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Edmundson AB, Harris DL, Tribbick G, Geysen HM. Binding of peptides to proteins: an exercise in molecular design. CIBA FOUNDATION SYMPOSIUM 2007; 158:213-25; discussion 225-30. [PMID: 1935422 DOI: 10.1002/9780470514085.ch14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptides coupled to solid supports were systematically tested for binding activity with a polyreactive immunoglobulin light chain dimer by the methods of Geysen and colleagues. Once identified, peptides of progressively increasing affinity for the dimer were synthesized in milligram quantities and diffused into crystals of the protein. The three-dimensional structures of the peptide-protein complexes were determined by X-ray analysis and crystallographic refinement. Criteria for the design of ligands to fill the binding cavity in incremental stages could be formulated from the combined results of peptide scanning and crystallographic analyses. Histidine proved to be an important substituent in the binding series. It was possible to manipulate the properties of this amino acid residue to alter the structures and binding patterns of the ligands. For example, if two beta-alanine residues were added to the carboxyl end of a tetrapeptide ligand, the terminal carboxyl group formed an intramolecular ion pair with the imidazolium group (N-3) of histidine. This interaction was accompanied by cleavage of the intra molecular hydrogen bond between N-1 of histidine and the amide group of a glutamine side chain. The shape of the ligand shifted from a compact to an extended form and the mode of binding changed from a lock-and-key to an induced-fit type. The direction of entry of dipeptides of histidine and proline into the binding cavity (normally amino end first) could be reversed (carboxyl end first) by protonation of the histidine ring.
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2
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Peabody DS. A Viral Platform for Chemical Modification and Multivalent Display. J Nanobiotechnology 2003; 1:5. [PMID: 12890286 PMCID: PMC169181 DOI: 10.1186/1477-3155-1-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 07/15/2003] [Indexed: 11/10/2022] Open
Abstract
The ability to chemically modify the surfaces of viruses and virus-like particles makes it possible to confer properties that make them potentially useful in biotechnology, nanotechnology and molecular electronics applications. RNA phages (e.g. MS2) have characteristics that make them suitable scaffolds to which a variety of substances could be chemically attached in definite geometric patterns. To provide for specific chemical modification of MS2's outer surface, cysteine residues were substituted for several amino acids present on the surface of the wild-type virus particle. Some substitutions resulted in coat protein folding or stability defects, but one allowed the production of an otherwise normal virus-like particle with an accessible sulfhydryl on its surface.
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Affiliation(s)
- David S Peabody
- Department of Molecular Genetics and Microbiology and the Cancer Research and Treatment Center University of New Mexico School of Medicine Albuquerque, New Mexico, USA 87131.
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Edmundson AB. Reminiscences: joyous moments along the road from here to there and back again. J Mol Recognit 2002; 15:227-39. [PMID: 12447899 DOI: 10.1002/jmr.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Allen B Edmundson
- The Crystallography Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City 73104, USA.
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Guddat LW, Shan L, Broomell C, Ramsland PA, Fan Z, Anchin JM, Linthicum DS, Edmundson AB. The three-dimensional structure of a complex of a murine Fab (NC10. 14) with a potent sweetener (NC174): an illustration of structural diversity in antigen recognition by immunoglobulins. J Mol Biol 2000; 302:853-72. [PMID: 10993728 DOI: 10.1006/jmbi.2000.4083] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three-dimensional structure of a complex of an Fab from a murine IgG2b(lambda) antibody (NC10.14) with a high potency sweet tasting hap- ten, N-(p-cyanophenyl)-N'-(diphenylmethyl)-N"-(carboxymethyl)guan idine (NC174), has been determined to 2.6 A resolution by X-ray crystallography. This complex crystallized in the triclinic space group P1, with two molecules in the asymmetric unit. In contrast to a companion monoclonal antibody (NC6.8) with a kappa-type light chain and similar high affinity for the NC174 ligand, the NC10.14 antibody possessed a large and deep antigen combining site bounded primarily by the third complementarity-determining regions (CDR3s) of the light and heavy chains. CDR3 of the heavy chain dominated the site and its crown protruded into the external solvent as a type 1' beta-turn. NC174 was nested against HCDR3 and was held in place by two tryptophan side-chains (L91 and L96) from LCDR3. The diphenyl rings were accommodated on an upper tier of the binding pocket that is largely hydrophobic. At the floor of the site, a positively charged arginine side-chain (H95) stabilized the orientation of the electronegative cyano group of the hapten. The negative charge on the acetate group was partially neutralized by a hydrogen bond with the phenolic hydroxyl group of tyrosine H58. Comparisons of the modes of binding of NC174 to the NC6.8 and NC10.14 antibodies illustrate the enormous structural and mechanistic diversity manifest by immune responses.
