Conservation of water molecules in an antibody-antigen interaction

Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations

We have carried out a long-timescale simulation study on crystal structures of nine antibody-antigen pairs, in antigen-bound and antibody-only forms, using molecular dynamics with enhanced sampling and an explicit water model to explore interface conformation and hydration. By combining atomic level simulation and replica exchange to enable full protein flexibility, we find significant numbers of bridging water molecules at the antibody-antigen interface. Additionally, a higher proportion of interactions excluding bulk waters and a lower degree of antigen bound CDR conformational sampling are correlated with higher antibody affinity. The CDR sampling supports enthalpically driven antibody binding, as opposed to entropically driven, in that the difference between antigen bound and unbound conformations do not correlate with affinity. We thus propose that interactions with waters and CDR sampling are aspects of the interface that may moderate antibody-antigen binding, and that explicit hydration and CDR flexibility should be considered to improve antibody affinity prediction and computational design workflows.

Key role of a structural water molecule for the specificity of 14F7-An antitumor antibody targeting the NeuGc GM3 ganglioside

Tumor-associated glycolipids such as NeuGc GM3 are auspicious molecular targets in antineoplastic therapies and vaccine strategies. 14F7 is a monoclonal IgG1 with high clinical potential in cancer immunotherapy as it displays extraordinary specificity for NeuGc GM3, while it does not recognize the very similar, ubiquitous NeuAc GM3. Here we present the 2.3 Å crystal structure of the 14F7 antigen-binding domain (14F7 scFv) in complex with the NeuGc GM3 trisaccharide. Modeling analysis and previous mutagenesis data suggest that 14F7 may also bind to an alternative NeuGc GM3 conformation, not observed in the crystal structure. The most intriguing finding, however, was that a water molecule centrally placed in the complementarity-determining region directly mediates the specificity of 14F7 to NeuGc GM3. This has profound impact on the complexity of engineering in the binding site and provides an excellent example of the importance in understanding the water structure in antibody-antigen interactions.

A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection

Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.

A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection

Coronaviruses have caused several epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Some prophylactic vaccines and therapeutic antibodies have already showed striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody CV38-142 in complex with the receptor binding domains from SARS-CoV-2 and SARS-CoV. Our structural findings provide mechanistic insights into how this antibody can accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, in particular COVA1-16, to enhance neutralization of SARS-CoV-2 and SARS-CoV. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic coronaviruses.

Structural Aspects of the Allergen-Antibody Interaction

The development of allergic disease involves the production of IgE antibodies upon allergen exposure in a process called sensitization. IgE binds to receptors on the surface of mast cells and basophils, and subsequent allergen exposure leads to cross-linking of IgE antibodies and release of cell mediators that cause allergy symptoms. Although this process is quite well-understood, very little is known about the epitopes on the allergen recognized by IgE, despite the importance of the allergen-antibody interaction for the allergic response to occur. This review discusses efforts to analyze allergen-antibody interactions, from the original epitope mapping studies using linear peptides or recombinant allergen fragments, to more sophisticated technologies, such as X-ray crystallography and nuclear magnetic resonance. These state-of-the-art approaches, combined with site-directed mutagenesis, have led to the identification of conformational IgE epitopes. The first structures of an allergen (egg lysozyme) in complex with Fab fragments from IgG antibodies were determined in the 1980s. Since then, IgG has been used as surrogate for IgE, due to the difficulty of obtaining monoclonal IgE antibodies. Technical developments including phage display libraries have contributed to progress in epitope mapping thanks to the isolation of IgE antibody constructs from combinatorial libraries made from peripheral blood mononuclear cells of allergic donors. Most recently, single B cell antibody sequencing and human hybridomas are new breakthrough technologies for finally obtaining human IgE monoclonal antibodies, ideal for epitope mapping. The information on antigenic determinants will facilitate the design of hypoallergens for immunotherapy and the investigation of the fundamental mechanisms of the IgE response.

