Interactions of lysozyme in guanidinium chloride solutions from static and dynamic light-scattering measurements

Recent Advances in Overexpression of Functional Recombinant Lipases

Heterologous functional expression of the recombinant lipases is typically a bottleneck due to the expression in the insoluble fraction as inclusion bodies (IBs) which are in inactive form. Due to the importance of lipases in various industrial applications, many investigations have been conducted to discover suitable approaches to obtain functional lipase or increase the expressed yield in the soluble fraction. The utilization of the appropriate prokaryotic and eukaryotic expression systems, along with the suitable vectors, promoters, and tags, has been recognized as a practical approach. One of the most powerful strategies to produce bioactive lipases is using the molecular chaperones co-expressed along with the target protein's genes into the expression host to produce the lipase in soluble fraction as a bioactive form. The refolding of expressed lipase from IBs (inactive) is another practical strategy which is usually carried out through chemical and physical methods. Based on recent investigations, the current review simultaneously highlights strategies to express the bioactive lipases and recover the bioactive lipases from the IBs in insoluble form.

Protein solutions close to liquid-liquid phase separation exhibit a universal osmotic equation of state and dynamical behavior

Liquid-liquid phase separation (LLPS) of protein solutions is governed by highly complex protein-protein interactions. Nevertheless, it has been suggested that based on the extended law of corresponding states (ELCS), as proposed for colloids with short-range attractions, one can rationalize not only the thermodynamics, but also the structure and dynamics of such systems. This claim is systematically and comprehensively tested here by static and dynamic light scattering experiments. Spinodal lines, the isothermal osmotic compressibility κ_T and the relaxation rate of concentration fluctuations Γ are determined for protein solutions in the vicinity of LLPS. All these quantities are found to exhibit a corresponding-states behavior. This means that, for different solution conditions, these quantities are essentially the same if considered at similar reduced temperature or second virial coefficient. For moderately concentrated solutions, the volume fraction ϕ dependence of κ_T and Γ can be consistently described by Baxter's model of adhesive hard spheres. The off-critical, asymptotic T behavior of κ_T and Γ close to LLPS is consistent with the scaling laws predicted by mean-field theory. Thus, the present work aims at a comprehensive experimental test of the applicability of the ELCS to structural and dynamical properties of concentrated protein solutions.

Phase separation and dynamical arrest of protein solutions dominated by short-range attractions

The interplay of liquid-liquid phase separation (LLPS) and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as condensed matter physics, materials science, food engineering, and the pharmaceutical industry. In this context, protein solutions exhibit remarkable equilibrium and non-equilibrium behaviors. In the regime where attractive and repulsive forces compete, it has been demonstrated, for example, that the location of the dynamical arrest line seems to be independent of ionic strength, so that the arrest lines at different ionic screening lengths overlap, in contrast to the LLPS coexistence curves, which strongly depend on the salt concentration. In this work, we show that the same phenomenology can also be observed when the electrostatic repulsions are largely screened, and the range and strength of the attractions are varied. In particular, using lysozyme in brine as a model system, the metastable gas-liquid binodal and the dynamical arrest line as well as the second virial coefficient have been determined for various solution conditions by cloud-point measurements, optical microscopy, centrifugation experiments, and light scattering. With the aim of understanding this new experimental phenomenology, we apply the non-equilibrium self-consistent generalized Langevin equation theory to a simple model system with only excluded volume plus short-range attractions, to study the dependence of the predicted arrest lines on the range of the attractive interaction. The theoretical predictions find a good qualitative agreement with experiments when the range of the attraction is not too small compared with the size of the protein.

