Close-up of the immunogenic α1,3-galactose epitope as defined by a monoclonal chimeric immunoglobulin E and human serum using saturation transfer difference (STD) NMR

Anaphylaxis mediated by carbohydrate structures is a controversially discussed phenomenon. Nevertheless, IgE with specificity for the xenotransplantation antigen α1,3-Gal (α-Gal) are associated with a delayed type of anaphylaxis, providing evidence for the clinical relevance of carbohydrate epitopes in allergy. The aim of this study was to dissect immunoreactivity, interaction, and fine epitope of α-Gal-specific antibodies to obtain insights into the recognition of carbohydrate epitopes by IgE antibodies and their consequences on a molecular and cellular level. The antigen binding moiety of an α-Gal-specific murine IgM antibody was employed to construct chimeric IgE and IgG antibodies. Reactivity and specificity of the resulting antibodies were assessed by means of ELISA and receptor binding studies. Using defined carbohydrates, interaction of the IgE and human serum was assessed by mediator release assays, surface plasmon resonance (SPR), and saturation transfer difference NMR analyses. The α-Gal-specific chimeric IgE and IgG antibodies were proven functional regarding interaction with antigen and Fc receptors. SPR measurements demonstrated affinities in the micromolar range. In contrast to a reference antibody, anti-Gal IgE did not induce mediator release, potentially reflecting the delayed type of anaphylaxis. The α1,3-Gal epitope fine structures of both the recombinant IgE and affinity-purified serum were defined by saturation transfer difference NMR, revealing similar contributions of carbohydrate residues and participation of both galactose residues in interaction. The antibodies generated here constitute the principle underlying α1,3-Gal-mediated anaphylaxis. The complementary data of affinity and fine specificity may help to elucidate the recognition of carbohydrates by the adaptive immune response and the molecular requirements of carbohydrate-based anaphylaxis.     

Unique assignment of inter-subunit association in GABAA α1β3γ2 receptors determined by molecular modeling

Recent publications defined requirements for inter-subunit contacts in a benzodiazepine-sensitive GABA_A receptor (GABA_ARα1β3γ2). There is strong evidence that the heteropentameric receptor contains two α1, two β3, and one γ2 subunit. However, the available data do not distinguish two possibilities: When viewed clockwise from an extracellular viewpoint the subunits could be arranged in either γ2β3α1β3α1 or γ2α1β3α1β3 configurations. Here we use molecular modeling to thread the relevant GABA_AR subunit sequences onto a template of homopentameric subunits in the crystal structure of the acetylcholine binding protein (AChBP). The GABA_A sequences are known to have 15-18% identity with the acetylcholine binding protein and nearly all residues that are conserved within the nAChR family are present in AChBP. The correctly aligned GABA_A sequences were threaded onto the AChBP template in the γ2β3α1β3α1 or γ2α1β3α1β3  arrangements. Only the γ2α1β3α1β3 arrangement satisfied three known criteria: (1) α1 His¹⁰² binds at the γ2 subunit interface in proximity to γ2 residues Thr¹⁴², Phe⁷⁷, and Met¹³⁰; (2) α1 residues 80-100 bind near γ2 residues 91-104; and (3) α1 residues 58-67 bind near the β3 subunit interface. In addition to predicting the most likely inter-subunit arrangement, the model predicts which residues form the GABA and benzodiazepine binding sites.     

Structural Analysis of a Protective Epitope of the Francisella tularensis O-Polysaccharide

Francisella tularensis (Ft), the Gram-negative facultative intracellular bacterium that causes tularemia, is considered a biothreat because of its high infectivity and the high mortality rate of respiratory disease. The Ft lipopolysaccharide (Ft LPS) is thought to be a main protective antigen in mice and humans, and we have previously demonstrated the protective effect of the Ft LPS-specific monoclonal antibody Ab52 in a mouse model of respiratory tularemia. Immunochemical characterization has shown that the epitope recognized by Ab52 is contained within two internal repeat units of the O-polysaccharide [O-antigen (OAg)] of Ft LPS. To further localize the Ab52 epitope and understand the molecular interactions between the antibody and the saccharide, we determined the X-ray crystal structure of the Fab fragment of Ab52 and derived an antibody-antigen complex using molecular docking. The docked complex, refined through energy minimization, reveals an antigen binding site in the shape of a large canyon with a central pocket that accommodates a V-shaped epitope consisting of six sugar residues, α-d-GalpNAcAN(1→4)-α-d-GalpNAcAN(1→3)-β-d-QuipNAc(1→2)-β-d-Quip4NFm(1→4)-α-d-GalpNAcAN(1→4)-α-d-GalpNAcAN. These results inform the development of vaccines and immunotherapeutic/immunoprophylactic antibodies against Ft by suggesting a desired topology for binding of the antibody to internal epitopes of Ft LPS. This is the first report of an X-ray crystal structure of a monoclonal antibody that targets a protective Ft B cell epitope.     

Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody

The anti-nerve growth factor (NGF) monoclonal antibody αD11 is a potent antagonist that neutralizes the biological functions of its antigen in vivo. NGF antagonism is expected to be a highly effective and safe therapeutic approach in many pain states. A comprehensive functional and structural analysis of αD11 monoclonal antibody was carried out, showing its ability to neutralize NGF binding to either tropomyosine receptor kinase A (TrkA) or p75 receptors. The 3-D structure of the αD11 Fab fragment was solved at 1.7 Å resolution. A computational docking model of the αD11 Fab-NGF complex, based on epitope mapping using a pool of 44 NGF mutants and experimentally validated by small-angle X-ray scattering, provided the structural basis for identifying the residues involved in αD11 Fab binding. The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor.     

Species- and Subtype-Specific Recognition by Antibody WF6 of a Sequence Segment Forming an α-Bungarotoxin Binding Site on the Nicotinic Acetylcholine Receptor α Subunit

Abstract

The monoclonal antibody WF6 competes with acetylcholine and α-bungarotoxin (α-BGT) for binding to the Torpedo nicotinic acetylcholine receptor (nAChR) α1 subunit. Using synthetic peptides corresponding to the complete Torpedo nAChR α1 subunit, we previously mapped a continuous epitope recognized by WF6, and the prototope for α-BGT, to the sequence segment α1(181–200). Single amino acid substitution analogs have been used as an initial approach to determine the critical amino acids for WF6 and α-BGT binding. In the present study, we continue our analysis of the structural features of the WF6 epitope by comparing its cross-reactivity with synthetic peptides corresponding to the α1 subunits from the muscle nAChRs of different species, the rat brain α2, α3, α4 and α5 nAChR subtypes, and the chick brain α-BGT binding protein subunits, αBGTBP α1 and αBGTBP α2. Our results indicate that WF6 is able to cross-react with the muscle α1 subunits of different species by virtue of conservation of several critical amino acid residues between positions 190–198 of the α1 subunit. These studies further define the essential structural features of the sequence segment α1(181–200) required to form the epitope for WF6.     

Epitope mapping of function‐blocking monoclonal antibody CM6 suggests a “weak” integrin binding site on the laminin‐332 LG2 domain

Laminin‐332 (Ln‐332) is an extracellular matrix molecule that regulates cell adhesion, spreading, and migration by interaction with cell surface receptors such as α3β1 and α6β4. Previously, we developed a function‐blocking monoclonal antibody against rat Ln‐332, CM6, which blocks hemidesmosome assembly induced by Ln‐332‐α6β4 interactions. However, the location of its epitope on Ln‐332 has remained unclear. In this study, we show that the CM6 epitope is located on the laminin G‐like (LG)2 module of the Ln‐332 α3 chain. To specify the residues involved in this epitope, we produced a series of GST‐fused α3 LG2 mutant proteins in which rat‐specific acids were replaced with human acids by a site‐directed mutagenesis strategy. CM6 reactivity against these proteins showed that CM6 binds to the ¹⁰⁸⁹NERSVR¹⁰⁹⁴ sequence of rat Ln‐332 LG2 module. In a structural model, this sequence maps to an LG2 loop sequence that is exposed to solvent according to predictions, consistent with its accessibility to antibody. CM6 inhibits integrin‐dependent cell adhesion on Ln‐332 and inhibits cell spreading on both Ln‐332 and recombinant LG2 (rLG2; but not rLG3), suggesting the presence of an α3β1 binding site on LG2. However, we were unable to show that rLG2 supports adhesion in standard assays, suggesting that LG2 may contain a “weak” integrin binding site, only detectable in spreading assays that do not require washes. These results, together with our previous findings, indicate that binding sites for α3β1 and α6β4 are closely spaced in the Ln‐332 LG domains where they regulate alternative cell functions, namely adhesion/migration or hemidesmosome anchoring. J. Cell. Physiol. 223:541–548, 2010. © 2010 Wiley‐Liss, Inc.     

