Protein surface area and retention in hydrophobic interaction chromatography

Summary Molecular surface areas accessible to a 4 ? diameter spherical probe were calculated from crystallographic data for five proteins: α-chymotrypsinogen A, lysozyme, trypsinogen, ribonuclease A and ribonuclease S. The retention factors of various proteins were measured on stationary phases having polyether- and phenylligates and with aqueous eluents containing (NH₄)₂SO₄, Na₂SO₄ or NaCl at pH 7.0. The logarithmic retention factors were plotted against the salt molality and the hydrophobic interaction parameters evaluated from the limiting slopes of the plots at high salt concentrations for the proteins in the chromatographic systems investigated. The hydrophobic interaction parameters thus obtained were linear in both the molecular surface areas of the proteins and the molal surface tension increments of the salts. The experimental results obtained with these relatively simple proteins of known molecular structure, which were available in high purity, support earlier theoretical predictions for the dependence of the hydrophobic interaction parameter on the surface area of the protein and the surface tension raising effect of the salt.     

Prediction of retention times of proteins in hydrophobic interaction chromatography using only their amino acid composition

This paper focuses on the prediction of the dimensionless retention time of proteins (DRT) in hydrophobic interaction chromatography (HIC) by means of mathematical models based, essentially, only on aminoacidic composition. The results show that such prediction is indeed possible. Our main contribution was the design of models that predict the DRT using the minimal information concerning a protein: its aminoacidic composition. The performance is similar to that observed in models that use much more sophisticated information such as the three-dimensional structure of proteins. Three models that, in addition to the amino acid composition, use different assumptions about the amino acids tendency to be exposed to the solvent, were evaluated in 12 proteins with known experimental DRT. In all the cases analyzed, the model that obtained the best results was the one based on a linear estimation of the aminoacidic surface composition. The models were adjusted using a collection of 74 vectors of aminoacidic properties plus a set of 6388 vectors derived from these using two mathematical tools: k-means and self-organizing maps (SOM) algorithms. The best vector was generated by the SOM algorithm and was interpreted as a hydrophobicity scale based partly on the tendency of the amino acids to be hidden in proteins. The prediction error (MSE(JK)) obtained by this model was almost 35% smaller than that obtained by the model that supposes that all the amino acids are completely exposed and 40% smaller than that obtained by the model that uses a simple correction factor considering the general tendency of each amino acid to be exposed to the solvent. In fact, the performance of the best model based on the aminoacidic composition was 5% better than that observed in the model based on the three-dimensional structure of proteins.     

Prediction of protein retention times in gradient hydrophobic interaction chromatographic systems

A two-step methodology has been developed for the prediction of protein retention time in linear-gradient HIC systems. Isocratic retention parameters were determined from ln(k')-salt concentration plots for a number of commercially available proteins with a range of properties. Quantitative structure property relationship (QSPR) models based on a support vector machine (SVM) approach were generated for predicting isocratic retention parameters for proteins not included in the model generation. The predicted parameters were then used to calculate protein gradient retention times and the results indicate that this approach is well suited for predicting experimental gradient retention data. The approach presented in this paper may have implications for HIC methods development at both the bench and process scales.     

Prediction of retention time of phenols in liquid chromatography

The chromatographic behavior of phenols in reversed-phase mode liquid chromatography differs from that of non-ionic compounds such as alkyl alcohols, alkylbenzenes, halogenated benzenes, polyaromatic hydrocarbons, and aromatic acids. Therefore, the retention times of 61 phenols were measured in a system of an octadecyl bonded silica gel and acetonitrile/water mixtures. The logarithm of the capacity ratio (log k') was found to be a linear function of the hydrophobicity (log P) in acidic acetonitrile/water mixtures. This result was applied to a different octadecyl bonded silica gel. Eight phenols were selected as standard compounds, and their log k' values were measured in 0.05 M phosphoric acid in 10 to 90% acetonitrile/water mixtures. An empirical polynomial relation was obtained between the concentration of acetonitrile and the slope of the log k' vs log P curve. Finally the capacity ratio of all phenols were calculated in given eluents by the equations derived from the measurements of standard compounds and the calculated log P values. The difference between predicted capacity ratios and measured ones was within 10%.     