The influence of excipients on the viscosity of monoclonal antibody solutions

The aggregation propensity of monoclonal antibodies can be modified by adding different cosolutes into the solution. A simple coarse-grained model in the combination with the thermodynamic perturbation theory was used to predict cluster distribution and viscosity of the solutions of IgG4 monoclonal anibody in the presence of L-Arginine Hydrochloride. The data were analysed using binding polynomial to describe the binding of cosolute (Arginine) to the antibody molecule. The results show that by binding to the antibody molecule the cosolute occupies some of the binding sites of the antibody, and in this way reduces the amount of binding sites available to other antibody molecules. The aggregation propensity of the antibody molecules is therefore reduced.

Universal effective interactions of globular proteins close to liquid–liquid phase separation: Corresponding-states behavior reflected in the structure factor

Intermolecular interactions in protein solutions, in general, contain many contributions. If short-range attractions dominate, the state diagram exhibits liquid–liquid phase separation (LLPS) that is metastable with respect to crystallization. In this case, the extended law of corresponding states (ELCS) suggests that thermodynamic properties are insensitive to details of the underlying interaction potential. Using lysozyme solutions, we investigate the applicability of the ELCS to the static structure factor and how far effective colloidal interaction models can help to rationalize the phase behavior and interactions of protein solutions in the vicinity of the LLPS binodal. The (effective) structure factor has been determined by small-angle x-ray scattering. It can be described by Baxter’s adhesive hard-sphere model, which implies a single fit parameter from which the normalized second virial coefficient b2 is inferred and found to quantitatively agree with previous results from static light scattering. The b2 values are independent of protein concentration but systematically vary with temperature and solution composition, i.e., salt and additive content. If plotted as a function of temperature normalized by the critical temperature, the values of b2 follow a universal behavior. These findings validate the applicability of the ELCS to globular protein solutions and indicate that the ELCS can also be reflected in the structure factor.

Physicochemical and Biological Insights Into the Molecular Interactions Between Extracellular DNA and Exopolysaccharides in Myxococcus xanthus Biofilms

Extracellular DNA (eDNA) is a critical component in the extracellular matrix (ECM) of bacterial biofilms, while little is known about the mechanisms underlying how eDNA integrates into the ECM through potential macromolecular interactions. Myxococcus xanthus biofilm was employed as a suitable model for the investigation due to the co-distribution of eDNA and exopolysaccharides (EPS) owing to their direct interactions in the ECM. DNA is able to combine with M. xanthus EPS to form a macromolecular conjugate, which is dominated by the electrostatic forces participating in the polymer-polymer interactions. Without intercalation binding, DNA-EPS interactions exhibit a certain degree of reversibility. Acting as a strong extracellular framework during biofilm formation process, the eDNA-EPS complex not only facilitates the initial cell adhesion and subsequent establishment of ECM architecture, but also renders cells within biofilms stress resistances that are relevant to the survival of M. xanthus in some hostile environments. Furthermore, the EPS protects the conjugated DNA from the degradation by nucleic acid hydrolases, which leads to the continuous and stable existence of eDNA in the native ECM of M. xanthus biofilms. These results will shed light on developing prevention and treatment strategies against biofilm-related risks.

Structurally distinct unfolding intermediates formed from a staphylococcal capsule-producing enzyme retained NADPH binding activity

CapF, a capsule-producing enzyme expressed by Staphylococcus aureus, binds NADPH and exists as a dimer in the aqueous solution. Many other capsule-producing virulent bacteria also express CapF orthologs. To understand the folding-unfolding mechanism of S. aureus CapF, herein a recombinant CapF (rCapF) was individually investigated using urea and guanidine hydrochloride (GdnCl). Unfolding of rCapF by both the denaturants was reversible but proceeded via the synthesis of a different number of intermediates. While two dimeric intermediates (rCapF4 and rCapF5) were formed at 0.5 M and 1.5 M GdnCl, three dimeric intermediates (rCapF1, rCapF2, and rCapF3) were produced at 1 M, 2 M, and 3 M urea, respectively. rCapF5 showed 3.6 fold less NADPH binding activity, whereas other intermediates retained full NADPH binding activity. Compared to rCapF, all of the intermediates (except rCapF3) had a compressed shape. Conversely, rCapF3 possessed a native protein-like shape. The maximum shape loss was in rCapF4 though its secondary structure remained unperturbed. Additionally, the tertiary structure and hydrophobic surface area of the intermediates neither matched with each other nor with those of the native rCapF. Of the four Trp residues in rCapF, one or more Trp residues in the intermediates may have higher solvent accessibility. Using sequence alignment and a tertiary structural model of CapF, we have demonstrated that the region around Trp 137 of CapF may be most sensitive to unfolding, whereas the NADPH binding motif carrying region at the N-terminal end of this protein may be resistant to unfolding, particularly at the low denaturant concentrations.Communicated by Ramaswamy H. Sarma.

