Probing multimodal ligand binding regions on ubiquitin using nuclear magnetic resonance, chromatography, and molecular dynamics simulations.

Site-directed mutagenesis, nuclear magnetic resonance (NMR) chemical shift perturbation experiments, and molecular dynamics (MD) simulations are employed in concert with chromatographic experiments to provide insight into protein-ligand interactions in multimodal chromatographic systems. In previous studies, a preferred binding region was identified on the surface of the protein ubiquitin for binding with a multimodal ligand. In this study, site-directed mutagenesis is used to enable direct NMR evaluation of the mutant protein as compared to the wild type. It is found that reversing the charge of a key residue (K6E) in the proposed preferred binding region results in substantial decreases in the magnitude of the ligand-induced NMR chemical shift perturbations relative to those detected for the wild type protein, particularly for residues located within the preferred binding region. These NMR results also indicate a decrease in ligand affinity, consistent with the weaker chromatographic retention observed for the mutant as compared to the wild type on a multimodal cation exchange resin. MD simulation results provide additional insight at a molecular level and demonstrate that many residues located within the preferred binding region exhibit weaker binding interactions due to the mutation. The analysis suggests that multimodal ligand binding consists of initial localization of the ligand by long-ranged electrostatic interactions followed by multiple short-ranged synergistic interactions to attain high affinities of the ligand to specific residues.

Molecular simulations of multimodal ligand-protein binding: elucidation of binding sites and correlation with experiments.

Multimodal chromatography, which employs more than one mode of interaction between ligands and proteins, has been shown to have unique selectivity and high efficacy for protein purification. To test the ability of free solution molecular dynamics (MD) simulations in explicit water to identify binding regions on the protein surface and to shed light on the "pseudo affinity" nature of multimodal interactions, we performed MD simulations of a model protein ubiquitin in aqueous solution of free ligands. Comparisons of MD with NMR spectroscopy of ubiquitin mutants in solutions of free ligands show a good agreement between the two with regard to the preferred binding region on the surface of the protein and several binding sites. MD simulations also identify additional binding sites that were not observed in the NMR experiments. "Bound" ligands were found to be sufficiently flexible and to access a number of favorable conformations, suggesting only a moderate loss of ligand entropy in the "pseudo affinity" binding of these multimodal ligands. Analysis of locations of chemical subunits of the ligand on the protein surface indicated that electrostatic interaction units were located on the periphery of the preferred binding region on the protein. The analysis of the electrostatic potential, the hydrophobicity maps, and the binding of both acetate and benzene probes were used to further study the localization of individual ligand moieties. These results suggest that water-mediated electrostatic interactions help the localization and orientation of the MM ligand to the binding region with additional stability provided by nonspecific hydrophobic interactions.

Protein-surface interaction maps for ion-exchange chromatography.

In this paper, protein-surface interaction maps were generated by performing coarse-grained protein-surface calculations. This approach allowed for the rapid determination of the protein-surface interaction energies at a range of orientations and distances. Interaction maps of lysozyme indicated that there was a contiguous series of orientations corresponding to several adjacent preferred binding regions on the protein surface. Examination of these orientations provided insight into the residues involved in surface interactions, which qualitatively agreed with the retention data for single-site mutants. Interaction maps of lysozyme single-site mutants were also generated and provided significant insight into why these variants exhibited significant differences in their chromatographic behavior. This approach was also employed to study the binding behavior of CspB and related mutants. The results indicated that, in addition to describing general trends in the data, these maps provided significant insight into retention data of the single-site mutants. In particular, subtle retention trends observed with the K12 and K13 mutants were well-described using this interaction map approach. Finally, the number of interaction points with energies stronger than -2 kcal/mol was shown to be able to semi-quantitatively predict the behavior of most of the mutants. This rapid approach for calculating protein-surface interaction maps is expected to facilitate future method development for separating closely related protein variants in ion-exchange systems.

Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR.

