Antibody-antigen Interface Research Articles

Neutralizing epitopes on the extracellular interferon γ receptor (IFNγR) α-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 Fab-IFNγR1-108 complex

The extracellular interferon γ receptor α-chain comprises two immunoglobulin-like domains, each with fibronectin type-III topology, which are responsible for binding interferon γ at the cell surface. The epitopes on the human receptor recognized by three neutralizing antibodies, A6, γR38 and γR99, have been mapped by homolog scanning mutagenesis. In this way, a loop connecting β-strands C and C′ in the N-terminal domain was identified as a key component of the epitopes bound by A6 and γR38, whereas γR99 binds to the C-terminal domain in a region including strands A and B and part of the large C′E loop. The epitope for A6 was confirmed in a crystal structure of a complex between a recombinant N-terminal receptor domain and the Fab fragment from A6, determined by X-ray diffraction to 2.8 Å resolution. The antibody-antigen interface buries 1662 Å2 of protein surface, including 22 antibody residues from five complementarity determining regions, primarily through interactions with the CC′ surface loop of the receptor. The floor of the antigen binding cavity is formed mainly by residues from CDR L3 and CDR H3 while a surrounding ridge is formed by residues from all other CDRs except L2. Many potential polar interactions, as well as 13 aromatic side-chains, four in VL, six in VH and three in the receptor, are situated at the interface. The surface of the receptor contacted by A6 overlaps to a large extent with that contacted by interferon-γ, in the ligand-receptor complex. However, the conformation of this epitope is very different in the two complexes, demonstrating that conformational mobility in a surface loop on this cytokine receptor permits steric and electrostatic complementarity to two quite differently shaped binding sites.

Three-dimensional structure of an fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody

F11.2.32, a monoclonal antibody raised against HIV-1 protease ( K d=5 nM), which inhibits proteolytic activity of the enzyme ( K inh=35(±3) nM), has been studied by crystallographic methods. The three-dimensional structure of the complex between the Fab fragment and a synthetic peptide, spanning residues 36 to 46 of the protease, has been determined at 2.2 Å resolution, and that of the Fab in the free state has been determined at 2.6 Å resolution. The refined model of the complex reveals ten well-ordered residues of the peptide (P36 to P45) bound in a hydrophobic cavity at the centre of the antigen-binding site. The peptide adopts a β hairpin-like structure in which residues P38 to P42 form a type II β-turn conformation. An intermolecular antiparallel β-sheet is formed between the peptide and the CDR3-H loop of the antibody; additional polar interactions occur between main-chain atoms of the peptide and hydroxyl groups from tyrosine residues protruding from CDR1-L and CDR3-H. Three water molecules, located at the antigen-antibody interface, mediate polar interactions between the peptide and the most buried hypervariable loops, CDR3-L and CDR1-H. A comparison between the free and complexed Fab fragments shows that significant conformational changes occur in the long hypervariable regions, CDR1-L and CDR3-H, upon binding the peptide. The conformation of the bound peptide, which shows no overall structural similarity to the corresponding segment in HIV-1 protease, suggests that F11.2.32 might inhibit proteolysis by distorting the native structure of the enzyme.

Refined structure of the monoclonal antibody HyHEL-5 with its antigen hen egg-white lysozyme.

The crystal structure of the complex of the antibody Fab, HyHEL-5, with its antigen, hen egg-white lysozyme, has been refined at 2.65 A resolution to an R value of 0.196. The resulting model has significantly better stereochemistry than the previously reported model of the complex, PDB reference 2HFL, and sufficiently improved phases, permitting the reliable location of a number of water molecules. No major conformational differences are observed between this structure and that previously reported, although small differences occur throughout the complex. 82 water molecules have been assigned, of which three are in the antibody-antigen interface involved in a hydrogen-bonding network. Three other waters are trapped within the interface between V(H) and V(L) and a fourth water molecule is observed near the interface but buried below the lysozyme surface as observed in crystal structures of lysozyme alone.

The crystal structures of complexes formed between lysozyme and antibody fragments.