High-Throughput Screening for Colloidal Stability of Peptide Formulations Using Dynamic and Static Light Scattering

Selection of an appropriate formulation to stabilize therapeutic proteins against aggregation is one of the most challenging tasks in early-stage drug product development. The amount of aggregates is more difficult to quantify in the case of peptides due to their small molecular size. Here, we investigated the suitability of diffusion self-interaction parameters (k_D) and osmotic second virial coefficients (B₂₂) for high-throughput (HT) screening of peptide formulations regarding their aggregation risk. These parameters were compared to the effect of thermal stress on colloidal stability. The formulation matrix comprised six buffering systems at two selected pH values, four tonicity agents, and a common preservative. The results revealed that electrostatic interactions are the main driver to control colloidal stability. Preferred formulations consisted of acetate and succinate buffer at pH 4.5 combined with glycerol or mannitol and optional m-cresol. k_D proved to be a suitable surrogate for B₂₂ as an indicator of high colloidal stability in the case of peptides as was previously described for globular proteins and antibodies. Formulation assessment solely based on k_D obtained by HT methods offers important insights into the optimization of colloidal stability during the early development of peptide-based liquid formulations and can be performed with a limited amount of peptide (∼360 mg).

Structural characterization with light scattering: A tool for rationally designing protein formulations

Here we explore the possibility of using light scattering technologies as an analytical tool for understanding structural features of a protein that might be responsible for initiating aggregative interactions. Using widely independent complementary experimental and computational techniques, we found that interaction parameters like K_m in particular possess good correlation with residue specific descriptors for the model protein Bovine Serum Albumin. Such information can help rationally design protein engineering and/or formulation strategies for prolonged shelf-life of such products.

Ionic liquids in protein amyloidogenesis: a brief screenshot of the state-of-the-art

Ionic liquids (ILs) are a vast class of organic non-aqueous electrolytes whose interaction with biomolecules is receiving great attention for potential applications in bio-nano-technology. Recently, it has been shown that ILs can affect protein amyloidogenesis. Whereas some ILs favour the aggregation of proteins into amyloids, others inhibit their formation. Moreover, ILs can dissolve mature fibrils and restore the protein biochemical function. In this letter, we present a brief state-of-the-art summary of this emerging field that holds the promise of important developments both in basic science and in applications from bio-medicine to material science, and bio-nano-technology. The huge variety of ILs offers a vast playground for future studies and potential applications.

Tuning protein-protein interactions using cosolvents: specific effects of ionic and non-ionic additives on protein phase behavior