Antigen-Antibody Complexes

In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an integral role in the armamentarium of immune defense against various pathogens. After an antigenic challenge, antibodies are secreted by differentiated B cells called plasma cells. Antibodies have two predominant roles that involve specific binding to antigens to launch an immune response, along with activation of other components of the immune system to fight pathogens. The ability of immunoglobulins to fight against innumerable and diverse pathogens lies in their intrinsic ability to discriminate between different antigens. Due to this specificity and high affinity for their antigens, antibodies have been a valuable and indispensable tool in research, diagnostics and therapy. Although seemingly a simple maneuver, the association between an antibody and its antigen, to make an antigen-antibody complex, is comprised of myriads of non-covalent interactions. Amino acid residues on the antigen binding site, the epitope, and on the antibody binding site, the paratope, intimately contribute to the energetics needed for the antigen-antibody complex stability. Structural biology methods to study antigen-antibody complexes are extremely valuable tools to visualize antigen-antibody interactions in detail; this helps to elucidate the basis of molecular recognition between an antibody and its specific antigen. The main scope of this chapter is to discuss the structure and function of different classes of antibodies and the various aspects of antigen-antibody interactions including antigen-antibody interfaces-with a special focus on paratopes, complementarity determining regions (CDRs) and other non-CDR residues important for antigen binding and recognition. Herein, we also discuss methods used to study antigen-antibody complexes, antigen recognition by antibodies, types of antigens in complexes, and how antigen-antibody complexes play a role in modern day medicine and human health. Understanding the molecular basis of antigen binding and recognition by antibodies helps to facilitate the production of better and more potent antibodies for immunotherapy, vaccines and various other applications.

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle

Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H₃O⁺ through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O₂ bound to heme a₃ To block backward proton movement, the water channel remains closed after O₂ binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O₂ binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg²⁺ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu¹⁹⁸, which bridges the Mg²⁺ and Cu_A (the initial electron acceptor from cytochrome c) sites, suggest that the Cu_A-Glu¹⁹⁸-Mg²⁺ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg²⁺-containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO.

Synchrotron X-ray footprinting as a method to visualize water in proteins

The vast majority of biomolecular processes are controlled or facilitated by water interactions. In enzymes, regulatory proteins, membrane-bound receptors and ion-channels, water bound to functionally important residues creates hydrogen-bonding networks that underlie the mechanism of action of the macromolecule. High-resolution X-ray structures are often difficult to obtain with many of these classes of proteins because sample conditions, such as the necessity of detergents, often impede crystallization. Other biophysical techniques such as neutron scattering, nuclear magnetic resonance and Fourier transform infrared spectroscopy are useful for studying internal water, though each has its own advantages and drawbacks, and often a hybrid approach is required to address important biological problems associated with protein-water interactions. One major area requiring more investigation is the study of bound water molecules which reside in cavities and channels and which are often involved in both the structural and functional aspects of receptor, transporter and ion channel proteins. In recent years, significant progress has been made in synchrotron-based radiolytic labeling and mass spectroscopy techniques for both the identification of bound waters and for characterizing the role of water in protein conformational changes at a high degree of spatial and temporal resolution. Here the latest developments and future capabilities of this method for investigating water-protein interactions and its synergy with other synchrotron-based methods are discussed.

Structural and biochemical characterization of the vaccinia virus envelope protein D8 and its recognition by the antibody LA5

Smallpox vaccine is considered a gold standard of vaccines, as it is the only one that has led to the complete eradication of an infectious disease from the human population. B cell responses are critical for the protective immunity induced by the vaccine, yet their targeted epitopes recognized in humans remain poorly described. Here we describe the biochemical and structural characterization of one of the immunodominant vaccinia virus (VACV) antigens, D8, and its binding to the monoclonal antibody LA5, which is capable of neutralizing VACV in the presence of complement. The full-length D8 ectodomain was found to form a tetramer. We determined the crystal structure of the LA5 Fab-monomeric D8 complex at a resolution of 2.1 Å, as well as the unliganded structures of D8 and LA5-Fab at resolutions of 1.42 Å and 1.6 Å, respectively. D8 features a carbonic anhydrase (CAH) fold that has evolved to bind to the glycosaminoglycan (GAG) chondroitin sulfate (CS) on host cells. The central positively charged crevice of D8 was predicted to be the CS binding site by automated docking experiments. Furthermore, sequence alignment of various poxvirus D8 orthologs revealed that this crevice is structurally conserved. The D8 epitope is formed by 23 discontinuous residues that are spread across 80% of the D8 protein sequence. Interestingly, LA5 binds with a high-affinity lock-and-key mechanism above this crevice with an unusually large antibody-antigen interface, burying 2,434 Å(2) of protein surface.

Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies

Thermodynamic and structural studies addressed the increased affinity due to L-chain somatic mutations in the HyHEL-10 family of affinity matured IgG antibodies, using ITC, SPR with van't Hoff analysis, and X-ray crystallography. When compared to the parental antibody H26L26, the H26L10 and H26L8 chimeras binding to lysozyme showed an increase in favorable DeltaG(o) of -1.2+/-0.1 kcal mol(-1) and -1.3+/-0.1 kcal mol(-1), respectively. Increase in affinity of the H26L10 chimera was due to a net increase in favorable enthalpy change with little difference in change in entropy compared to H26L26. The H26L8 chimera exhibited the greatest increase in favorable enthalpy but also showed an increase in unfavorable entropy change, with the result being that the affinities of both chimeras were essentially equivalent. Site-directed L-chain mutants identified the shared somatic mutation S30G as the dominant contributor to increasing affinity to lysozyme. This mutation was not influenced by H-chain somatic mutations. Residue 30L is at the periphery of the binding interface and S30G effects an increase in hydrophobicity and decrease in H-bonding ability and size, but does not make any new energetically important antigen contacts. A new 1.2-A structure of the H10L10-HEL complex showed changes in the pattern of both inter- and intra-molecular water bridging with no other significant structural alterations near the binding interface compared to the H26L26-HEL complex. These results highlight the necessity for investigating both the structure and the thermodynamics associated with introduced mutations, in order to better assess and understand their impact on binding. Furthermore, it provides an important example of how backbone flexibility and water-bridging may favorably influence the thermodynamics of an antibody-antigen interaction.

Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen

The virulence of Bacillus anthracis is critically dependent on the cytotoxic components of the anthrax toxin, lethal factor (LF) and edema factor (EF). LF and EF gain entry into host cells through interactions with the protective antigen (PA), which binds to host cellular receptors such as CMG2. Antibodies that neutralize PA have been shown to confer protection in animal models and are undergoing intense clinical development. A murine monoclonal antibody, 14B7, has been reported to interact with domain 4 of PA (PAD4) and block its binding to CMG2. More recently, the 14B7 antibody was used as the platform for the selection of very high affinity, single-chain antibodies that have tremendous potential as a combination anthrax prophylactic and treatment. Here, we report the high-resolution X-ray structures of three high-affinity, single-chain antibodies in the 14B7 family; 14B7 and two high-affinity variants 1H and M18. In addition, we present the first neutralizing antibody-PA structure, M18 in complex with PAD4 at 3.8 A resolution. These structures provide insights into the mechanism of neutralization, and the effect of various mutations on antibody affinity, and enable a comparison between the binding of the M18 antibody and CMG2 with PAD4.

The immunoglobulin constant region contributes to affinity and specificity

A central dogma in immunology is that antibody specificity is solely the result of variable (V)-region interactions with an antigen. However, this view is not tenable in light of numerous reports that constant heavy (C(H)) domains can affect binding affinity and specificity and V-region structure. Kinetic and thermodynamic proof for the occurrence of this phenomenon is now available. C(H)-region effects on affinity and specificity suggest new mechanisms for generating antibody diversity and polyreactivity (multispecificity) that impact current views on idiotype regulation, autoimmunity, and B cell selection and change our understanding of vaccine responses.

Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface

The redesign of protein-protein interactions is a stringent test of our understanding of molecular recognition and specificity. Previously we engineered a modest specificity switch into the colicin E7 DNase-Im7 immunity protein complex by identifying mutations that are disruptive in the native complex, but can be compensated by mutations on the interacting partner. Here we extend the approach by systematically sampling alternate rigid body orientations to optimize the interactions in a binding mode specific manner. Using this protocol we designed a de novo hydrogen bond network at the DNase-immunity protein interface and confirmed the design with X-ray crystallographic analysis. Subsequent design of the second shell of interactions guided by insights from the crystal structure on tightly bound water molecules, conformational strain, and packing defects yielded new binding partners that exhibited specificities of at least 300-fold between the cognate and the non-cognate complexes. This multi-step approach should be applicable to the design of polar protein-protein interactions and contribute to the re-engineering of regulatory networks mediated by protein-protein interactions.

Determination of the interfacial water content in protein-protein complexes from free energy simulations

The question as to how many tightly or weakly bound water molecules are located in interfaces between protein-protein complex constituents is addressed from a phase equilibrium point of view by developing a theory in the canonical ensemble. A fast method based on free energy simulations is described for computing the number of water molecules in the interface regions. Results are given for 211 interfacial cavities of 26 antigen-antibody complexes for which experimentally determined structures are found in the Protein Data Bank. The accuracy of the method is assessed and the computational water content is compared with experimental data, revealing the amount of water molecules not resolved by experimental approaches.

