Study of Conformation Effects on the Retention of Small Peptides in Reversed-Phase Chromatography by Thermodynamic Analysis and Molecular Dynamics Simulation

Computational prediction of diastereomeric separation behavior of fluorescent o-phthalaldehyde derivatives of amino acids

We have developed a convenient method for predicting the LC resolution of amino acid diastereomers through computational calculations. For acquiring experimental data, we derivatized 10 amino acids using o-phthalaldehyde and N-acetyl-L-cysteine as fluorogenic diastereomer-forming reagents and analyzed the diastereomers using reversed-phase LC and fluorescence detection. For theoretical chemical calculations, we used the publicly available semi-empirical calculation software MOPAC2012. Using the obtained experimental and theoretical data, we determined the change in analytical resolution with differences in the structure of the diastereomers. From the results obtained, we concluded that greater conformational change through diastereomeric derivatization induced an increase in the contact area with the stationary phase, leading to higher resolution.

HPLC retention thermodynamics of grape and wine tannins

The effect of grape and wine tannin structure on retention thermodynamics under reversed-phase high-performance liquid chromatography conditions on a polystyrene divinylbenzene column was investigated. On the basis of retention response to temperature, an alternative retention factor was developed to approximate the combined temperature response of the complex, unresolvable tannin mixture. This alternative retention factor was based upon relative tannin peak areas separated by an abrupt change in solvent gradient. Using this alternative retention factor, retention thermodynamics were calculated. Van't Hoff relationships of the natural log of the alternative retention factor against temperature followed Kirchoff's relationship. An inverse quadratic equation was fit to the data, and from this the thermodynamic parameters for tannin retention were calculated. All tannin fractions exhibited exothermic, spontaneous interaction, with enthalpy-entropy compensation observed. Normalizing for tannin size, distinct tannin compositional effects on thermodynamic parameters were observed. The results of this study indicate that HPLC can be valuable for measuring the thermodynamics of tannin interaction with a hydrophobic surface and provides a potentially valuable alternative to calorimetry. Furthermore, the information gathered may provide insight into understanding red wine astringency quality.

Molecular simulation studies of reversed-phase liquid chromatography

Over the past 20 years, molecular simulation methods have been applied to the modeling of reversed-phase liquid chromatography (RPLC). The purpose of these simulations was to provide a molecular-level understanding of: (i) the structure and dynamics of the bonded phase and its interface with the mobile phase, (ii) the interactions of analytes with the bonded phase, and (iii) the retention mechanism for different analytes. However, the investigation of chromatographic systems poses significant challenges for simulations with respect to the accuracy of the molecular mechanics force fields and the efficiency of the sampling algorithms. This review discusses a number of aspects concerning molecular simulation studies of RPLC systems including the historical development of the subject, the background needed to understand the two prevalent techniques, molecular dynamics (MD) and Monte Carlo (MC) methods, and the wealth of insight provided by these simulations. Examples from the literature employing MD approaches and from the authors' laboratory using MC methods are discussed. The former can provide information on chain dynamics and transport properties, whereas the latter techniques are uniquely suited for the investigation of phase and sorption equilibria that underly RPLC retention, and both can be used to elucidate the bonded-chain conformations and solvent distributions.

Retention prediction of peptide diastereomers in reversed-phase liquid chromatography assisted by molecular dynamics simulation

In this study, we explored the relationship between the retention factors and structural flexibilities of peptide diastereomers in reversed-phase chromatography (RPC) based on thermodynamic interpretations. The RPC retention order of antimicrobial peptides, IL-K7F89 (H-ILPWKWKFFPWRR-NH(2)), and its four diastereomers were well correlated with the order of their conformation energies in elution solvent. In particular, when the composition of the sample loading solvent was altered, the retention order changed accordingly. The thermodynamic analysis revealed that the peptide adsorption was driven by adsorption enthalpy, but the retention order was dominated by adsorption entropy. To further understand the relationships between the retention factor and conformation energy, the intramolecular van der Waals energy of peptides and the ordered water molecules associated with peptides were analyzed by all-atom molecular dynamics (MD) simulation. The results showed that the flexible peptide with larger conformation energy had weaker intramolecular hydrophobic interaction and associated with more ordered water molecules. For this peptide diastereomer set, the elution difference is derived by the difference in adsorption entropy gain from repelling the ordered water molecules around the peptide. Consequently, we suggested that the separation of peptide diastereomers could be achieved by RPC, and the elution order could be predicted by their structural flexibilities.

Adsorption of antimicrobial indolicidin-derived peptides on hydrophobic surfaces

The hydrophobic interaction between antimicrobial peptides and membrane hydrophobic cores is usually related to their cytotoxicity. In this study, the adsorption mechanism of five plasma membrane-associated peptides, indolicidin (IL) and its four derivatives, with hydrophobic ligands was investigated to understand the relationship between peptide hydrophobicity and bioactivity. The hydrophobic adsorption mechanisms of IL and its derivatives were interpreted thermodynamically and kinetically by reversed-phase chromatography (RPC) analysis and surface plasmon resonance (SPR) measurement, respectively. IL and its derivatives possess a similar random coil structure in both aqueous and organic solvents. Thermodynamic analysis showed that the binding enthalpy of peptides with higher electropositivity was lower than those with lower electropositivity and exhibited unfavorable binding entropy. Higher electropositivity peptides adsorbed to the hydrophobic surface arising from the less bound solvent on the peptide surface. A comparison with the kinetic analysis showed that IL and its derivatives adopt a two-state binding model (i.e., adsorption onto and self-association on the hydrophobic acyl chain) to associate with the hydrophobic surface, and the binding affinity of peptide self-association correlates well with peptide hemolysis. Consequently, this study provided a novel concept for understanding the action of plasma membrane-associated peptides.

Comparison of molecular dynamics simulation methods for amyloid β(1-42) monomers containing D-aspartic acid residues for predicting retention times in chromatography

Molecular dynamics simulations of amyloid β(1-42) containing D-aspartic acid residues were performed using several continuous solvent models to investigate the usefulness of simulation methods for D-amino acid-containing proteins and peptides. Normal molecular dynamics simulations and replica exchange molecular dynamics simulations, which are one of the generalized-ensemble algorithms, were performed. Because the β-structure contents of amyloid β(1-42) peptides obtained by replica exchange molecular dynamics simulations with Onufriev-Bashford-Case generalized Born implicit solvent were qualitatively consistent with experimental data, replica exchange molecular dynamics rather than other methods appeared to be more reasonable for calculations of amyloid β(1-42) containing D-aspartic acid residues. Computational results revealed that peptides with stereoinversion of Asp23 tend to form β-sheet structures by themselves, in contrast to the wild-type peptides that form β-sheet structures only after aggregation. These results are expected to be useful for computational investigations of proteins and peptides such as prediction of retention time of peptides and proteins containing D-aspartic acid residues.