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Affiliation(s)
- L W Guddat
- Crystallography Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
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Faber C, Shan L, Fan Z, Guddat LW, Furebring C, Ohlin M, Borrebaeck CA, Edmundson AB. Three-dimensional structure of a human Fab with high affinity for tetanus toxoid. IMMUNOTECHNOLOGY : AN INTERNATIONAL JOURNAL OF IMMUNOLOGICAL ENGINEERING 1998; 3:253-70. [PMID: 9530559 DOI: 10.1016/s1380-2933(97)10003-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The wide range of antibody specificity and affinity results from the differing shapes and chemical compositions of their binding sites. These shapes range from discrete grooves in antibodies elicited by linear oligomers of nucleotides and carbohydrates to shallow depressions or flat surfaces for accommodation of proteins, peptides and large organic compounds. OBJECTIVES To determine the Fab structure of a high-affinity human antitoxin antibody. To explore structural features which enable the antibody to bind to intact tetanus toxoid, peptides derived from the sequence of the natural immunogen and antigenic mimics identified by combinatorial chemistry. To explain why this Fab shows a remarkable tendency to produce crystals consistently diffracting to d spacings of 1.7-1.8 A. To use this information to engineer a strong tendency to crystallize into the design of other Fabs. STUDY DESIGN The protein was crystallized in hanging or sitting drops by a microseeding technique in polyethylene glycol (PEG) 8000. Crystals were subjected to X-ray analysis and the three-dimensional structure of the Fab was determined by the molecular replacement method. Interactive computer graphics were employed to fit models to electron density maps, survey the structure in multiple views and discover the crystal packing motif of the protein. RESULTS Exceptionally large single crystals of this protein have been obtained, one measuring 5 x 3 x 2 mm (l x w x d). The latter was cut into six irregular pieces, each retaining the features of the original in diffracting to high resolution (1.8 A) with little decay in the X-ray beam. In an individual Fab, the active site is relatively flat and it seems likely that the protein antigen and derivative peptides are tightly held on the outer surface without significant penetration into the interior. There is no free space to accommodate even a dipeptide between VH and VL. One of the unique features of the B7-15A2 Fab is a large aliphatic ridge dominating the center of the active site. The CDR3 of the H chain contributes significantly to this ridge, as well as to adjoining regions projected to be important for the docking of the antigen. Both the ease of crystallization and the favorable diffraction properties are mainly attributable to the tight packing of the protein molecules in the crystal lattice. DISCUSSION The B7-15A2 active site provides a stable and well defined platform for high affinity docking of proteins, peptides and their mimotopes. The advantages for future developments are suggested by the analysis of the crystal properties. It should be possible to incorporate the features promoting crystallization, close packing and resistance to radiation damage into engineered human antibodies without altering the desired specificities and affinities of their active sites.
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Affiliation(s)
- C Faber
- Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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6
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Edmundson AB, Borrebaeck CA. Progress in programming antibody fragments to crystallize. IMMUNOTECHNOLOGY : AN INTERNATIONAL JOURNAL OF IMMUNOLOGICAL ENGINEERING 1998; 3:309-17. [PMID: 9530564 DOI: 10.1016/s1380-2933(97)10002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Completion of the X-ray analysis of the human B7-15A2 Fab opened a new vista (Immunotechnology 3, no. 4). In the crystal lattice, both the lambda-type light chain (CL domain) and gamma 1-type heavy chain (CH1 domain) participated in formation of antiparallel beta-pleated sheets with neighboring molecules related to the reference Fab by 2-fold axes. This observation evoked memories of the first description of this type of packing for human Bence-Jones (lambda chain) dimers 20 years ago (Ely K.R. et al. Biochemistry 1978;17:158-167). Reexamination of packing interactions in selected crystal systems revealed that the C domains of lambda and gamma 1 chains were structurally amenable to the formation of such cross-molecule beta-structures, but kappa chain CL domains were not. In the latter, a single proline residue disrupted the order of beta-strand 3-3 in the middle of the surface used in lambda and gamma 1 chains for intermolecular interactions with symmetry-related molecules. For the packing of Fv molecules, the VL domains are structurally well suited for analogous packing interactions through antiparallel 4-1 beta-strands in adjacent molecules. Such interactions have been shown to provide the driving force in the crystal packing of a human (Pot) Fv from an IgM-kappa cryoglobulin. Together, these observations suggest several avenues through which propensity to crystallize can be programmed into the designs of synthetic human Fabs, Fvs and single-chain antibodies.
