold at room temperature. Eventually, we challenged the ability of these intermediate structures to form supramolecular aggregates by heating experiments at different TFE concentrations.

The effects of organic solvents on the efficiency and regioselectivity of N-acetyl-lactosamine synthesis, using the β-galactosidase from Bacillus circulans in hydro-organic media

The enzymatic synthesis of N-acetyl-lactosamine (LacNAc) by the transgalactosylation of N-acetyl-D-glucosamine (GlcNAc), catalyzed by the β-galactosidase from Bacillus circulans (BcβGal), was studied in hydro-organic media, starting from o-nitrophenyl-β-D-galactopyranoside (oNPG) as a galactosyl donor. Thermal stability and synthesis activity of BcβGal were shown to depend on the organic solvent polarity, characterized by its Log P value. BcβGal was thus most stable in 10% (v/v) t-BuOH, an organic solvent found to have a stabilizing and/or weakly denaturing property, which was confirmed for high t-BuOH concentrations. In the same manner, the optimal synthesis yield increased as the Log P value of the organic solvent increased. The best results were obtained for reactions carried out in 10% (v/v) pyridine or 2-methyl-2-butanol, which gave 47% GlcNAc transgalactosylation yield based on starting oNPG, of which 23% (11 mM; 4.3 g/L) consisted in LacNAc synthesis. Furthermore, it was also established that both the GlcNAc transgalactosylation yield and the enzyme regioselectivity depended on the percentage of organic solvent used, the optimal percentage varying from 10 to 40% (v/v), depending on the solvent. This phenomenon was found to correlate mainly with the thermodynamic activity of water (a(w)) in the aqueous organic solvent mixture, which was found to be optimal when close to 0.96, whatever the organic solvent used. Finally, this study highlighted the fact that the regioselectivity of BcβGal for 1-4 linkage formation could be advantageously managed by controlling the a(w) parameter.

Protein stability modulated by a conformational effector: effects of trifluoroethanol on bovine serum albumin

The link between the thermodynamic properties of a solution and the conformational space explored by a protein is of fundamental importance to understand and control solubility, misfolding and aggregation processes. Here, we study the thermodynamic and conformational stability of a model protein, bovine serum albumin (BSA), by addition of trifluoroethanol (TFE), which is known to affect both the solvent properties and the protein structure. The solvent-mediated pair-wise interactions are investigated by static and dynamic light scattering, and by small angle X-ray scattering. The protein conformational details are studied by far- and near-UV circular dichroism (CD), and steady state fluorescence from tryptophan and from 1-anilino-8-naphthalene sulfonate (ANS). At low TFE concentrations, our results show that protein-protein interaction is dominated by steric repulsion accompanied by a consistent protein solvation. Minor local conformational changes also occur, but they do not affect the stability of BSA. At TFE concentrations above the threshold of 16% v/v, attractive interactions become prevalent, along with conformational changes related to a loosening of BSA tertiary structure. The onset of thermodynamic instability is triggered by the enhancement of hydrophobic attraction over repulsion, due to minor local changes of protein conformation and hydration. In the present context, TFE acts as a conformational effector, since it affects the intermolecular interaction and the activity of the proteins in solution through a direct mechanism.

Protein phase behavior and crystallization: Effect of glycerol

Glycerol is widely used as an additive to stabilize proteins in aqueous solution. We have studied the effect of up to 40 wt % glycerol on the crystallization of lysozyme from brine. As the glycerol concentration increased, progressively larger amounts of salt were needed to crystallize the protein. Like previous authors, we interpret this as evidence for glycerol changing the interaction between lysozyme molecules. We quantitatively model the interprotein interaction using a Derjaguin-Landau-Verwey-Overbeek potential. We find that the effect of glycerol can be entirely accounted for by the way it modifies the dielectric constant and refractive index of the solvent. Quantifying the interprotein interaction by the second virial coefficient, B(2), we find a universal crystallization boundary for all glycerol concentrations.