Mathematical correlations for predicting protein retention times in hydrophobic interaction chromatography

In our work we performed a combinatorial synthesis in aqueous medium to prepare peptide libraries from which we would select amino acid sequences with binding properties towards estrogens. We prepared an affinity solid-phase by using a tetrapeptide with good selectivity and affinity towards the estradiol (K> 10(4) M(-1)). Samples of estrogens in buffer, in tap water and in river water were applied to our column in which they were retained (k' > 116). These could only be eluted in a few millilitres of methanol mobile phase. In all cases there were quantitative recoveries. The pre-concentration studies were promising.     

Hydrophobic contribution of amino acids in peptides measured by hydrophobic interaction chromatography

The adsorption behaviors of amino acids in short chain peptides were examined. Each amino acid, aliphatic or charged, was inserted between the two tryptophans of a peptide, GWWG. The capacity factors of these peptides on an Ocytl-Sepharose column were measured. The adsorption enthalpies, entropies, and the number of repelled water molecules after adsorption were estimated to analyze the contribution of each different amino acid to its hydrophobic adsorption. The peptides inserted with aliphatic amino acids owned the highest capacity factors but released the least amount of adsorption heat among all the peptides under examination. It was found that the hydrophobic contribution of aliphatic amino acids was derived from the entropy gain by repelling the ordered water surrounding them. The insertion of negatively charged amino acids greatly reduced the capacity factors but still repelled a significant number of water molecules after adsorption. This indicated that the water molecules surrounding ionic amino acids were not orderly aligned. The dehydration cost energy but the water repelling did not offer enough entropy to drive the adsorption. Subsequently, lower retention was obtained from the peptides inserted with negatively charged ionic amino acids. The insertion of lysine increased the adsorption enthalpy but repelled no water molecules after adsorption. It was speculated that the inserted lysine still interacted with hydrophobic ligands but disturbed the interaction between ligands and adjacent tryptophans. Therefore, the adsorption enthalpy increased and the capacity factors decreased. Different amino acids contributed to hydrophobic interaction in different ways. The simultaneous analysis of capacity factor, adsorption enthalpy, adsorption entropy, and the number of repelled water molecules facilitated the understanding of the adsorption processes.     

Effect of surface hydrophobicity distribution on retention of ribonucleases in hydrophobic interaction chromatography

The effect of surface hydrophobicity distribution of proteins on retention in hydrophobic interaction chromatography (HIC) was investigated. Average surface hydrophobicity as well as hydrophobic contact area between protein and matrix were estimated using a classical thermodynamic model. The applicability of the model to predict protein retention in HIC was investigated on ribonucleases with similar average surface hydrophobicity but different surface hydrophobicity distribution. It was shown experimentally that surface hydrophobicity distribution could have an important effect on protein retention in HIC. The parameter "hydrophobic contact area," which comes from the thermodynamic model, was able to represent well the protein retention in HIC with salt gradient elution. Location and size of the hydrophobic patches can therefore have an important effect on protein retention in HIC, and the hydrophobic contact area adequately describes this.     

Applying flexible molecular docking to simulate protein retention behavior in hydrophobic interaction chromatography

Interaction between proteins and stationary phase in hydrophobic interaction chromatography (HIC) is differentiated into two thermodynamic processes involving direct nonbonding/conformation interac- tion and surface hydrophobic effect of proteins, hence quantitatively giving rise to a binary linear rela- tion between HIC retention time (RT) at concentrated salting liquid and ligand-protein binding free en- ergy. Then, possible binding manners for 27 proteins of known crystal structures with hydrophobic ligands are simulated and analyzed via ICM flexible molecular docking and genetic algorithm, with re- sults greatly consistent with experimental values. By investigation, it is confirmed local hydrophobic effects of proteins and nonbinding/conformation interaction between ligand and protein both notably influence HIC chromatogram retention behaviors, mainly focusing on exposed portions on the protein surface.     

Prediction of peptide retention time in reversed-phase high-performance liquid chromatography.