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Affiliation(s)
- A B Edmundson
- Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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7
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Grégoire C, Rebaï N, Schweisguth F, Necker A, Mazza G, Auphan N, Millward A, Schmitt-Verhulst AM, Malissen B. Engineered secreted T-cell receptor alpha beta heterodimers. Proc Natl Acad Sci U S A 1991; 88:8077-81. [PMID: 1716770 PMCID: PMC52449 DOI: 10.1073/pnas.88.18.8077] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have produced a soluble form of a mouse alpha beta T-cell antigen receptor (TCR) by shuffling its variable (V) and constant (C) domains to the C region of an immunoglobulin kappa light chain. These chimeric molecules composed of V alpha C alpha C kappa and V beta C beta C kappa chains were efficiently secreted (up to 1 micrograms/ml) by transfected myeloma cells as noncovalent heterodimers of about 95-kDa molecular mass. In the absence of direct binding measurement, we have refined the epitopic analysis of the soluble V alpha C alpha C kappa-V beta C beta C kappa dimers and shown that they react with an anti-clonotypic antibody and two antibodies directed to the C domain of the TCR alpha and beta chains. Conversely, we have raised three distinct monoclonal antibodies against the soluble TCR heterodimers and shown that they recognize surface-expressed TCRs. Two of these antibodies were found to react specifically with the products of the V alpha 2 (V delta 8) and V beta 2 gene segments, respectively. When considered together, these data suggest that these soluble TCR molecules are folded in a conformation indistinguishable from that which they assume at the cell surface.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal
- Base Sequence
- Epitopes
- Genes, Immunoglobulin
- Macromolecular Substances
- Mice
- Molecular Sequence Data
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/immunology
- Recombinant Proteins
- Restriction Mapping
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Affiliation(s)
- C Grégoire
- Centre d'Immunologie, Institut National de la Santé et de la Recherche Médicale, Marseille, France
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Ely KR, Herron JN, Edmundson AB. Three-dimensional structure of a hybrid light chain dimer: protein engineering of a binding cavity. Mol Immunol 1990; 27:101-14. [PMID: 2108322 DOI: 10.1016/0161-5890(90)90105-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An attempt was made to engineer a binding site and check its structure by X-ray analysis. Two human light chains (Mcg and Weir), with "variable" domain sequences differing in 36 positions, were hybridized into a heterologous dimer and crystallized in ammonium sulfate by the same procedure used for the trigonal form of the Mcg dimer. The three-dimensional structure of the hybrid was determined at 3.5-A resolution by difference Fourier analysis, interactive model building with computer graphics and crystallographic refinement. In the heterologous dimer, the Weir protein behaved as the structural analog of the heavy chain in an antigen binding fragment, while the Mcg protein assumed the role of the light chain component. The hybrid and the Mcg dimer were closely similar in overall structure, an observation probably correlated with the deliberate cleavage of the intrachain disulfide bond in the variable domain of the Weir protein during the hybridization procedure. Examination of the crystal structure of the hybrid suggested that the cleavage resulted in the relaxation of restraints which might otherwise have interfered with the formation of an Mcg-like dimer. There were six substitutions among the residues lining the binding cavities of the hybrid and Mcg dimer. These substitutions significantly affected the sizes, shapes and binding properties of the two cavities.