Hydration of protein-protein interfaces

We present an analysis of the water molecules immobilized at the protein-protein interfaces of 115 homodimeric proteins and 46 protein-protein complexes, and compare them with 173 large crystal packing interfaces representing nonspecific interactions. With an average of 15 waters per 1000 A2 of interface area, the crystal packing interfaces are more hydrated than the specific interfaces of homodimers and complexes, which have 10-11 waters per 1000 A2, reflecting the more hydrophilic composition of crystal packing interfaces. Very different patterns of hydration are observed: Water molecules may form a ring around interfaces that remain "dry," or they may permeate "wet" interfaces. A majority of the specific interfaces are dry and most of the crystal packing interfaces are wet, but counterexamples exist in both categories. Water molecules at interfaces form hydrogen bonds with protein groups, with a preference for the main-chain carbonyl and the charged side-chains of Glu, Asp, and Arg. These interactions are essentially the same in specific and nonspecific interfaces, and very similar to those observed elsewhere on the protein surface. Water-mediated polar interactions are as abundant at the interfaces as direct protein-protein hydrogen bonds, and they may contribute to the stability of the assembly.

Hyperglycosylated mutants of human immunodeficiency virus (HIV) type 1 monomeric gp120 as novel antigens for HIV vaccine design

The ability to induce broadly neutralizing antibodies should be a key component of any forthcoming vaccine against human immunodeficiency virus type 1. One potential vaccine candidate, monomeric gp120, has generally failed to elicit such antibodies. We postulated that gp120 might be a better immunogen if it could be engineered to preferentially bind known broadly neutralizing antibodies. In a first study, we found that four alanine substitutions on the perimeter of the so-called Phe-43 cavity of gp120 could reduce binding of weakly neutralizing CD4-binding site antibodies (R. Pantophlet, E. O. Saphire, P. Poignard, P. W. H. I. Parren, I. A. Wilson, and D. R. Burton, J. Virol. 77:642-658, 2003), while slightly enhancing binding of the potent, broadly neutralizing antibody b12. In the present study, we sought to reduce or abolish the binding of a wider range of nonneutralizing antibodies, by incorporating extra N-glycosylation motifs at select positions into the hypervariable loops and the gp120 core. A hyperglycosylated mutant containing seven extra glycosylation sequons (consensus sequences) and the four alanine substitutions described above did not bind an extensive panel of nonneutralizing and weakly neutralizing antibodies, including a polyclonal immunoglobulin preparation (HIVIG) of low neutralizing potency. Binding of b12, at lowered affinity, and of four antibodies to the C1 and C5 regions was maintained. Removal of N- and C-terminal residues in the C1 and C5 regions, respectively, reduced or abolished binding of the four antibodies, but this also adversely affected b12 binding. The hyperglycosylated mutant and its analogues described here are novel antigens that may provide a new approach to eliciting antibodies with b12-like neutralizing properties.

Molecular recognition in antibody-antigen complexes

With the numerous detailed molecular descriptions of antibody-antigen interfaces, the structual study of these molecular interactions has evolved from an attempt to understand to immunological function to their use as model systems for protein-protein interactions. In this chapter, we describe the structual aspects common to antibody-antigen interfaces and discuss the roles they may play in antibody cross-rectivity and molecular mimicry. More detailed analysis of these interfaces has required the marriage of structural studies with extensive mutagenesis and thermodynamic analysis efforts. Here, we discuss the thermodynamic mapping of interfaces for two model antibody-antigen complexes, including the identification of thermodynamic hot spots in binding and the various mechanism used to accommodate interface mutations. We also discuss the functional roles for protein plasticity in antigen recognition, including the entropic control of antibody affinity maturation and the use of induced fit mechanism of different types and to varying degrees by mature antibodies in binding their specific antigens.

The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction

To study the role of hydrogen bonding via interfacial water molecules in protein-protein interactions, we examined the interaction between hen egg white lysozyme (HEL) and its HyHEL-10 variable domain fragment (Fv) antibody. We constructed three antibody mutants (l-Y50F, l-S91A, and l-S93A) and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the mutations significantly decreased the negative enthalpy change (8-25 kJ mol(-1)), despite some offset by a favorable entropy change. X-ray crystallography demonstrated that the complexes had nearly identical structures, including the positions of the interfacial water molecules. Taken together, the isothermal titration calorimetric and x-ray crystallographic results indicate that hydrogen bonding via interfacial water enthalpically contributes to the Fv-HEL interaction despite the partial offset because of entropy loss, suggesting that hydrogen bonding stiffens the antigen-antibody complex.

Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface

Macrophages and neutrophils protect animals from microbial infection in part by issuing a burst of toxic superoxide radicals when challenged. To counteract this onslaught, many Gram-negative bacterial pathogens possess periplasmic Cu,Zn superoxide dismutases (SODs), which act on superoxide to yield molecular oxygen and hydrogen peroxide. We have solved the X-ray crystal structure of the Cu,Zn SOD from Actinobacillus pleuropneumoniae, a major porcine pathogen, by molecular replacement at 1.9 A resolution. The structure reveals that the dimeric bacterial enzymes form a structurally homologous class defined by a water-mediated dimer interface, and share with all Cu,Zn SODs the Greek-key beta-barrel subunit fold with copper and zinc ions located at the base of a deep loop-enclosed active-site channel. Our structure-based sequence alignment of the bacterial enzymes explains the monomeric nature of at least two of these, and suggests that there may be at least one additional structural class for the bacterial SODs. Two metal-mediated crystal contacts yielded our C222(1) crystals, and the geometry of these sites could be engineered into proteins recalcitrant to crystallization in their native form. This work highlights structural differences between eukaryotic and prokaryotic Cu,Zn SODs, as well as similarities and differences among prokaryotic SODs, and lays the groundwork for development of antimicrobial drugs that specifically target periplasmic Cu,Zn SODs of bacterial pathogens.

Immunoelectrodes in protein detection: comparison between glassy carbon and a semimetallic Ni/P thin film as binding support. Biological applications

Though immunoelectrodes can allow direct detection of very low protein amounts (about 0.1 pmol) in vitro and in vivo, they are not yet widely used because they need quality improvement. Based on a few works devoted to the basic electrochemical phenomenon occurring when antibodies are linked onto a solid support and during antigen/antibody complex formation, we have coated two different supports with antibodies: the classical glassy carbon fiber or an epoxy plate covered with an amorphous semimetallic (nickel/phosphorus) thin film obtained by means of an electrochemical deposit. The antibody/antigen complex formation induces direct and/or indirect ionic movements and a current flow through the conductive support toward a very low-noise and high-sensitivity preamplifier stage in an I/V configuration. The proposed electrochemical treatment (hydrophilization), applied to both carbon and Ni/P electrodes, improves antibody binding and reliability of the response to antigens. The Ni/P probes present several advantages when compared to carbon fiber: better conductivity, possibility of surface quality control, and semimetallic nature, making them unbreakable. Several applications were proposed: somatostatin-14 detection with both carbon fiber and Ni/P plate electrodes, and histamine detection in simple and complex fluid media. Dose-response curves and analysis of the results lead us to conclude that the obtained currents are directly related to the quantity of antigen.

Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity

Cluster analysis is presented as a technique for analyzing the conservation and chemistry of water sites from independent protein structures, and applied to thrombin, trypsin, and bovine pancreatic trypsin inhibitor (BPTI) to locate shared water sites, as well as those contributing to specificity. When several protein structures are superimposed, complete linkage cluster analysis provides an objective technique for resolving the continuum of overlaps between water sites into a set of maximally dense microclusters of overlapping water molecules, and also avoids reliance on any one structure as a reference. Water sites were clustered for ten superimposed thrombin structures, three trypsin structures, and four BPTI structures. For thrombin, 19% of the 708 microclusters, representing unique water sites, contained water molecules from at least half of the structures, and 4% contained waters from all 10. For trypsin, 77% of the 106 microclusters contained water sites from at least half of the structures, and 57% contained waters from all three. Water site conservation correlated with several environmental features: highly conserved microclusters generally had more protein atom neighbors, were in a more hydrophilic environment, made more hydrogen bonds to the protein, and were less mobile. There were significant overlaps between thrombin and trypsin conserved water sites, which did not localize to their similar active sites, but were concentrated in buried regions including the solvent channel surrounding the Na+ site in thrombin, which is associated with ligand selectivity. Cluster analysis also identified water sites conserved in thrombin but not trypsin, and vice versa, providing a list of water sites that may contribute to ligand discrimination. Thus, in addition to facilitating the analysis of water sites from multiple structures, cluster analysis provides a useful tool for distinguishing between conserved features within a protein family and those conferring specificity.

Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution

A complete understanding of antibody-antigen association and specificity requires the stereochemical description of both antigen and antibody before and upon complex formation. The structural mechanism involved in the binding of the IgG1 monoclonal antibody E8 to its highly charged protein antigen horse cytochrome c (cyt c) is revealed by crystallographic structures of the antigen-binding fragment (Fab) of E8 bound to cyt c (FabE8-cytc), determined to 1.8 A resolution, and of uncomplexed Fab E8 (FabE8), determined to 2.26 A resolution. E8 antibody binds to three major discontiguous segments (33 to 39; 56 to 66; 96 to 104), and two minor sites on cyt c opposite to the exposed haem edge. Crystallographic definition of the E8 epitope complements and extends biochemical mapping and two-dimensional nuclear magnetic resonance with hydrogen-deuterium exchange studies. These combined results demonstrate that antibody-induced stabilization of secondary structural elements within the antigen can propagate locally to adjacent residues outside the epitope. Pre-existing shape complementarity at the FabE8-cytc interface is enhanced by 48 bound water molecules, and by local movements of up to 4.2 A for E8 antibody and 8.9 A for cyt c. Glu62, Asn103 and the C-terminal Glu104 of cyt c adjust to fit the pre-formed VL "hill" and VH "valley" shape of the grooved E8 paratope. All six E8 complementarity determining regions (CDRs) contact the antigen, with CDR L1 forming 46% of the total atomic contacts, and CDRs L1 (29%) and H3 (20%) contributing the highest percentage of the total surface area of E8 buried by cyt c (550 A2). The E8 antibody covers 534 A2 of the cyt c surface. The formation of five ion pairs between E8 and flexible cyt c residues Lys60, Glu62 and Glu104 suggests the importance of mobile regions and electrostatic interactions in providing the exquisite specificity needed for recognition of this extremely conserved protein antigen. The highly homologous VL domains of E8 and anti-lysozyme antibody D1. 3 achieve their distinct antigen-binding specificities by expanding the impact of their limited sequence differences through the recruitment of different sets of conserved residues and distinctly different CDR L3 conformations.

Anatomy of an antibody molecule: structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1.3

Using site-directed mutagenesis, x-ray crystallography, microcalorimetric, equilibrium sedimentation and surface plasmon resonance detection techniques, we have examined the structure of an antibody-antigen complex and the structural and thermodynamic consequences of removing specific hydrogen bonds and van der Waals interactions in the antibody-antigen interface. These observations show that the complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody and antigen side chains that form contacts. Alterations in interface solvent structure for two of the mutant complexes appear to compensate for the unfavorable enthalpy changes when antibody-antigen 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. In concert, data from structural studies, reaction rates, calorimetric measurements and site directed mutations are beginning to detail the nature of antibody-protein antigen interactions.

Affinity selection and repertoire shift: paradoxes as a consequence of somatic mutation?

Affinity selection of antibodies during immune responses relies on two mechanisms, one molecular that involves the targeted introduction of somatic mutations into rearranged immunoglobulin genes and one cellular that involves the clonal expansion of B cells expressing a surface immunoglobulin with a higher affinity for antigen compared to their competitors. In this review we focus on the conditions for affinity selection during the establishment, expansion and memory phases of the immune response. We postulate that somatic mutation evolved prior to affinity selection and we present a model for selection of B cells in germinal centres. We also discuss the possibility that antibody repertoire shift occurs during the memory maintenance phase. Finally, we argue that a significant affinity selection and a selection for polyclonality of immune responses occur during this stage of the immune response.