Type c lysozymes, and hen egg lysozyme in particular, have been extensively used to study the immune response because of their strong immunogenicity, the availability of many natural variants to study cross-reactivity, and the possibility to correlate these results with the known three-dimensional structure of lysozymes from several species. To date, the structure of six different murine monoclonal anti-lysozyme antibodies has been studied as a complex between the Fab fragment and antigen. In some cases, the structure of the uncomplexed Fab is also available, giving detail at the atomic level of the changes which take place during the formation of the antibody-antigen complex. The bacterially-expressed Fv molecule, the simplest fragment of an immunoglobulin retaining an intact antigen-binding site, has been studied for three of the monoclonal anti-lysozyme antibodies. Recombinant Fv fragments have opened up the possibility of using site-directed mutagenesis to study the effect of amino acid changes at the antibody-antigen interface. The six monoclonal antibodies appear to recognize epitopes which are localised on three different regions of the lysozyme surface.

Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.

Using site-directed mutagenesis, X-ray crystallography, and titration calorimetry, we have examined the structural and thermodynamic consequences of removing specific hydrogen bonds in an antigen-antibody interface. Crystal structures of three antibody FvD1.3 mutants, VLTyr50Ser (VLY50S), VHTyr32Ala (VHY32A), and VHTyr101Phe (VHY101F), bound to hen egg white lysozyme (HEL) have been determined at resolutions ranging from 1.85 to 2.10 A. In the wild-type (WT) FvD1.3-HEL complex, the hydroxyl groups of VLTyr50, VHTyr32, and VHTyr101 each form at least one hydrogen bond with the lysozyme antigen. Thermodynamic parameters for antibody-antigen association have been measured using isothermal titration calorimetry, giving equilibrium binding constants Kb (M-1) of 2.6 x 10(7) (VLY50S), 7.0 x 10(7) (VHY32A), and 4.0 x 10(6) (VHY101F). For the WT complex, Kb is 2.7 x 10(8) M-1; thus, the affinities of the mutant Fv fragments for HEL are 10-, 4-, and 70-fold lower than that of the original antibody, respectively. In all three cases entropy compensation results in an affinity loss that would otherwise be larger. Comparison of the three mutant crystal structures with the WT structure demonstrates that the removal of direct antigen-antibody hydrogen bonds results in minimal shifts in the positions of the remaining protein atoms. These observations show that this complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody side chains that form hydrogen bonds with the antigen. Alterations in interface solvent structure for two of the mutant complexes (VLY50S and VHY32A) appear to compensate for the unfavorable enthalpy changes when protein-protein interactions are removed. These changes in solvent structure, along with the increased mobility of side chains near the mutation site, probably contribute to the observed entropy compensation. For the VHY101F complex, the nature of the large entropy compensation is not evident from a structural comparison of the WT and mutant complexes. Differences in the local structure and dynamics of the uncomplexed Fv molecules may account for the entropic discrepancy in this case.

Conservation of water molecules in an antibody-antigen interaction.

The solvation of the antibody-antigen Fv D1.3-lysozyme complex is investigated through a study of the conservation of water molecules in crystal structures of the wild-type Fv fragment of antibody D1.3, 5 free lysozyme, the wild-type Fv D1.3-lysozyme complex, 5 Fv D1.3 mutants complexed with lysozyme and the crystal structure of an idiotope (Fv D1.3)-anti-idiotope (Fv E5.2) complex. In all, there are 99 water molecules common to the wild-type and mutant antibody-lysozyme complexes. The antibody-lysozyme interface includes 25 well-ordered solvent molecules, conserved among the wild-type and mutant Fv D1.3-lysozyme complexes, which are bound directly or through other water molecules to both antibody and antigen. In addition to contributing hydrogen bonds to the antibody-antigen interaction the solvent molecules fill many interface cavities. Comparison with x-ray crystal structures of free Fv D1.3 and free lysozyme shows that 20 of these conserved interface waters in the complex were bound to one of the free proteins. Up to 23 additional water molecules are also found in the antibody-antigen interface, however these waters do not bridge antibody and antigen and their temperature factors are much higher than those of the 25 well-ordered waters. Fifteen water molecules are displaced to form the complex, some of which are substituted by hydrophilic protein atoms, and 5 water molecules are added at the antibody- antigen interface with the formation of the complex. While the current crystal models of the D1.3-lysozyme complex do not demonstrate the increase in bound waters found in a physico-chemical study of the interaction at decreased water activities, the 25 well- ordered interface waters contribute a net gain of 10 hydrogen bonds to complex stability.