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Affiliation(s)
- K R Ely
- Department of Biology, University of Utah, Salt Lake City 84112
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Tribbick G, Edmundson AB, Mason TJ, Geysen HM. Similar binding properties of peptide ligands for a human immunoglobulin and its light chain dimer. Mol Immunol 1989; 26:625-35. [PMID: 2779586 DOI: 10.1016/0161-5890(89)90044-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The urinary light chain dimer and serum monoclonal IgG1 protein from a patient (Mcg) with multiple myeloma and amyloidosis were systematically tested for their binding activities to peptides presented on solid supports. The system was validated using a series of enkephalins, beta-casomorphins and DNP-lysine derivatives which were known to complex with the dimer. Sets of peptide ligands binding to the proteins were constructed by incremental additions of amino acid residues to minimal binding units [Geysen et al., J. Immun. Meth. 102, 259-274 (1987)]. Both the amino acid sequences and the combinations of optical isomers were optimized at each stage of the syntheses. Binding could be demonstrated for ligands ranging in size from a tethered single amino acid to pentapeptides. At the dipeptide levels, the dimer and the IgG1 protein showed different preferences (Hp versus qf, where lower case letters designate D-amino acid residues). However, in a tetrapeptide ligand (qfHp) for the dimer, both of these initial preferences had converged. With few exceptions, the IgG1 molecule showed binding activity for the ligands developed for the dimer. Two sets of selected peptides, one based on Hp and the other on mW, were synthesized for diffusion into crystals of the dimer. X-ray analyses showed that these peptides bound exclusively in the main binding cavity between the "variable" domains of the dimer. As predicted from the ELISA results with tethered ligands, the relative occupancies in the crystals followed the order of tetrapeptide greater than tripeptide much greater than dipeptide. The crystallographic studies confirmed that peptides with very different sequences can bind in the same cavity.
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Affiliation(s)
- G Tribbick
- Coselco Mimotopes Pty Ltd, Commonwealth Serum Laboratories, Parkville, Victoria, Australia
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10
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Edmundson AB, Ely KR, He XM, Herron JN. Cocrystallization of an immunoglobulin light chain dimer with bis(dinitrophenyl) lysine: tandem binding of two ligands, one with and one without accompanying conformational changes in the protein. Mol Immunol 1989; 26:207-20. [PMID: 2495436 DOI: 10.1016/0161-5890(89)90074-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Previous studies showed that the Mcg dimer of immunoglobulin light chains bound bis(dinitrophenyl)lysine both in trigonal crystals and in solution. On prolonged storage in ammonium sulfate, mixtures of ligand and protein produced small trigonal cocrystals in low frequency. These crystals were nearly isomorphous with those of the unliganded dimer in which the subunits were covalently linked by an interchain disulfide bond. By difference Fourier analyses at 3.5 A resolution and subsequent crystallographic refinement, the cocrystals were found to contain molecules with two ligands aligned in tandem along the interface of the variable (V) domains of the protein. One ligand molecule adopted an almost fully extended conformation, with the epsilon-DNP ring situated near the floor, the alpha-carboxyl group directed toward the solvent at the entry, and the alpha-DNP ring outside the rim of the main cavity. As if architecturally designed, the ligand was located symmetrically between the two domains in an orientation that was compatible with both the unaltered structure of the cavity lining and with the known crystal packing interactions of neighboring protein molecules. The second ligand molecule in the cocrystal lodged in the deep pocket immediately under the floor of the main cavity. The ligand adopted a very compact conformation with the two DNP rings roughly antiparallel to each other. This molecule appeared to be semi-permanently sequestered in the pocket since it could not be dislodged by exhaustive perfusion with ammonium sulfate crystallizing media. Relative to its volume in the native dimer, the pocket was expanded to accommodate the oversized ligand. Within a single protein molecule, therefore, two types of binding of a flexible ligand were observed, one with and one without accompanying conformational changes in the protein. The number of cocrystals which could be produced was markedly increased if the interchain disulfide bond between the Mcg monomers was first reduced and alkylated.