Peptide retention in reversed-phase chromatography depends mainly on the amino acid composition of peptides and can therefore be predicted by summing the relative hydrophobic contributions of each constitutive amino acid residue. The prediction is correct for small peptides but overestimates the retention times of peptides larger than 10-15 residues. A new prediction model is proposed in which the contribution to peptide retention of each amino acid residue is not a constant but a decreasing function of peptide length. From the retention times of 104 peptides, the parameters of decreasing functions were estimated by a non-linear multiple regression analysis. The contribution to peptide retention of charged, polar and non-polar residues appears to be differently affected by peptide length. The secondary structure of most peptides during reversed-phase high-performance liquid chromatography could be responsible for this. The high correlation between the predicted and observed retention times of peptides which were not used to establish the model indicates a good predictive accuracy of the new model.     

Prediction of peptides retention behavior in reversed-phase liquid chromatography based on their hydrophobicity

Hydrophobicity is an important physicochemical property of peptides and proteins. It is responsible for their conformational changes, stability, as well as various chemical intramolecular and intermolecular interactions. Enormous efforts have been invested to study the extent of hydrophobicity and how it could influence various biological processes, in addition to its crucial role in the separation and purification endeavor as well. Here, we have reviewed various studies that were carried out to determine the hydrophobicity starting from (i) simple amino acids solubility behavior, (ii) experimental approach that was undertaken in the reversed-phase liquid chromatography mode, and ending with (iii) some examples of more advanced computational and machine learning models.     

Two-step recovery process for tryptophan tagged cutinase: interfacing aqueous two-phase extraction and hydrophobic interaction chromatography

In this work, the interfacing of a poly(ethylene glycol) (PEG)-phosphate aqueous two-phase system with hydrophobic interaction chromatography (HIC) for primary recovery of an intracellular protein was evaluated. As a model protein, a recombinant cutinase furnished with a tryptophan-proline (WP) peptide tag was used and produced intracellularly in Escherichia coli (E. coli). E. coli cell homogenate was partitioned in a two-phase system and the top phase yield, concentration and purity of the tagged ZZ-cutinase-(WP)4 was evaluated as function of polymer sizes, system pH and phase volume ratio. The partition behaviour of cell debris, total protein and endotoxin was also monitored. In the HIC part, the chromatographic yield and purity was investigated with respect to ligand hydrophobicity, dilution of loaded top phase and elution conditions. Based on the results, a recovery process was demonstrated where a PEG 1500-K-Na phosphate salt aqueous two-phase system was interfaced with a HIC column. The interfacing was facilitated by the Trp-tagged peptide. The tagged ZZ-cutinase-(WP)4 was obtained in a PEG-free phase and purified to >95% purity according to silver stained sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels with a total yield of 83% during the two-step recovery process.     

A theory of protein-resin interaction in hydrophobic interaction chromatography

Docking simulations were performed in order to investigate surface area of interaction between several ribonucleases and a reduced model for the hydrophobic moiety used in Phenyl Sepharose using the program AutoDock 3.0. For each ribonucelase, 80 independent simulations with populations consisting of 100 random structures were performed and from these the most probable docked protein-ligand conformations were obtained. A new methodology was used to select the most probable conformations, based on qualitative and quantitative considerations. The interacting amino acids in each protein were identified. The average surface hydrophobicity of the interfacial zone (local hydrophobicity, LH) was determined. The LH showed a high correlation level (r2 = 0.99) with the "hydrophobic contact area" (HCA) experimentally determined for the different ribonucleases as well as with the dimensionless retention time (r2 = 0.90). This study allowed us to identify the zones on the protein surface most probably involved in protein retention in HIC, without tedious experimental work. Given the good correlation level obtained, this new methodology may constitute a novel approach that could be used to predict protein behavior in HIC.     

