Antibody recognition of chiral surfaces. Structural models of antibody complexes with leucine-leucine-tyrosine crystal surfaces

Conformational adaptability determining antibody recognition to distomer: structure analysis of enantioselective antibody against chiral drug gatifloxacin

Enantioselective antibodies have great potential to separate and detect chiral compounds. However, cross-reactivity of enantioselective antibodies to the distomer may limit the application. An in-depth understanding of interactions between antibodies and chiral drugs could be helpful to investigate antibody recognition to the distomer. In this study, a monoclonal antibody against chiral quinolone S-(−)-gatifloxacin (S-GAT) was produced and its Fab fragment was prepared by proteolysis. The S-GAT Fab exhibited 10% cross-reactivity against the R-enantiomer compared to that of the S-enantiomer in an indirect competitive enzyme-linked immunosorbent assay (icELISA). The crystal structures of the S-GAT Fab apo form and complex with S-GAT were analyzed, and molecular docking of the R-enantiomer was carried out. The ligand conformation was further studied using molecular dynamics simulations. The results showed that the distomer R-enantiomer could enter the chiral center recognition region of the antibody by adjusting the piperazine ring conformation. Meanwhile, the antibody binding cavity had obvious conformational adaptability during ligand binding. It demonstrated that conformational change of both ligand and antibody was the key reason why antibodies recognize the distomer. Restricting conformational adaptability could improve the enantioselective recognition ability of antibodies. This study provided a new explanation for the cross-reactivity of enantioselective antibodies to the distomer, and could help to modulate antibody enantioselectivity for immunoassay of chiral drugs.

The conformational adaptability of both antibody and ligand could determine the antibody enantioselectivity in chiral drug immunoassay.

On the limited recognition of inorganic surfaces by short peptides compared with antibodies

The vast potential applications of biomolecules that bind inorganic surfaces led mostly to the isolation of short peptides that target selectively specific materials. The demonstrated differential affinity toward certain surfaces created the impression that the recognition capacity of short peptides may match that of rigid biomolecules. In the following, we challenge this view by comparing the capacity of antibody molecules to discriminate between the (100) and (111A) facets of a gallium arsenide semiconductor crystal with the capacity of short peptides to do the same. Applying selection from several peptide and single chain phage display libraries, we find a number of antibody molecules that bind preferentially a given crystal facet but fail to isolate, in dozens of attempts, a single peptide capable of such recognition. The experiments underscore the importance of rigidity to the recognition of inorganic flat targets and therefore set limitations on potential applications of short peptides in biomimetics.

Two and three-dimensional pattern recognition of organized surfaces by specific antibodies

Understanding molecular recognition of supramolecules for solid substrates is essential for designing chemical sensors and molecular devices. The rules of molecular recognition are well established at the level of single molecules. However, during the transition from molecular-scale devices to macroscopic devices, issues concerning control over recognition that are well-established at the molecular level become much more complex. Hopefully, the conceptual and practical considerations reported here will clarify some of these issues. The immune system uses antibodies to identify molecular surfaces through molecular recognition. Antibodies are thus appropriate tools to study the rules of macromolecule-surface interactions, and this was done using crystal surfaces as substrates. Crystals can be formed or introduced into organisms and should be thus treated by the organism as any other intruder, by eliciting antibodies specific to their surfaces. A structure-recognizing antibody is defined here as complementary to a certain ordered supramolecular organization. It can be considered as a mold bearing in its binding site memory of the organization against which it was elicited. On the surface of a crystal composed of relatively small organic molecules, an antibody binding site would encompass an array of 10-20 molecular moieties. The antibody binding site would not detect one molecule, but rather a two- or three-dimensional molecular arrangement on the surface, similar to a macromolecular surface. The complementarity between antibody binding site and surface is supported by stereoselective supramolecular interactions to the repetitive structural motifs that are exposed at the surface. A procedure was developed in order to isolate monoclonal antibodies that specifically recognize a certain crystalline surface. The procedure was applied in particular to crystals of cholesterol monohydrate, of 1,4-dinitrobenzene, and of the tripeptide (S)leucine-(S)leucine-(S)tyrosine (LLY). A series of antibodies were selected and studied, three of which provided reliable specific antibody-antigen structural models. The three docking models show an astounding geometrical and chemical match of the antibody binding sites on the respective crystal surfaces. We also showed that antibodies are intrinsically capable of recognition at the length scale necessary for detection of chirality. Once the structural parameters determining the antibody specificity to the target surfaces are characterized, the antibodies may be conceivably used as reporters of the existence and location of target domains with similar structure in biological milieus. In this context, we developed and characterized monoclonal antibodies specific to crystalline mixed monolayers of cholesterol and ceramide, fundamental building blocks of lipid microdomains in cellular membranes. When used on cells, one antibody indeed labels cell membrane domains composed of cholesterol and ceramide. The fundamental contribution of the approach developed here may be in the antibody ability to report on the structural organization of paracrystalline domains that cannot be determined by other means. Alternatively, structure-recognizing antibodies may be conceivably used to carry information or build connections to specific targets, which may offer interesting developments in medicine or electronics.

On proteins, grids, correlations, and docking

The activity of a living cell can be portrayed as a network of interactions involving proteins and nucleic acids that transfer biological information. Intervention in cellular processes requires thorough understanding of the interactions between the molecules, which can be provided by docking techniques. Docking methods attempt to predict the structures of complexes given the structures of the component molecules. We focus hereby on protein-protein docking procedures that employ grid representations of the molecules, and use correlation for searching the solution space and evaluating putative complexes. Geometric surface complementarity is the dominant descriptor in docking. Inclusion of electrostatics often improves the results of geometric docking for soluble proteins, whereas hydrophobic complementarity is more important in construction of oligomers. Using binding-site information in the scan or as a filter helps to identify and up-rank nearly correct solutions.