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Affiliation(s)
- A B Edmundson
- Department of Biology, University of Utah, Salt Lake City 84112
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Kabat EA. Antibody combining sites: how much of the antibody repertoire are we seeing? How does it influence our understanding of the structural and genetic basis of antibody complimentarity? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1988; 228:1-45. [PMID: 3051914 DOI: 10.1007/978-1-4613-1663-3_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- E A Kabat
- Department of Microbiology, College of Physicians and Surgeons Columbia University, New York, N.Y. 10032
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12
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Edmundson AB, Ely KR, Herron JN, Cheson BD. The binding of opioid peptides to the Mcg light chain dimer: flexible keys and adjustable locks. Mol Immunol 1987; 24:915-35. [PMID: 3116411 DOI: 10.1016/0161-5890(87)90003-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Enkephalins and beta-casomorphins (opioid peptides) were found to bind in a variety of conformations to a human light chain (Bence-Jones) dimer from a patient (Mcg) with amyloidosis. The peptides were diffused into crystals of the protein and their positions, relative occupancies and modes of binding were determined at 2.7 A resolution by difference Fourier analyses. Collectively, the opioid peptides occupied practically all of the available space in the concave, internal parts of the binding region, as well as flat or convex external surfaces around the rim of the binding cavity. Suitable ligands ranged in size from four to seven residues. As many as five residues could be accommodated inside the binding region, and there was space for at least four residues on the external surfaces. External binding was influenced by solvent effects and local packing interactions among adjacent protein molecules in the crystal lattice. In the enkephalin series the presence of amino-terminal tyrosine was necessary, but not sufficient for binding. [Met]-enkephalin, a pentapeptide, showed two different modes of binding in overlapping subsites. In one subsite, preferred over the second in a ratio of 1.3:1.0, the side chain of amino-terminal tyrosine penetrated through the floor of the main cavity to lodge in the deep binding pocket about 20 A from the entrance. The remainder of the peptide spanned the length of the main cavity in an extended conformation. In the second subsite the amino end was restricted to the main cavity and the peptide backbone turned abruptly upward at residue 3 to interact with external surfaces. An (Arg-6, Phe-7) heptapeptide extension of [Met]-enkephalin entered the deep pocket and assumed an extended conformation in the main cavity like the pentapeptide. Its last two residues flattened against the external surfaces. [Leu]-enkephalin and its analogues displayed a combination of internal and external binding like [Met]-enkephalin in its secondary subsite. Enkephalin analogues with D-amino acids in position 2 generally adopted conformations which were more convoluted than those in the L-isomers. Moreover, external interactions tended to be more prominent in the D-derivatives. The beta-casomorphin-7 heptapeptide penetrated into the deep pocket and traversed the main cavity in as extended a conformation as the presence of two proline residues would permit. On removal of the ligand there was an unexpected hysteresis effect involving permanent structural alterations in the walls of the binding region. beta-casomorphins-4 and -5 were bound in the main cavity with the carboxyl ends protruding from the entrance.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- A B Edmundson
- Department of Biology, University of Utah, Salt Lake City 84112
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Raison RL, Edmundson AB. Localization of an idiotope on the L chain dimer and intact IgG1 immunoglobulin from the patient Mcg. Mol Immunol 1987; 24:937-43. [PMID: 3116412 DOI: 10.1016/0161-5890(87)90004-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A monoclonal anti-idiotype (M3.9) raised against the covalently linked Mcg lambda chain dimer binds with a similar affinity to the Mcg IgG immunoglobulin and covalent heterodimers of Mcg with other human L chains. Despite having identical amino acid sequences, the two light chains in the Mcg dimer adopt different conformations with monomer 1 acting as a heavy chain analog and monomer 2 behaving like a light chain component of an Fab. As the lambda chain in the Mcg IgG and at least one hybrid L chain dimer (Mcg X Weir) assumes a conformation similar to that of monomer 2 and the binding of anti-idiotype requires only the presence of a single Mcg lambda chain, we conclude that the idiotope is restricted to the monomer 2 type of the Mcg lambda chain conformational isomer. Cooperative binding of two molecules of rhodamine 123 in the main cavity of the Mcg dimer block the binding of the anti-idiotype whereas the binding of one molecule of bis(DNP)lysine has no significant effect on the idiotype-anti-idiotype system. Previous crystallographic analyses indicated that bound rhodamine 123 protrudes outside the rim while bis(DNP)lysine is completely immersed in the cavity. At high concns bis(DNP)lysine penetrates through the floor of the main cavity and forms a virtually irreversible complex with the dimer. Production of this complex is accompanied by conformational changes, which are presumed to be correlated with observed inhibition of binding with the anti-idiotype M3.9. Expression of the idiotope probably involves more than one linear sequence since reduction and alkylation of the intra- and inter-chain disulphide bonds in 8 M urea leads to a complete loss of binding of the anti-idiotype. The inhibition data suggest involvement of residues on or near the rim of the main cavity. Distribution of potential contact residues for rhodamine 123 is asymmetric only in the case of aspartic acid 97, which is located on the cavity rim in only one conformational isomer (monomer 2). The homologous residue in monomer 1 is directed away from the cavity and is unlikely to participate in the epitope recognized by M3.9. Attempts to define the epitope in more detail by simulation with multiple peptides have been initiated in collaboration with the laboratory of H. M. Geysen.