Patterns of protein protein interactions in salt solutions and implications for protein crystallization

The second osmotic virial coefficients of seven proteins-ovalbumin, ribonuclease A, bovine serum albumin, alpha-lactalbumin, myoglobin, cytochrome c, and catalase-were measured in salt solutions. Comparison of the interaction trends in terms of the dimensionless second virial coefficient b(2) shows that, at low salt concentrations, protein-protein interactions can be either attractive or repulsive, possibly due to the anisotropy of the protein charge distribution. At high salt concentrations, the behavior depends on the salt: In sodium chloride, protein interactions generally show little salt dependence up to very high salt concentrations, whereas in ammonium sulfate, proteins show a sharp drop in b(2) with increasing salt concentration beyond a particular threshold. The experimental phase behavior of the proteins corroborates these observations in that precipitation always follows the drop in b(2). When the proteins crystallize, they do so at slightly lower salt concentrations than seen for precipitation. The b(2) measurements were extended to other salts for ovalbumin and catalase. The trends follow the Hofmeister series, and the effect of the salt can be interpreted as a water-mediated effect between the protein and salt molecules. The b(2) trends quantify protein-protein interactions and provide some understanding of the corresponding phase behavior. The results explain both why ammonium sulfate is among the best crystallization agents, as well as some of the difficulties that can be encountered in protein crystallization.

Biophysical characterization of anticoagulant hemextin AB complex from the venom of snake Hemachatus haemachatus

Hemextin AB complex from the venom of Hemachatus haemachatus is the first known natural anticoagulant that specifically inhibits the enzymatic activity of blood coagulation factor VIIa in the absence of factor Xa. It is also the only known heterotetrameric complex of two three-finger toxins. Individually only hemextin A has mild anticoagulant activity, whereas hemextin B is inactive. However, hemextin B synergistically enhances the anticoagulant activity of hemextin A and their complex exhibits potent anticoagulant activity. In this study we characterized the nature of molecular interactions leading to the complex formation. Circular dichroism studies indicate the stabilization of beta-sheet in the complex. Hemextin AB complex has an increased apparent molecular diameter in both gas and liquid phase techniques. The complex formation is enthalpically favorable and entropically unfavorable with a negative change in the heat capacity. Thus, the anticoagulant complex shows less structural flexibility than individual subunits. Both electrostatic and hydrophobic interactions are important for the complexation; the former driving the process and the latter helping in the stabilization of the tetramer. The tetramer dissociates into dimers and monomers with the increase in the ionic strength of the solution and also with increase in the glycerol concentration in the buffer. The two dimers formed under each of these conditions display distinct differences in their apparent molecular diameters and anticoagulant properties. Based on these results, we have proposed a model for this unique anticoagulant complex.

Hydrophobic interaction chromatography of proteins

A general thermodynamic relation was derived to correlate protein solubility to retention in hydrophobic interaction chromatography (HIC). This relation is built on a thermodynamic formulation presented previously by Melander, Horváth and co-workers in the context of the solvophobic theory, but the final result is independent of this model framework. The relation reflects an increase in protein retention in HIC under conditions that promote precipitation or crystallization, consistent with early descriptions of HIC. To examine the contribution of protein solubility to retention in HIC, isocratic elution experiments were performed with four different commercially available agarose media and four model proteins (ribonuclease A (RNA), lysozyme (LYS), myoglobin (MYO), and ovalbumin (OVA)). A wide variety of retention trends were observed as a function of protein, adsorbent type, salt type and concentration, and pH. In general, however, the results show that solubility, or its surrogate, the second osmotic virial coefficient, which reflects solution thermodynamic properties, correlates well with HIC retention in many cases; this includes correctly predicting reverse Hofmeister effects, which cannot be explained by retention models based on the solvophobic theory and preferential interaction theory. However, solution properties could not explain retention behavior under some conditions. In those cases, effects such as protein-surface interactions or conformational change could be important determinants of protein adsorption.