Mechanistic studies of displacer–protein binding in chemically selective displacement systems using NMR and MD simulations

Abstract

A parallel batch screening technique was employed to identify chemically selective displacers which exhibited exclusive separation behavior for the protein pair a-chymotrypsin/ribonuclease A on a strong cation exchange resin. Two selective displacers, 1-(4-chlorobenzyl)piperidin-3-aminesulfate and N 0 1 0 -(4-methyl-quinolin-2-yl)-ethane-1,2-diamine dinitrate, and one non-selective displacer, spermidine, were selected as model systems to investigate the mechanism of chemically selective displacement chromatography. Saturation transfer difference (STD) NMR was used to directly evaluate displacer-protein binding. The results indicated that while binding occurred between the two chemically selective displacers and the more hydrophobic protein, a-chymotrypsin, no binding was observed with ribonuclease A. Further, the non-selective displacer, spermidine, was not observed to bind to either protein. Importantly, the binding event was observed to occur primarily on the aromatic portion of the selective displacers. Extensive molecular dynamic simulations of protein-displacer-water solution were also carried out. The MD results corroborated the NMR findings demonstrating that the binding of selective displacers occurred primarily on hydrophobic surface patches of a-chymotrypsin, while no significant long term binding to ribonuclease A was observed. The non-selective displacer did not show significant binding to either of the proteins. MD simulations also indicated that the charged amine group of the selective displacers in the bound state was primarily oriented towards the solvent, potentially facilitating their interaction with a resin surface. These results directly confirm that selective binding between a protein and displacer is the mechanism by which chemically selective displacement occurs. This opens up many possibilities for future molecular design of selective displacers for a range of applications.

Unique selectivity windows using selective displacers/eluents and mobile phase modifiers on hydroxyapatite

“…A Jupiter 5 m C4 300A column (4.6 mm × 50 mm) was purchased from Phenomenex (Torrance, CA). Ribonuclease A from bovine pancreas (RNaseA), ribonuclease B from bovine pancreas (RNaseB), ␣-chymotrypsinogen A from bovine pancreas (␣-ChyA), cytochrome C from equine heart (CytC), lysozyme from chicken egg white (Lys), conalbumin from chicken egg white (Conal), hemoglobin from bovine blood (Hemo), myoglobin from equine heart (Myo), avidin from chicken egg white, subtilisin A from Bacillus, elastase from porcine pancreas, papain from papaya latex, bromelain from pineapple stem, alcohol dehydrogenase from equine liver, trypsinogen from bovine pancreas, catalase from bovine liver, aprotinin from bovine lung, aconitase from porcine heart, albumin from bovine serum, neomycin sulfate (displacer 1), paromomycin sulfate (2), bekanamycin sulfate (3), amikacin sulfate (4), spermine (5), bis(hexamethylene)triamine (7), spermidine (8), 1,4-bis(3-aminopropyl)piperazine (9), diethylenetriamine (10), 4,7,10-trioxa-1,13-tridecanediamine (11), N,Ndiethyl-1,3-propanediamine (12), N,N-diethyldiethylenetriamine (13), 2-(2-aminoethylamino)ethanol (14), spectinomycin dihydrochloride pentahydrate (15), l-arginine methyl ester dihydrochloride (16), l-lysine methyl ester dihydrochloride (17), N-hexylethylenediamine (18), piperazine (19), cyclohexylamine (20), acetic acid (21), malonic acid (22), succinic acid (23), adipic acid (24), isocitric acid lactone (25), trans-aconitic acid (26), 1,2,4-butanetricarboxylic acid (27), 1,2,3,4-butanetetracarboxylic acid (28), glycine (29), 3-guanidinopropionic acid (30), 5-aminovaleric acid (31), pantothenic acid (32), aspartic acid (33), l-␤-homoglutamic acid hydrochloride (34), guanidinosuccinic acid (35), l-2,3-diaminopropionic acid hydrochloride (36), lysine (37), arginine (38), meso-2,3,-diaminosuccinic acid (39), ethylenediaminetetrapropionic acid (40), glycerol (41), threitol (42), adonitol (43), dulcitol (44), malic acid (45), tartaric acid (46), mucic acid …”

“…There are two classes of selective displacers, mass action and chemically selective displacers. Chemically selective displacement has been shown to be caused by a selective binding event between the displacer and the protein which is retained in the displacer zone [18][19][20][21][22]. Mass action selective displacers typically have an affinity for the resin that lies between that of the two solutes being separated and can be readily predicted using the steric mass action formalism [23,24].…”

NMR Spectroscopy for Studying Interactions of Bioactive Molecules

“…Those findings demonstrated the specificity of anaesthetics for a particular protein conformation. Several research groups have proposed the implementation of STD-NMR spectroscopy in chromatographic optimisation studies [74,75]. STD-NMR in combination with molecular dynamics simulations can be used to screen chiral stationary phases for evidence of molecular interactions as a predictor of chiral column selection and to study the mechanism of chemically selective displacement chromatography.…”

Application of a Spherical Harmonics Expansion Approach for Calculating Ligand Density Distributions around Proteins

“…For complex multisite ligands, which have multiple binding sites around the protein, similar free solution simulations can be carried out and calculations of spatial distribution of ligands can be performed based on the probability of finding a ligand atom (or center of mass) within a certain distance from the atoms/residues on the protein. , These calculations are, however, limited to a local region around the protein, and the directional dependence of ligand distribution in the three-dimensional (3D) space around the proteins becomes difficult to quantify. Grid-based calculations can also be performed by keeping track of the location of ligand atoms during the simulation.…”