NMR titration experiments with labeled human ubiquitin were employed in concert with chromatographic data obtained with a library of ubiquitin mutants to study the nature of protein adsorption in multimodal (MM) chromatography. The elution order of the mutants on the MM resin was significantly different from that obtained by ion-exchange chromatography. Further, the chromatographic results with the protein library indicated that mutations in a defined region induced greater changes in protein affinity to the solid support. Chemical shift mapping and determination of dissociation constants from NMR titration experiments with the MM ligand and isotopically enriched ubiquitin were used to determine and rank the relative binding affinities of interaction sites on the protein surface. The results with NMR confirmed that the protein possessed a distinct preferred binding region for the MM ligand in agreement with the chromatographic results. Finally, coarse-grained ligand docking simulations were employed to study the modes of interaction between the MM ligand and ubiquitin. The use of NMR titration experiments in concert with chromatographic data obtained with protein libraries represents a previously undescribed approach for elucidating the structural basis of protein binding affinity in MM chromatographic systems.

The effect of feed composition on the behavior of chemically selective displacement systems.

In this paper we examine whether adding a more retained protein to the feed will mitigate displacer-protein interactions in the column, thus affecting the displacement modality that occurs (chemically selective vs. traditional displacement chromatography). STD-NMR experiments were carried out to probe displacer-protein interactions for the chemically selective displacer chloroquine diphosphate and the results indicated that this displacer only had measurable interactions with the protein alpha-chymotrypsinogen A. For a two component feed mixture containing ribonuclease A and alpha-chymotrypsinogen A, the separation resulted in the displacement of ribonuclease A, with the more hydrophobic alpha-chymotrypsinogen A remaining on the column. On the other hand, when the experiment was repeated with cytochrome c added to the feed, all three feed proteins were displaced. Column simulations indicated that the combination of sample self-displacement occurring during the introduction of the feed, along with the dynamics of the initial displacement process at the column inlet was responsible for this behavior. These results indicate that for this class of hydrophobic-based selective displacers, in order for the protein to be selectively retained, the protein should be the most strongly retained feed component.

Utilization of lysozyme charge ladders to examine the effects of protein surface charge distribution on binding affinity in ion exchange systems.

A lysozyme library was employed to study the effects of protein surface modification on protein retention and to elucidate preferred protein binding orientations for cation exchange chromatography. Acetic anhydride was used as an acetylating agent to modify protein surface lysine residues. Partial acetylation of lysozyme resulted in the formation of a homologous set of modified proteins with varying charge densities and distribution. The resulting protein charge ladder was separated on a cation exchange column, and eluent fractions were subsequently analyzed using capillary zone electrophoresis and direct infusion electrospray ionization mass spectrometry. The ion exchange separation showed a significant degree of variation in the retention time of the different variants. Several fractions contained coelution of variants, some with differing net charge. In addition, several cases were observed where variants with more positive surface charge eluted from the column prior to variants with less positive charge. Enzymatic digest followed by mass spectrometry was performed to determine the sites of acetylation on the surface of the variants eluting in various fractions. Electrostatic potential maps of these variants were then generated to provide further insight into the elution order of the variants.

Investigation of protein binding affinity in multimodal chromatographic systems using a homologous protein library.

A library of cold shock protein B mutant variants was employed to examine differences in protein binding behavior in ion exchange and multimodal chromatography. Single site mutations introduced at charged amino acids on the protein surface resulted in a homologous protein set with varying charge density and distribution. The retention times of the mutants varied significantly during linear gradient chromatography in both systems. The majority of the proteins were more strongly retained on the multimodal cation exchange resin as compared to the traditional cation exchanger. Further, the elution order of the mutants on the multimodal resin was different from that obtained with the ion exchanger. Quantitative structure-property relationship models generated using a support vector regression technique were shown to provide good predictions for the retention times of protein mutants on the multimodal resin. A coarse-grained ligand docking package was employed to examine the various interactions between the proteins and ligands in free solution. The multimodal ligand was shown to utilize multiple interaction types to achieve stronger retention on the protein surface. The use of this protein library in concert with the qualitative and quantitative analyses presented in this paper provides an improved understanding of protein behavior in multimodal chromatographic systems.

Investigation of protein binding affinity and preferred orientations in ion exchange systems using a homologous protein library.