α1-Adrenergic Receptors of A Smooth Muscle Cell Line: Guanine Nucleotides Do Not Regulate Agonist Affinities

Abstract

Using [³H]-dihydroergocryptine, we have identified in membranes prepared from the DDT₁ MF-2 smooth muscle cell line a binding site with characteristics of the α₁-adrenergic receptor. Specific binding (90–95% of total binding) was saturable with a binding site concentration of 197±44 fmol/mg protein and was of high affinity with a dissociation constant of 1.7±0.4 nM. The order of agonist competition for the binding site was epinephrine (K_i=2.3±0.5μM) ≥ norepinephrine (K_i=4.4±1.3μM) ? isoproterenol (K_i=195.5±27.6μM), consistent with an α-adrenergic interaction. Computer modelling of competition curves obtained with prazosin (α₁-selective) and yohimbine (α₂-selective) indicated that the DDT₁ cell αa-adrenergic receptor was predominantly (>95%) of the α₁-subtype. Guanine nucleotides, either GTP or 5'-guanylylimidodiphosphate, did not reduce the affinity of either epinephrine of phenylephrine for the [3H]-dihydroergocryptine binding site.     

Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide

The three-dimensional structure of the Fab fragment of a monoclonal antibody (LNKB-2) to human interleukin-2 (IL-2) complexed with a synthetic antigenic nonapeptide, Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-OMe, has been determined at 3.0 A resolution. In the structure, four out of the six hypervariable loops of the Fab (complementarity determining regions [CDRs] L1, H1, H2, and H3) are involved in peptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. The Tyr residues in the Fab antigen binding site play a major role in antigen-antibody recognition. The structures of the complexed and uncomplexed Fab were compared. In the antigen binding site the CDR-L1 loop of the antibody shows the largest structural changes upon peptide binding. The peptide adopts a mostly alpha-helical conformation similar to that in the epitope fragment 64-72 of the IL-2 antigen. The side chains of residues Leu 66, Val 69, and Leu 70, which are shielded internally in the IL-2 structure, are involved in interactions with the Fab in the complex studied. This indicates that antibody-antigen complexation involves a significant rearrangement of the epitope-containing region of the IL-2 with retention of the alpha-helical character of the epitope fragment.     

Characterization of a high-affinity human antibody with a disulfide bridge in the third complementarity-determining region of the heavy chain

Disulfide bridges are common in the antigen-binding site from sharks (new antigen receptor) and camels (single variable heavy-chain domain, VHH), in which they confer both structural diversity and domain stability. In human antibodies, cysteine residues in the third complementarity-determining region of the heavy chain (CDR-H3) are rare but naturally encoded in the IGHD germline genes. Here, by panning a phage display library designed based on human germline genes and synthetic CDR-H3 regions against a human cytokine, we identified an antibody (M3) containing two cysteine residues in the CDR-H3. It binds the cytokine with high affinity (0.4?nM), recognizes a unique epitope on the antigen, and has a distinct neutralization profile as compared with all other antibodies selected from the library. The two cysteine residues form a disulfide bridge as determined by mass spectrometric peptide mapping. Replacing the cysteines with alanines did not change the solubility and stability of the monoclonal antibody, but binding to the antigen was significantly impaired. Three-dimensional modeling and dynamic simulations were employed to explore how the disulfide bridge influences the conformation of CDR-H3 and binding to the antigen. On the basis of these results, we envision that designing human combinatorial antibody libraries to contain intra-CDR or inter-CDR disulfide bridges could lead to identification of human antibodies with unique binding profiles.     