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Affiliation(s)
- R L Raison
- Clinical Immunology Research Centre, University of Sydney, Australia
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14
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Shaw DC, Harris DL, He XM, Oster JA, Montgomery DL, Ely KR, Edmundson AB. A mild method for the preparation of disulfide-linked hybrids of immunoglobulin light chains. Mol Immunol 1987; 24:267-74. [PMID: 3112562 DOI: 10.1016/0161-5890(87)90145-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A method is described for the hybridization of immunoglobulin light chains (Bence-Jones proteins) from different patients. The interchain half-cystine residues in the light chains from one subject are converted into mixed disulfides with 2,2'-dithiodipyridine. In the Bence-Jones dimer from a second patient the interchain disulfide bond is reduced with dithiothreitol. A covalently linked hybrid molecule is produced by the reaction of the mixed disulfide with the reduced thiol. In favorable cases the mild treatment yields heterodimers which can be crystallized for X-ray diffraction studies. The procedure can also be employed for converting a monomer into a covalent dimer. The engineered dimer of one kappa chain (Jen) crystallizes in the same space group as an aggregate of monomers, but the unit cell is only one-third as large.
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Abstract
IgG Gar, a human myeloma protein that binds riboflavin with a high affinity, was used to derive variable region fragments from the heavy chain and the light chain. Riboflavin binding ability of the active site generated by V(H) and light chain and the active site generated by V(H) and V(L) was compared to riboflavin binding by the F(ab) fragment. The riboflavin binding ability of the F(ab) fragment is the same as the intact molecule, while the binding ability of the active site formed by V(H) and light chain is lowered by two to three orders of magnitude, indicating that the removal of C(H1) domain decreases the interaction between riboflavin and the amino acids that is important in tight binding of riboflavin. Removal of the third hypervariable region and the constant region domain from the light chain further lowers the binding constant by one order of magnitude. The results indicate that the V(H) and V(L) segments of IgG Gar can reconstitute a riboflavin binding site. The decrease in affinity probably reflects a decrease in the rigidity with which the hypervariable loops are held together to place the contact amino acid residues in optimal contact with the hapten.
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Affiliation(s)
- J Sen
- Department of Biological Sciences, Columbia University, New York, New York 10027
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16
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Edmundson AB, Ely KR. The Mcg light chain: multiple conformations derived from a single amino acid sequence. ANNALES DE L'INSTITUT PASTEUR. IMMUNOLOGIE 1985; 136C:276-82. [PMID: 3923898 DOI: 10.1016/s0769-2625(85)80059-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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Ely KR, Wood MK, Rajan SS, Hodsdon JM, Abola EE, Deutsch HF, Edmundson AB. Unexpected similarities in the crystal structures of the Mcg light-chain dimer and its hybrid with the Weir protein. Mol Immunol 1985; 22:93-100. [PMID: 3919281 DOI: 10.1016/s0161-5890(85)80002-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The covalently linked hybrid of two human lambda-type light chains (Mcg and Weir) crystallizes as trigonal bipyramids in ammonium sulfate [Ely et al., Molec. Immun. 22, 85-92 (1985)]. While markedly different in appearance from the barrel-shaped crystals of the parental Mcg dimer, the bipyramids of the hybrid have the same space group: trigonal P3(1)21. Moreover, the unit cell dimensions are practically identical: a = 72.3 A in both proteins; c = 188.1 A in the hybrid and 185.9 A in the Mcg dimer. These observations imply that the crystal packing and the main features of the three-dimensional structures are closely similar in the Mcg X Weir hybrid and the Mcg dimer. The "constant" domains of the Mcg and Weir proteins belong to the same genetic subclass and were expected to interact in comparable ways in hybrids and parental dimers. However, the overall similarities in the "variable" domain pairs in the hybrid and Mcg dimer were completely unpredicted, since the amino acid sequences of the heterologous variable domains differ by 36 residues. By difference Fourier analysis the Weir light chain has been tentatively identified as monomer 1 (heavy-chain analogue) and the Mcg protein as monomer 2 (light-chain analogue) in the hybrid dimer. Substitutions in key positions in the hypervariable loops explain the differences in binding activity of the Mcg and Weir dimers. In the Mcg dimer bis(dinitrophenyl)lysine spans two relatively spacious subsites (A and B), with primary contacts involving tyrosines 34 and 38 of monomer 2. The Weir dimer, which does not bind dinitrophenyl ligands, has serine and phenylalanine in homologous positions. Moreover, the bilateral replacement of valine 48 and serine 91 in Mcg by leucine and methionine in the Weir dimer should effectively block access to subsite B. In the hybrid binding activity for bis(dinitrophenyl)lysine is restored because the Mcg light chain is present as the monomer 2 subunit.