Cosolvents are routinely used to modulate the (thermal) stability of proteins and, hence, their interactions with proteins have been studied intensely. However, less is known about their specific effects on protein-protein interactions, which we characterize in terms of the protein phase behavior. We analyze the phase behavior of lysozyme solutions in the presence of sodium chloride (NaCl), guanidine hydrochloride (GuHCl), glycerol, and dimethyl sulfoxide (DMSO). We experimentally determined the crystallization boundary (XB) and, in combination with data on the cloud-point temperatures (CPTs), the crystallization gap. In agreement with other studies, our data indicate that the additives might affect the protein phase behavior through electrostatic screening and additive-specific contributions. At high salt concentrations, where electrostatic interactions are screened, both the CPT and the XB are found to be linear functions of the additive concentration. Their slopes quantify the additive-specific changes of the phase behavior and thus of the protein-protein interactions. While the specific effect of NaCl is to induce attractions between proteins, DMSO, glycerol and GuHCl (with increasing strength) weaken attractions and/or induce repulsions. Except for DMSO, changes of the CPT are stronger than those of the XB. Furthermore, the crystallization gap widens in the case of GuHCl and glycerol and narrows in the case of NaCl. We relate these changes to colloidal interaction models, namely square-well and patchy interactions.

Preferential Interactions and the Effect of Protein PEGylation

Background

PEGylation is a strategy used by the pharmaceutical industry to prolong systemic circulation of protein drugs, whereas formulation excipients are used for stabilization of proteins during storage. Here we investigate the role of PEGylation in protein stabilization by formulation excipients that preferentially interact with the protein.

Methodology/Principal Findings

The model protein hen egg white lysozyme was doubly PEGylated on two lysines with 5 kDa linear PEGs (mPEG-succinimidyl valerate, MW 5000) and studied in the absence and presence of preferentially excluded sucrose and preferentially bound guanine hydrochloride. Structural characterization by far- and near-UV circular dichroism spectroscopy was supplemented by investigation of protein thermal stability with the use of differential scanning calorimetry, far and near-UV circular dichroism and fluorescence spectroscopy. It was found that PEGylated lysozyme was stabilized by the preferentially excluded excipient and destabilized by the preferentially bound excipient in a similar manner as lysozyme. However, compared to lysozyme in all cases the melting transition was lower by up to a few degrees and the calorimetric melting enthalpy was decreased to half the value for PEGylated lysozyme. The ratio between calorimetric and van’t Hoff enthalpy suggests that our PEGylated lysozyme is a dimer.

Conclusion/Significance

The PEGylated model protein displayed similar stability responses to the addition of preferentially active excipients. This suggests that formulation principles using preferentially interacting excipients are similar for PEGylated and non-PEGylated proteins.

Accurate Diffusion Coefficients of Organosoluble Reference Dyes in Organic Media Measured by Dual-Focus Fluorescence Correlation Spectroscopy

Dual-focus fluorescence correlation spectroscopy (2fFCS) is a versatile method to determine accurate diffusion coefficients of fluorescent species in an absolute, reference-free manner. Whereas (either classical or dual-focus) FCS has been employed primarily in the life sciences and thus in aqueous environments, it is increasingly being used in materials chemistry, as well. These measurements are often performed in nonaqueous media such as organic solvents. However, the diffusion coefficients of reference dyes in organic solvents are not readily available. For this reason we determined the translational diffusion coefficients of several commercially available organosoluble fluorescent dyes by means of 2fFCS. The selected dyes and organic solvents span the visible spectrum and a broad range of refractive indices, respectively. The diffusion coefficients can be used as absolute reference values for the calibration of experimental FCS setups, allowing quantitative measurements to be performed. We show that reliable information about the hydrodynamic dimensions of the fluorescent species (including noncommercial compounds) within organic media can be extracted from the 2fFCS data.

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies.

Buffers more than buffering agent: introducing a new class of stabilizers for the protein BSA

In this study, we have analyzed the influence of four biological buffers on the thermal stability of bovine serum albumin (BSA) using dynamic light scattering (DLS).