Association and dissociation kinetics of anti-hen egg lysozyme monoclonal antibodies HyHEL-5 and HyHEL-10

The immunoglobulin G1 (IgG1) kappa antibodies HyHEL-5 and HyHEL-10 interact with nonoverlapping epitopes on hen egg lysozyme (HEL); the HyHEL-5/HEL interface has two energetically and structurally important salt links, whereas the HyHEL-10/HEL interface involves predominantly hydrogen bonds and van der Waals interactions. The kinetics of association and dissociation of antibodies HyHEL-5 and HyHEL-10 with HEL under a variety of conditions were investigated in this study. The association of each antibody with HEL follows second-order kinetics. The association process is significantly diffusion-limited, as indicated by the viscosity dependence of the interaction of both antibodies with HEL, although detailed energetics suggest that the association process may be more complex. The association rate constant for the HyHEL-5/HEL system is within a factor of 2 of the modified Smoluchowski estimate for proteins of this size, whereas HyHEL-10 interacts with HEL with an association rate an order of magnitude lower. The association reactions are insensitive to ionic strength, showing only a twofold decrease in the association rate constant when the ionic strength was increased from 27 mM to 500 mM. Interestingly, the association rate constant for the interaction of HyHEL-5 with HEL varies with pH in the range 6.0-10.0, whereas HyHEL-10/HEL association is not affected by pH in the same range. The dissociation of the HyHEL-5/HEL and HyHEL-10/HEL complexes follow first-order kinetics with half-lives at 25 degrees C of approximately 3,150 s and approximately 21,660 s, respectively.

Conformational correction mechanisms aiding antigen recognition by a humanized antibody

The crystal structure of the complex between hen egg lysozyme and the Fv fragment of a humanized antilysozyme antibody was determined to 2.7-A resolution. The structure of the antigen combining site in the complex is nearly identical to that of the complexed form of the parent mouse antibody, D1.3. In contrast, the combining sites of the unliganded mouse and humanized antilysozymes show moderate conformational differences. This disparity suggests that a conformational readjustment process linked to antigen binding reverses adverse conformations in the complementarity determining regions that had been introduced by engineering these segments next to human framework regions in the humanized antibody.

pH dependence of antibody/lysozyme complexation

Association between proteins often depends on the pH and ionic strength conditions of the medium in which it takes place. This is especially true in complexation involving titratable residues at the complex interface. Continuum electrostatics methods were used to calculate the pH-dependent energetics of association of hen egg lysozyme with two closely related monoclonal antibodies raised against it and the association of these antibodies against an avian species variant. A detailed analysis of the energetic contributions reveals that even though the hallmark of association in the two complexes is the presence of conserved charged-residue interactions, the environment of these interactions significantly influences the titration behavior and concomitantly the energetics. The contributing factors include minor structural rearrangements, buried interfacial area, dielectric environment of the key titratable residues, and geometry of the residue dispositions. Modeled structures of several mutant complexes were also studied so as to further delineate the contribution of individual factors to the titration behavior.

Involvement of water molecules in the association of monoclonal antibody HyHEL-5 with bobwhite quail lysozyme

Fluorescence polarization spectroscopy and isothermal titration calorimetry were used to study the influence of osmolytes on the association of the anti-hen egg lysozyme (HEL) monoclonal antibody HyHEL-5 with bobwhite quail lysozyme (BWQL). BWQL is an avian species variant with an Arg-->Lys mutation in the HyHEL-5 epitope, as well as three other mutations outside the HyHEL-5 structural epitope. This mutation decreases the equilibrium association constant of HyHEL-5 for BWQL by over 1000-fold as compared to HEL. The three-dimensional structure of this complex has been obtained recently. Fluorescein-labeled BWQL, obtained by labeling at pH 7.5 and purified by hydrophobic interaction chromatograpy, bound HyHEL-5 with an equilibrium association constant close to that determined for unlabeled BWQL by isothermal titration calorimetry. Fluorescence titration, stopped-flow kinetics, and isothermal titration calorimetry experiments using various concentrations of the osmolytes glycerol, ethylene glycol, and betaine to perturb binding gave a lower limit of the uptake of approximately 6-12 water molecules upon formation of the HyHEL-5/BWQL complex.

Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope

A modeling analysis has been conducted to assess the determinants of binding strength and specificity for three crystal complexes; the anti-hen egg white lysozyme antibody D1.3 complexed with hen egg white lysozyme (HEL), the D1.3 antibody complexed with the anti-lysozyme antibody E5.2, and barnase complexed with barstar. The strengths of individual binding components within these interfaces are evaluated using a model of binding free energy that is based on pairwise surface preferences. In all cases the energetics of binding are dominated by a relatively small number of interfacial residues that define the binding epitope. A precise geometric arrangement of these residues was not found; they were either localized to one region, or distributed throughout the binding interface. Surprisingly, interfacial crystal water molecules were calculated to contribute around 25% of the total calculated binding strength. Theoretical alanine mutations were completed by atomic deletions of the wild-type complexes. Strong correlations were observed between the calculated changes in binding free energy (deltadeltaG(calculated)) and the experimental values (deltadeltaG(observed)) for all but three of the 30 single residue mutations in the D1.3-HEL, D1.3-E5.2 and barnase-barstar systems and for all of the double mutations in the barnase-barstar system. This analysis finds that the observed differences in binding strength are consistent with a model that accounts for the changes in binding energy from the direct contacts between each member of the complex and indirect changes due to released crystallographic water molecules that are near the mutation site. The observed energy changes for double mutations in the barnase-barstar system is fully accounted for by considering water molecules bound jointly by each member of the complex.