Thermodynamics of Antigen-antibody Binding using Specific Anti-lysozyme Antibodies

Titration calorimetry measurements on the binding of hen lysozyme to the specific monoclonal IgG antibodies D1.3, D11.15, D44.1, F9.13.7, F10.6.6, their papain-cleaved antigen binding fragments (Fab) and their protein-engineered fragments consisting of non-covalently linked heavy variable chain and light variable chain domains (Fv) were performed between 6-50 degrees C in 0.15 M NaCl, 0.01 M sodium phosphate pH 7.1. The binding thermodynamic free energy change (delta G degrees b), enthalpy change (delta Hb), and entropy change (delta Sb) were the same for the whole IgG and its Fv and Fab fragments. With the exception of F9.13.7 at 13 degrees C, all the binding reactions were enthalpically driven with enthalpy changes ranging from -129 +/- 7 kJ mol-1 (D1.3 at 49.8 degrees C) to -26.2 +/- 0.6 kJ mol-1 (D44.1 at 8.0 degrees C). The heat capacity changes for the binding reaction (delta Cp) ranged from -2.72 +/- 0.16 kJ mol-1 K-1 (F9.13.7) to -0.95 +/- 0.06 kJ mol-1 K-1 (F10.6.6). The apolar surface areas buried at the binding sites estimated from the heat capacity changes indicate that the binding reactions are primarily hydrophobic, contrary to the mainly observed enthalpy-driven nature of the reactions. Conformational stabilization and the presence of water at the antigen-antibody interface may account for this discrepancy.

Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1

The three-dimensional structures of the free and antigen-complexed Fabs from the mouse monoclonal anti-hen egg white lysozyme antibody D44. I have been solved and refined X-ray crystallography techniques. The crystals of the free and lysozyme-bound Fabs were grown under identical conditions and their X-ray diffraction data were collected to 2.1 and 2.5 Å, respectively. Two molecules of the Fab-lysozyme complex in the asymmetric unit of the crystals show nearly identical conformations and thus confirm the essential structural features of the antigen-antibody interface. Three buried water molecules enhance the surface complementarity at the interface and provide hydrogen bonds to stabilize the complex. Two hydrophobic buried holes are present at the interface which, although large enough to accomodate solvent molecules, are void. The combining site residues of the complexed FabD44.1 exhibit reduced temperature factors compared with those of the free Fab. Furthermore, small perturbations in atomic positions and rearrangements of side-chains at the combining site, and a relative rearrangement of the variable domains of the light (V 1) and the heavy (V H) chains, detail a Fab accommodation of the bound lysozyme. The amino acid sequence of the V H domain, as well as the epitope of lysozyme recognized by D44.1 are very close to those previously reported for the monoclonal antibody HyHEL-5. A feature centrel to the Fab44.1 and FabHyHEL-5 complexes with lysozyme are three salt bridges between V H glutamate residues 35 and 50 and lysozyme arginine residues 45 and 68. The presence of the three salt bridges in the D44.1-lysozyme interface indicates that these bonds are not responsible for the 1000-fold increase in affinity for lysozyme that HyHEL-5 exhibits relative to D44.1.