Effect of stationary and mobile phases on hydrophobic interaction chromatography of proteins and peptides

A number of different stationary phases designed for hydrophobic interaction chromatography have been examined to assess their efficiency and resolving capability with respect to protein and peptide mixtures. A packing with an ether-bonded phase was substantially less hydrophobic than those with propyl- or phenyl-bonded surface chemistry. While the overall efficiencies of most columns were broadly similar with respect to most proteins, some proteins did chromatograph with enhanced efficiency on specific packings. The elution order of individual proteins was, with one or two exceptions, similar for all columns tested using comparable mobile phases. It differed, however, substantially from orders obtained with conventional reversed-phase alkyl-bonded phases and from the elution orders obtained when the hydrophobic packings were used in a reversed-phase mode, i.e. with an organic modifier gradient. Varying the salt used in the mobile phase and its pH under hydrophobic interaction conditions (high ionic strength) changed overall retentivities and also altered specific retention orders, thus offering possibilities of selective resolution of some mixtures.     

Separations of hydrophobic synthetic peptides in counter-current chromatography

Synthetic peptides with many aromatic, aliphatic and especially acidic amino acid residues are not very soluble and require strong solvents for useful partitioning. A chloroform-methanol-acidic solvent system fractionates neutral and basically charged 26-mers to provide high yields. An insoluble 15-mer with 5 Trp residues and 60% overall hydrophobic amino acid content was purified in pyridine-acetic acid and in another basic t-butyl methyl ether-n-butanol-acetonitrile solvent system with high recovery. Two instruments were used, the eccentric-multi-layer hybrid coil planet centrifuge and the new spiral disk planet centrifuge that were able to retain the stationary phase of these solvent systems, some of which have low interfacial tension.     

Effects of thermal heterogeneity in hydrophobic interaction chromatography

Manipulating temperature and salt concentration can have a powerful effect on the separation effectiveness in hydrophobic interaction chromatography (HIC). However, use of temperature as an operating variable in large-scale applications may involve undesirable consequences such as radial heterogeneity of the column temperature. In this study non-ideal effects of heat transfer in HIC columns were analyzed. The radial temperature gradients were measured by thermocouples immersed in a bed packed into a preparative column. The column wall was either thermostatted by a water jacket or left under ambient conditions. The influence of ineffective column thermostatting and of heat losses on the radial temperature profiles was demonstrated and predicted by a model of heat dispersion in a packed bed. To analyze possible positive or negative effects of thermal heterogeneity on band propagation, non-isothermal chromatographic elution of a model protein (α-chymotrypsinogen A) was recorded under salt gradient conditions as well as at constant salt concentration. To predict temperature and concentration profiles a model of the column dynamics was used. The model accounted for kinetics of mass and heat transfer. A good agreement between experimental and simulated profiles was achieved. It was shown that by proper selection of the process conditions undesirable temperature effects can be avoided or controlled.     

Influence of the sample-solvent on protein retention,mass transfer and unfolding kinetics in hydrophobic interaction chromatography

Typical mobile phase employed in hydrophobic interaction chromatography contains cosmotropic salts, which promote retention and simultaneously reduce the protein solubility in the mobile phase. To increase mass overloading in the separation process the protein can be dissolved in a sample-solvent with concentration of salt lower than that in the mobile phase or in salt free solutions. However, this methodology may cause band splitting and band deformation, which results in yield losses. In this study, these phenomena were analyzed based on the retention behavior of two model proteins, i.e., lysozyme and bovine serum albumin. Retention of these proteins was accompanied by strong band broadening originated from slow rates of mass transfer and/or of adsorption–desorption process involving the protein conformational changes. The mass transport resistances and unfolding kinetics were found to contribute to the sample-solvent effects. To avoid band deformations the process variables such as the salt concentration and temperature were adjusted in such a way that complete resolution between band profile of the sample-solvent and the protein was achieved. For the process simulation a dynamic model, which accounted for underlying kinetics was used. General guidelines of the process design were developed.     

Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention

Hydrophobic interaction chromatography (HIC) is a key technique for protein separation and purification. Different methodologies to estimate the hydrophobicity of a protein are reviewed, which have been related to the chromatographic behavior of proteins in HIC. These methodologies consider either knowledge of the three-dimensional structure or the amino acid composition of proteins. Despite some restrictions; they have proven to be useful in predicting protein retention time in HIC.