Partial unfolding of a monoclonal antibody: role of a single domain in driving protein aggregation

We have examined the effect of incubating a monoclonal antibody (mAb) in low (0-2.0 M) concentrations of guanidine hydrochloride (GdnHCl) on the protein's conformation and aggregation during isothermal incubation. In GdnHCl solutions at concentrations from 1.2 to 1.6 M, the mAb was partially unfolded. As demonstrated by fluorescence and circular dichroism spectroscopy, the partially unfolded state of the antibody had perturbed tertiary structure but retained native secondary structure. Furthermore, partial unfolding of the antibody was documented by analytical ultracentrifugation, dynamic light scattering, and limited proteolysis. Subsequent aggregation of the antibody was characterized using size-exclusion chromatography, analytical ultracentrifugation, and dynamic light scattering. Over the entire concentration range (0-2.0 M) of GdnHCl, protein-protein interactions were attractive, as quantified by negative osmotic second virial coefficients measured with static light scattering. However, during isothermal incubation at 37 °C, the aggregation of the antibody was detected only in solutions that induced partial unfolding. Differential scanning calorimetry studies showed that the antibody's CH2 domains were unfolded in antibody molecules that had been incubated in 1.2 M and higher concentrations of GdnHCl. These results suggest that unfolding of the CH2 domains leads to aggregation.

Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies

Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies.

Fluorescence correlation spectroscopy (IUPAC Technical Report)

We present an overview on the applicability of fluorescence correlation spectroscopy (FCS) for the accurate determination of translational diffusion coefficients and thus, via the Stokes–Einstein relation, of molecular size. We consider several of the most common sources of optical aberrations and their impact on the outcome of conventional FCS measurements. We describe also a new variant of FCS, dual-focus FCS, which is robust against most of the considered aberrations, and we report reference values of diffusion coefficients for several fluorescent dyes across the visible spectrum.

Assessment of net charge and protein-protein interactions of different monoclonal antibodies

The purpose of this work was to compare biophysical properties of different monoclonal antibodies (mAbs). mAbs' theoretical isoelectric point (IEP) and theoretical net charge were compared with experimentally assessed values. IEP was determined by isoelectric focusing capillary electrophoresis, determination of zero electrophoretic mobility, or the minimum mutual diffusion coefficient during pH titration. Net charge was determined using electrophoretic mobility and self-diffusion coefficient. It was found that antibodies differ substantially in their biophysical properties, that is, in IEP, net charge, and zeta potential. Also, the importance of these properties was studied with respect to protein-protein interactions. This was achieved by assessing the second virial coefficient (A(2)) determined by static light scattering (SLS) and dynamic light scattering (DLS). It was found that at low ionic strength formulation conditions [20 mM histidine (His)/His-HCl buffer, pH 6.0] proteins' charge is the main driver for overall repulsive protein interactions. At high ionic strength conditions (20 mM His/His-HCl buffer, pH 6.0, + 150 mM NaCl), where counterions are shielding ionic interactions, proteins' repulsive forces were weakened, but to a different extent. Furthermore, a DLS method was developed allowing fast and easy assessment of A(2) by minimum need of material.

Structure and thermodynamics of colloidal protein cluster formation: comparison of square-well and simple dipolar models

Reversible formation of weakly associated protein oligomers or clusters is a key early step in processes such as protein aggregation and colloidal phase separation. A previously developed cell-based, quasichemical model for lattice fluids [T. M. Young and C. J. Roberts, J. Chem. Phys. 127, 165101 (2007)] is extended here to treat continuous-space systems. It is illustrated using two simplified limiting cases for globular proteins at the isoelectric point: spherical square-well (SW) particles with an isotropic short-ranged attraction and screened dipolar particles with SW attractions and square-shoulder repulsions. Cluster free energies (DeltaA(i)) and structures are analyzed as a function of the reduced second virial coefficient b(2)(*). DeltaA(i) values and the average structures of clusters up to pentamers have distinct differences due to the anisotropic nature of the dipolar interactions. However, DeltaA(i) values can be mapped semiquantitatively between the two cases if compared at common values of b(2)(*). Free energy landscapes of oligomerization are constructed, illustrating significant differences in landscape ruggedness for small clusters of dipolar versus SW fluids, and suggesting a possible molecular interpretation for empirical models of nucleation-dependent aggregation of proteins.