Binding of rat α1-inhibitor-3-methylamine to the α2-macroglobulin signaling receptor induces second messengers

Binding of receptor-recognized forms of tetrameric human α₂-macroglobulin (α₂M*) to a macrophage signaling receptor induces cAMP synthesis, increases in inositol 1,4,5-triphosphate (IP₃) synthesis, and a concomitant rise in cytosolic free calcium ([Ca²⁺]_i). The α₂M* signaling receptor is coupled to a pertussis-toxin insensitive G protein. Binding of α₂M* also occurs to the low density lipoprotein receptor-related protein/α₂M receptor (LRP/α₂MR), but this binding does not induce signal transduction. Rat α₁-inhibitor-3 (α₁I₃) is a monomeric member of the α-macroglobulin/complement superfamily. Like α₂M, it can react with proteinases or methylamine which induces a conformational change causing activated α₁I₃ to bind to LRP/α₂MR. We now report that α₁I₃-methylamine binds to the macrophage α₂M* signaling receptor inducing a rapid rise in the synthesis of IP₃ with a subsequent 1.5- to 3-fold rise in [Ca²⁺]_i. α₁I₃-methylamine binding to macrophages also caused a statistically significant elevation in cAMP. Native α₁I₃, like α₂M, was unable to induce signal transduction. α₁I₃ forms a complex with α₁-microglobulin, which has a distinct conformation from α₁I₃ and is recognized by LRP/α₂MR. This complex also induces an increase in [Ca²⁺]_i comparable to the effect of α₁I₃-methylamine on macrophages. It is concluded that activation of α₁I₃ by methylamine or binding of α₁-microglobulin causes similar conformational changes in the inhibitor, exposing the receptor recognition site for the α₂M* signaling receptor, as well as for LRP/α₂MR. © 1996 Wiley-Liss, Inc.     

Mutations within the agonist-binding site convert the homomeric α1 glycine receptor into a Zn2+-activated chloride channel

The divalent cation Zn²⁺ has been shown to regulate inhibitory neurotransmission in the mammalian CNS by affecting the activation of the strychnine-sensitive glycine receptor (GlyR). In spinal neurons and cells expressing recombinant GlyRs, low micromolar (10 µM) have an inhibitory effect. Mutational studies have localized the Zn²⁺ binding sites mediating allosteric potentiation and inhibition of GlyRs in distinct regions of the N-terminal extracellular domain of the GlyR α-subunits. Here, we examined the ZZn²⁺ sensitivity of different mutations within the agonist binding site of the homomeric α1-subunit GlyR upon heterologous expression in Xenopus oocytes. This revealed that 6 substitutions within the ligand-binding pocket result in a total loss of Zn²⁺ inhibition. Furthermore, substitution of the positively charged residues arginine 65 and arginine 131 by alanine (α1R65A, α1R131A), or of the aromatic residue phenylalanine 207 by histidine (α1F207H), converted the α1 GlyR into a chloride channel that was activated by Zn²⁺ alone. Dose-response analysis of the α1F207H GlyR disclosed an EC50 value of 1.2 µM for Zn²⁺ activation; concomitantly the apparent glycine affinity was 1000-fold reduced. Thus, single point mutations within the agonist-binding site of the α1 subunit convert the inhibitory GlyR from a glycine-gated into a selectively Zn²⁺-activated chloride channel. This might be exploited for the design of metal-specific biosensors by modeling-assisted mutagenesis.     

Studies of a Murine Monoclonal Antibody Directed against DARC: Reappraisal of Its Specificity

Duffy Antigen Receptor for Chemokines (DARC) plays multiple roles in human health as a blood group antigen, a receptor for chemokines and the only known receptor for Plasmodium vivax merozoites. It is the target of the murine anti-Fy6 monoclonal antibody 2C3 which binds to the first extracellular domain (ECD1), but exact nature of the recognized epitope was a subject of contradictory reports. Here, using a set of complex experiments which include expression of DARC with amino acid substitutions within the Fy6 epitope in E. coli and K562 cells, ELISA, surface plasmon resonance (SPR) and flow cytometry, we have resolved discrepancies between previously published reports and show that the basic epitope recognized by 2C3 antibody is ²²FEDVW²⁶, with ²²F and ²⁶W being the most important residues. In addition, we demonstrated that ³⁰Y plays an auxiliary role in binding, particularly when the residue is sulfated. The STD-NMR studies performed using 2C3-derived Fab and synthetic peptide corroborated most of these results, and together with the molecular modelling suggested that ²⁵V is not involved in direct interactions with the antibody, but determines folding of the epitope backbone.     

Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond

A recombinant Fv construct of the B1 monoclonal antibody that recognizes the Lewis^Y-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the V_H and V_L domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues V_L100 and V_H44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023–1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6₁22 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the Lewis^Y tetrasaccharide, Fuc–Gal–Nag–Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781–3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128–138, 1998. Published 1998 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

The Galα1,3Galβ1,4GlcNAc-R (α-Gal) epitope: A carbohydrate of unique evolution and clinical relevance

In 1985, we reported that a naturally occurring human antibody (anti-Gal), produced as the most abundant antibody (1% of immunoglobulins) throughout the life of all individuals, recognizes a carbohydrate epitope Galα1–3Galβ1–4GlcNAc-R (the α-gal epitope). Since that time, an extensive literature has developed on discoveries related to the α-gal epitope and the anti-Gal antibody, including the barrier they form in xenotransplantation and their reciprocity in mammalian evolution. This review covers these topics and new avenues of clinical importance related to this unique antigen/antibody system (α-gal epitope/anti-Gal) in improving the efficacy of viral vaccines and in immunotherapy against cancer.     

A multispecific monoclonal antibody G2 recognizes at least three completely different epitope sequences with high affinity

A monoclonal antibody (mAb) G2 possesses an unusual characteristic of reacting with at least three proteins (ATP6V1C1, SEPT3, and C6H10orf76) other than its original antigen, chicken prion protein (ChPrP). The epitopes on ChPrP and ATP6V1C1 have been identified previously. In this study, we identified the epitope in the third protein, SEPT3. Interestingly, there was no amino acid sequence similarity among the epitopes on the three proteins. These epitopes had high binding affinities to G2 (K _D = ～10^?7 M for monovalent binding and K _D = ～10^?9 M for divalent binding), as determined using a SPR biosensor. This is the first report on a three‐in‐one mAb recognizing completely different epitope sequences with high affinity. Additionally, competitive ELISA indicated that the binding sites on G2, specific for the three different epitopes, overlapped, suggesting that the antigen‐binding site may be flexible in the free form and capable of adapting to at least three different conformations to enable interactions with three different antigens.     

Structural consensus among antibodies defines the antigen binding site

The Complementarity Determining Regions (CDRs) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site. CDRs are typically discerned by searching for regions that are most different, in sequence or in structure, between different antibodies. Here, we show that ~20% of the antibody residues that actually bind the antigen fall outside the CDRs. However, virtually all antigen binding residues lie in regions of structural consensus across antibodies. Furthermore, we show that these regions of structural consensus which cover the antigen binding site are identifiable from the sequence of the antibody. Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically. Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding. These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.     

Goodpasture syndrome. Localization of the epitope for the autoantibodies to the carboxyl-terminal region of the alpha 3(IV) chain of basement membrane collagen.

The autoantibodies of patients with Goodpasture syndrome are primarily targeted to the noncollagenous (NC1) domain of the alpha 3(IV) chain of basement membrane collagen (Saus, J., Wieslander, J., Langeveld, J. P. M., Quinones, S., and Hudson, B. G. (1988) J. Biol. Chem. 263, 13374-13380). In the present study, the location of the Goodpasture epitope in human alpha 3NC1 was determined, and its structure was partially characterized. This was achieved by identification of regions of alpha 3NC1 which are candidates for the epitope and which are structurally unique among the five known homologous NC1 domains (alpha 1-alpha 5); amino acids that are critical for Goodpasture antibody binding, by selective chemical modifications; and regions that are critical for Goodpasture antibody binding, by synthesis of 12 alpha 3NC1 peptides and measurement of their antibody binding capacity. The carboxyl-terminal region, residues 198-233, was identified as the most likely region for the epitope. By experiment, lysine and cysteine were identified as critical amino acids for antibody binding. Three synthetic peptides were found to inhibit Goodpasture antibody binding to alpha 3NC1 markedly: a 36-mer (residues 198-233), a 12-mer (residues 222-233), and a 5-mer (residues 229-233). Together, these results strongly indicate that the Goodpasture epitope is localized to the carboxyl-terminal region of alpha 3NC1, encompassing residues 198-233 as the primary antibody interaction site and that its structure is discontinuous. These findings provide a conceptual framework for future studies to elucidate a more complete epitope structure by sequential replacement of residues encompassing the epitope using cDNA expression products and peptides synthesized chemically.     