Antibody-antigen interactions

The structural origins of antibody diversity are well understood as a result of X-ray crystallographic and molecular modelling studies of Fab fragments. A similar understanding of antibody specificity is beginning to emerge from an analysis of structures of hapten, peptide and protein antibody complexes. While the nature of the antibody-antigen interface, and any conformational changes that occur on complex formation, can be described in structural terms, a full explanation of the thermodynamic and mechanistic basis of affinity is less accessible from structure alone. A number of physiochemical studies carried out on wild type and mutant antibodies have raised questions about the nature of the energetics of the interaction, and the possibility of a key role for water molecules has been discussed. The possibility of ‘induced fit’ as a common mechanism for antigen-antibody interactions has been raised, and a molecular basis for hapten and protein cross-reactivity proposed. These recent contributions to the field, as well as providing partial solutions to old problems, have provided exciting new insights.

Antibody-Protein Complexes

The X-ray crystallographic structures of five antibody-protein antigen complexes are briefly described. The three-dimensional structure of the antibody-antigen interface is compared to the results obtained by two other techniques: analysis of mutant binding data and NMR hydrogen-deuterium exchange.

Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution

The three-dimensional crystal structure of the complex between the Fab from the monoclonal anti-lysozyme antibody D1.3 and the antigen, hen egg white lysozyme, has been refined by crystallographic techniques using x-ray intensity data to 2.5-A resolution. The antibody contacts the antigen with residues from all its complementarity determining regions. Antigen residues 18-27 and 117-125 form a discontinuous antigenic determinant making hydrogen bonds and van der Waals interactions with the antibody. Water molecules at or near the antigen-antibody interface mediate some contacts between antigen and antibody. The fine specificity of antibody D1.3, which does not bind (K alpha less than 10(5) M-1) avian lysozymes where Gln121 in the amino acid sequence is occupied by His, can be explained on the basis of the refined model.

Molecular Approaches to the Study of B Cell Epitopes

For some years, a major goal of immunochemistry has been to determine the molecular architecture of the antibody-combining site and its cognate surface on the antigen, the antigenic determinant or epitope, and to determine the molecular basis of specificity and affinity. In recent years, the crystal structures of several antigen-antibody complexes have been determined. In addition, recombinant DNA technology is beginning to play an increasingly important role in analysis of protein-protein interaction including the study of antigen structure and its interaction with antibody. The purpose of this review is to briefly present some of the major and common properties of the antigen-antibody interface as it is known today and to demonstrate, using a few selected studies, the efficacy of using site-directed mutagenesis to study the nature of the antigenic surface of protein molecules and its interaction with antibody.

Three-Dimensional Structure of an Antigen-Antibody Complex at 2.8 Å Resolution

The 2.8 A resolution three-dimensional structure of a complex between an antigen (lysozyme) and the Fab fragment from a monoclonal antibody against lysozyme has been determined and refined by x-ray crystallographic techniques. No conformational changes can be observed in the tertiary structure of lysozyme compared with that determined in native crystalline forms. The quaternary structure of Fab is that of an extended conformation. The antibody combining site is a rather flat surface with protuberances and depressions formed by its amino acid side chains. The antigen-antibody interface is tightly packed, with 16 lysozyme and 17 antibody residues making close contacts. The antigen contacting residues belong to two stretches of the lysozyme polypeptide chain: residues 18 to 27 and 116 to 129. All the complementarity-determining regions and two residues outside hypervariable positions of the antibody make contact with the antigen. Most of these contacts (10 residues out of 17) are made by the heavy chain, and in particular by its third complementarity-determining region. Antigen variability and antibody specificity and affinity are discussed on the basis of the determined structure.

Quantitative Analyses of Certain Enteric Bacteria and Bacterial Extracts

Bacterial extracts prepared by ultrasonic disruption were reacted with both narrow- and broad-spectrum reference (homologous) and cross-reacting (heterologous) precipitins produced in rabbits. Quantitation of the reaction was obtained by densitometry of the antigen-antibody interface. Comparisons were made of sonic extracts from various starting populations all equated to the same nitrogen concentrations, and of various nitrogen levels derived from five bacterial population levels prepared separately. Sources of error are probed to show under what circumstances cross-reactions would be of greater magnitude than reference ones. The feasibility was shown of using quantitative densitometry of the interface combined with broadly reacting precipitins to identify bacteria on an intergeneric and interspecies scale. Problems associated with the use of absorbed or monospecific precipitins are explained.