A library of cold shock protein B (CspB) mutant variants was employed to study protein binding affinity and preferred orientations in cation exchange chromatography. Single site mutations introduced at charged amino acids on the protein surface resulted in a homologous protein set with varying charge density and distribution. The retention times of the mutants varied significantly during linear gradient chromatography. While the expected trends were observed with increasing or decreasing positive charge on the protein surface, the degree of change was a strong function of the location and microenvironment of the mutated amino acid. Quantitative structure-property relationship (QSPR) models were generated using a support vector regression technique that was able to give good predictions of the retention times of the various mutants. Molecular descriptors selected during model generation were used to elucidate the factors affecting protein retention. Electrostatic potential maps were also employed to provide insight into the effects of protein surface topography, charge density and charge distribution on protein binding affinity and possible preferred binding orientations. The use of this protein mutant library in concert with the qualitative and quantitative analyses presented in the article provides an improved understanding of protein behavior in ion exchange systems.

Displacer concentration effects in displacement chromatography. Implications for trace solute detection.

In this paper, the utility of ion-exchange displacement chromatography for the concentration and enrichment of trace proteins is examined. Separations with varying displacer concentrations (1-25mM neomycin sulfate) indicate that higher concentrations result in elevated protein concentrations, at the price of reduced yields. The results demonstrate that displacement chromatography carried out at relatively low displacer concentrations (2.5mM) can produce significant concentration (8.5-fold) and enrichment (18-fold) of trace proteins present in the feed. Parametric simulations using the steric mass action model are carried out to investigate the concentration effects and enrichment factors observed over a wide range of feed, displacer and buffer counter-ion concentrations, and solute separation factors. The simulations confirm that trace components can be readily concentrated and enriched by displacement chromatography and that these effects will be more pronounced as the separation factor between trace and abundant components is increased. The results presented in this paper indicate the potential of displacement chromatography for improved separations where trace enrichment is critical such as proteomic applications.

Prediction of pH-dependent chromatographic behavior in ion-exchange systems.

In this study, predictive quantitative structure-property relationship (QSPR) models that employed a support vector machine regression algorithm and a set of novel pH-dependent descriptors were employed for the prediction of protein chromatographic behavior at any pH. The calculated pH-dependent descriptors were based on protein crystal structures and sequence information and represent charge and electrostatic potential properties on the protein surfaces. With this set of pH-dependent descriptors, proteins at different pH were treated as distinct molecules, thus enabling the generation of integrated QSPR models, which allow the prediction of chromatographic behavior of test set proteins across a wide range of mobile-phase pH conditions. The predictions from these integrated QSPR models in general showed good agreement with the experimental results. For proof of concept, the steric mass action adsorption isotherm parameters of a binary test set of proteins (lysozyme and aprotinin) at a pH not employed in the training set were predicted from the integrated QSPR models. Further, the predicted parameters were used in a macroscopic transport model to simulate the chromatographic separation of this binary protein mixture at this new pH. The simulated column behavior of these proteins showed good agreement with experimental results. The use of pH-dependent descriptors in this multiscale modeling approach now enables the prediction of various modes of protein chromatography at any mobile-phase pH, which may have significant implications for downstream bioprocessing.

Protein instability during HIC: describing the effects of mobile phase conditions on instability and chromatographic retention.

Hydrophobic interaction chromatography (HIC) is known to be potentially denaturing to proteins, but the effects of mobile phase conditions on chromatographic behavior are not well understood. In this study, we apply a model describing the effects of secondary protein unfolding equilibrium on chromatographic behavior, including the effects of salt concentration on both stability and adsorption. We use alpha-lactalbumin as a model protein that in the presence and absence of calcium, allows evaluation of adsorption parameters for folded and unfolded species independently. The HIC adsorption equilibrium under linear binding conditions and solution phase protein stability have been obtained from a combination of literature and new experiments. The effect of salt concentration on protein stability and the rate constant for unfolding on the chromatographic surface have been determined by fitting the model to isocratic chromatography data under marginally stable conditions. The model successfully describes the effects of added calcium and ammonium sulfate. The results demonstrate the importance of considering the effects on stability of mobile phase modifiers when applying HIC to marginally stable