Studies on the Antigenic Activity of Yeasts

In order to determine the determinant antigenic group of the mannan of Saccharomyces cerevisiae, a series of inhibition tests were carried out employing oligosaccharides which separated from the acetolyzate and the hydrolyzate of the mannan. Tetraose, Man α1→3 Man α1→2 Man α→2 Man², corresponding to the structure of the longer branching moieties of the mannan showed the strongest inhibition, while the isomer, Man α1→6 Man α1→6 Man, corresponding to the core moiety, produced only one-tenth the inhibition of the former. This provides evidence that the branching moieties of the mannan play important role in combining with antibody. The fact that the disaccharide, Man α→3, showed significantly stronger inhibition than those of the other disaccharides, Man α1→2 Man and Man α1→6 Man, indicates that the most important part of the determinant group of the mannan is α1→3 linked D-mannose residue. The antigenic inactivity of the periodate-oxidized mannan containing unoxidized mannose residues indicates that the presence of 3-O-substituted-D-mannose residues adjacent to the D-mannose residues and joined with α1→d2 linkages, are essential to fit the combining site of the antibody.     

Insights into binding modes of tumstatin peptide T7 with the active site of αvβ3 integrin

Through interaction with the active site of α_vβ₃ integrin, tumstatin T7 peptide inhibits both the angiogenesis and the proliferation of tumour cells. In this work, docking in conjunction with molecular dynamics simulation was used to explore the binding mode of T7 peptide and α_vβ₃ integrin. The binding mode analysis revealed that the residues Ser⁹⁰, Arg⁹¹, Asp⁹³ and Tyr⁹⁴ in T7 peptide, and (α)-Asp¹⁵⁰, (β)-Arg²¹⁴, (α)-Asp¹⁴⁸ (α)-Gln²¹⁴ and (α)-Glu¹²³ in the active site of α_vβ₃ integrin were most likely the key interaction sites. The hydroxyl of Tyr⁹⁴ coordinates α_vβ₃ via a Mn²⁺ ion, revealing that Mn²⁺ is also an important factor for the interaction. The insight into these key interaction sites not only suggests that the active site of α_vβ₃ integrin can bind to molecules through multiple binding mechanisms, but also provides some useful information for structure-based drug design.     

Nine Residues Influence the Binding of α-Bungarotoxin in α-Subunit Region 185–200 of Human Muscle Acetylcholine Receptor

Abstract: Identification of residues in the skeletal muscle nicotinic acetylcholine receptor (AChR) that bind snake venom a-neurotoxin antagonists of acetylcholine [e.g., α-bungarotoxin (α-BTx)] provides structural information about the neurotransmitter binding region of the receptor. Using synthetic peptides of the human AChR α-subunit region 177–208, we previously localized a pharmacologically specific binding site for α-BTx in segment 185–199. To define in more detail the residues that influence the binding of α-BTx to this region, we prepared 16 peptide analogues of the α-subunit segment 185–200, with the amino acid Lalanine sequentially replacing each native amino acid. Circular dichroism spectroscopy did not reveal changes in the secondary structure of the peptides except for the analogue in which Pro¹⁹⁴ was substituted with alanine. This implies that any change in α-BTx binding could be attributed to replacement of the native residue's side chain by alanine's methyl group, rather than to a change in the structure of the peptide. The influence of each substitution with alanine was determined by comparing the analogue to the parental sequence α 185–200 in solution-phase competition with native human AChR for binding of ¹²⁵I-labeled α-BTx. The binding of α-BTx by analogue peptides with alanine substituted for Tyr¹⁹⁰, Cys¹⁹², or Cys¹⁹³ was greatly diminished. Binding of α-BTx to peptides containing alanine replacements at Val¹⁸⁸, Thr¹⁸⁹, Pro¹⁹⁴, Asp¹⁹⁵, or Tyr¹⁹⁸ was also reduced significantly (p < 0.003). An unanticipated finding was that substitution of alanine for Ser¹⁹¹ significantly increased α-BTx binding (p < 0.003). The data imply that these nine amino acids influence the binding of the antagonist, α-BTx, to the nicotinic acetylcholine receptor of human skeletal muscle, and confirm previous reports for certain contact residues for α-BTX that were found in region α181-200 of the Torpedo AChR.