binding constants of levans and D-fructo-oligosaccharides to BALB/c and NZB D-fructan-specific, myeloma proteins, determined by affinity electrophoresis

New Insights into the Role of Hydrogen Bonding in Furanoside Binding to Protein

Furanosides have been subjected to extensive studies owing to their inherent flexibility, which is believed to play an important role in the survival and pathogenicity of different disease-causing organisms in the human body. This study reports the binding free energy (ΔG) and specificity of arabinofuranose oligosaccharides to a protein, arabinanase (Arb43A), with the use of potential of mean force (PMF) calculations using the umbrella-sampling simulations. Long molecular dynamics simulations have been carried out to understand intermolecular interactions in the arabinofuranose-protein complex. The PMF for pulling the α-(1 → 5)-linked L-arabinohexaose (ligand) from the protein provides a large free energy of binding, -16.8 kcal/mol. The ΔG of the nonreducing arabinotriose end is found to be -12.6 kcal/mol, while the ΔG of the reducing end is calculated to be -7.7 kcal/mol. In the absence of nonreducing arabinotrioside, the ΔG of the reducing arabinotrioside is -8.5 kcal/mol. Similarly, in the absence of reducing arabinotrioside, the ΔG of the nonreducing arabinotrioside is calculated to be -9.4 kcal/mol. The main contributing factor in the protein-arabinofuranose binding is hydrogen bonding. Acidic amino acid residues, Glu and Asp, with furanosides produce the strongest hydrogen bonding. Araf-A, B, and C construct the reducing arabinotriose, while Araf-D, E, and F construct the nonreducing arabinotriose. Since most of the hydrogen-bonding occupancies belong to Araf-D and Araf-E, the nonreducing arabinotriose is bound to protein more strongly than the reducing arabinotriose. This explains why the reducing arabinotriose can detach from the protein in nature.

Utilization of enzyme-substrate interactions in analytical chemistry

Enzymes are capable of a highly specific interaction with a variety of substances including their respective substrates. This review summarizes how such interactions may be used in analytical (bio-)chemistry, e.g., for the elucidation of the binding mechanism, the determination of the binding strength, the carting of the binding site, or the screening of possible substrate/inhibitor molecules. Possible assay formats such as analytical affinity chromatography, affinity capillary electrophoresis (ACE), conventional affinity gel electrophoresis (AEP), and related techniques are discussed together with examples of recent applications. In addition a brief section on enzyme-substrate reactions as tools in analytical chemistry is included, since these are perhaps even more important to analytical (bio-)chemistry. The development and application of bioanalytical systems and especially biosensors in various fields including medicine, biotechnology, agriculture, defense and foodstuffs are considered.

Affinity electrophoresis and its applications to studies of immune response

Affinity electrophoresis (AEP) is a useful technique for separation of biomolecules such as plasma proteins, enzymes, nucleic acids, lectins, receptors, and extracellular matrix proteins by specific interactions with their ligands in electric fields and for the determination of dissociation constants for those interactions. Two-dimensional affinity electrophoresis (2-D AEP), which was newly developed by a combination of isoelectric focusing with AEP, has been used for studies on immune response to haptens. Antihapten antibodies, which were induced by immunization of a mouse with the hapten-conjugated bovine serum albumin, were separated by 2-D AEP into a large number of groups of IgG spots with a few microliters of antiserum. Each group of spots showed an identical affinity for the hapten but different isoelectric points as in the case of monoclonal antibodies specific to the hapten. This enabled us to study the diversification and affinity maturation of antihapten antibodies in the course of immunization of a single mouse. Furthermore, effects of a carrier and a hapten array on the production of antihapten antibodies and the cause of charge heterogeneity of monoclonal antibodies were also examined to understand the molecular basis of the immune response in vivo.

Conformational analysis of beta-D-fructofuranosyl-(2-->6)-beta-D-glucopyranoside by molecular mechanics (MM2) calculations

Conformational energies for models of the disaccharide beta-D-fructofuranosyl-(2-->6)-beta-D-glucopyranoside were computed by molecular mechanics using MM2(87). An initial investigation of staggered forms examined the linkage bonds characterized by the torsion angles phi, psi, and omega, and subsequently the fructose hydroxymethyl side groups, characterized by the torsion angles chi-1 and chi-6. Then, in our major search of conformational space, the torsion angles of two linkage bonds, phi and omega, were driven through 360 degrees in 20 degree increments at all staggered side group combinations. From these results, the low-energy forms were minimized without the driver restrictions to generate the global minimum structure found and herein reported. This conformer was then used to map the conformational space of phi and omega by driving only those torsion angles through 360 degrees. Both the 4(3)T (northern) conformer (Cremer-Pople puckering phase angle of phi 2 = 265 degrees) and the 3(4)T, (southern) conformer (phi 2 = 80 degrees) of the fructofuranose ring were tested for comparison, and both were shown to be significant contributors of populated forms. As these two conformers had different minima for a number of important torsion angles, experimental studies may reveal different properties than those expected solely from the preferred northern conformer.

Binding specificities of inulin-binding immunoglobulins for sinistrin and oligosaccharides isolated from asparagus roots

The major aim of this study was to further investigate the fine specificity of myeloma proteins recognizing epitopes on fructans. Our studies showed that UPC 61, EPC 109, and a hybrid antibody composed of the heavy chain from UPC 61 and the light chain from EPC 109, UPC 61H:EPC 109L, not only bind to inulin which is a linear fructan of beta (2----1) fructofuranosyl linkages, but also bind to sinistrin, a branched molecule consisting of a beta (2----1) fructofuranosyl backbone with beta (2----6) branch points. The fine binding specificity of these three antibodies for the beta (2----1) fructofuranosyl linkages found in inulin-BSA can be further studied by their binding to fructan oligosaccharides isolated from asparagus roots. From a comparative analysis of the amino acid sequences and the apparent affinity constants (aKa) of UPC 61, EPC 109, and the hybrid for various fructan oligosaccharides, it appears that the light chain of the immunoglobulin molecule makes an important contribution to the binding specificity. Finally we report for the first time that a monoclonal antibody specific for beta (2----6) fructans can also bind specifically to inulin-BSA with a lower affinity. This antibody derives its VH and VL from the VHX24 and Vk10b gene families, respectively, which are different from the gene families utilized by UPC 61 and EPC 109 (VHJ606 and Vk11 gene families).