Thermodynamic analysis of antigen-antibody binding using biosensor measurements at different temperatures

The thermodynamic parameters of the interaction between hen egg white lysozyme and Fab D1.3 were determined by measuring the temperature dependence of the ratio of its kinetic association and dissociation rate constants. Biosensor technology (BIAcore 2000) was used to measure the rate constants at temperatures ranging from 5 to 40 degrees C. The value of DeltaG degrees at 25 degrees C (-49 kJ M-1) calculated by this method was very close to that obtained previously from fluorescence quenching measurements (-48.5 kJ M-1). However, the value of DeltaH degrees measured at 25 degrees C by biosensor technology (-35 kJ M-1) was smaller than that determined previously by microcalorimetry (-90 kJ M-1). Another difference was the limited variation of ln K and DeltaG with temperature observed with BIAcore compared to the steady decrease of ln K with temperature found by calorimetry. Our data showed that the binding reaction was driven only by enthalpy below 23 degrees C, by enthalpy and entropy between 23 and 35 degrees C, and only by entropy above 35 degrees C. This suggests, inter alia, that the contribution from the enthalpy of hydration due to the water molecules present at the interface in the lysozyme-antibody complex is progressively eliminated as the temperature increases. Whereas calorimetric data pertain to all the components present in the sample, including solvent molecules, BIAcore measurements monitor only the physical association and dissociation of the two macromolecular species. The difference between the two sets of data may also reflect the complexity of the binding mechanism between lysozyme and Fab D1.3.

Energetic and kinetic contributions of contact residues of antibody D1.3 in the interaction with lysozyme

Fully functional variable fragments (Fv) of D1.3, a mouse antibody directed against the hen egg lysozyme, were readily produced as hybrids (Fv-MalE) with the maltose-binding protein of Escherichia coli and purified independently of their antigen-binding properties. We used site-directed mutations of residues in the complementarity-determining regions (CDRs) of D1.3 as local conformational probes, and compared their effects on the binding of Fv and Fv-MalE to lysozyme. We found that the MalE moiety did not significantly interfere with the interaction between the antigen and the antibody Fv fragment. We then determined the contribution of several potential contact residues of D1.3 in the interaction with lysozyme, by assaying the effect of site-directed mutations on the kinetics of association and dissociation of the complex between Fv-MalE and immobilized lysozyme, using the BIAcore apparatus. While the k(on) values were virtually unaffected by the mutations, the k(off) values varied by more than three orders of magnitude. Both charged (aspartate and arginine) and aromatic (tyrosine and tryptophan) residues in the CDR3 regions of the heavy and light chains of D1.3, which form the center of its antigen-combining site, played a preponderant part in the binding of lysozyme. Our results also showed that indirect hydrogen bonds, bridged by water molecules, contributed significantly to the interaction between D1.3 and lysozyme, and that their energy could be estimated at 1 to 2 kcal.mol-1.

The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1

The reactions of lysozyme with the specific monoclonal antibody D1.3, its Fv fragment and a mutant of the Fv, were studied under conditions of reduced water activity through the addition of the cosolutes glycerol, ethanol, dioxane and methanol. Titration calorimetry, BIAcoreTM and ultracentrifugal analyses were used to determine enthalpy of reactions and affinity constants. There was a decrease in the values of the enthalpies of reactions as well as in the association constants which was proportional to the decrease in water activity. These results are consistent with a structural model in which water molecules bound to the antigen and the antibody are conserved upon complex formation and provide bonds which are important for the stability of the complex. In contrast, the reaction of lysozyme with the specific monoclonal antibody D44.1, or its Fab, showed the inverse effect: a small increase in the value of the association constant with decreasing water molarities. This is in agreement with a model in which binding of antigen to antibody D44.1 is accompanied by the release of a very small number of water molecules.