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Ely KR, Peabody DS, Holm TR, Cheson BD, Edmundson AB. Accessible intrachain disulfide bonds in hybrids of light chains. Mol Immunol 1985; 22:85-92. [PMID: 3919280 DOI: 10.1016/s0161-5890(85)80001-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The three-dimensional structure of the Mcg lambda-type Bence-Jones dimer crystallized in ammonium sulfate is known at 2.3-A resolution. A series of nine other human lambda-chains and two kappa-chains did not crystallize under the same conditions. After these proteins were hybridized with the Mcg light chain by the method of Peabody et al. [Biochemistry, 19, 2827 (1980)], however, crystals of six heterodimers were produced. Two of these (Mcg X Weir and Mcg X Hud) were suitable for X-ray analysis. The non-Mcg parental molecules in four of the crystallizable hybrids showed aberrant electrophoretic behavior after treatment with mild reducing agents. The results suggest that the intrachain disulfide bond in at least one domain (probably the variable domain) was susceptible to mild reductive cleavage in a significant proportion of light chains. Moreover, the loosening of the domain structure resulting from such disulfide cleavage in one parent appeared to promote the tendency of a hybrid molecule to crystallize.
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Sharon J, Gefter ML, Manser T, Morrison SL, Oi VT, Ptashne M. Expression of a VHC kappa chimaeric protein in mouse myeloma cells. Nature 1984; 309:364-7. [PMID: 6328310 DOI: 10.1038/309364a0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The heavy (H) and light (L) chains of antibodies consist of variable (V) and constant (C) regions. The V regions of the heavy and light chains form the antibody combining site. To determine whether a V region could be functional when joined to a polypeptide other than its own C region, we constructed a chimaeric gene encoding the V region of a mouse heavy chain and the C region of a mouse kappa light chain ( VHC kappa). The heavy-chain gene is derived from an A/J mouse hybridoma cell line 36-65 whose antibody product (gamma 1, kappa) is specific for the hapten azophenylarsonate. We report here that, when introduced into a mouse myeloma cell line, the chimaeric gene is expressed and a protein of the expected molecular weight is secreted into the medium. As light chains tend to dimerize we expected that the VHC kappa protein might associate with light chain from the cell line 36-65 to form an antibody-binding molecule. Affinity binding experiments and Ka determination indicate that this is the case. Dimers of this type offer a novel and interesting alternative to existing antibody-binding molecules.
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Davidson I, Katzav S, Ungar-Waron H, Eshhar Z, Haimovich J, Trainin Z. Somatic cell hybridization between bovine leukemia virus-infected lymphocytes and murine plasma cell tumors: cell fusion studies with bovine cells. Mol Immunol 1982; 19:893-9. [PMID: 6289087 DOI: 10.1016/0161-5890(82)90355-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hybridization of peripheral blood lymphocytes from bovine leukemia virus-infected cows with murine myeloma cells resulted in the generation of hybrid cells secreting immunoglobulins composed of various combinations of heavy and light chains of both bovine and murine Ig origin. Some hybrid cells derived from the light-chain producer, but non-secretor murine myeloma NSI cell line, secreted IgM molecules composed of bovine mu-chain linked to bovine and/or murine light chains. Other hybridomas secreted mouse and bovine light-chain dimers and/or monomers, or failed to secrete any Ig polypeptide chain whatsoever. Immunoglobulins secreted by hybridomas obtained upon hybridization of bovine cells with the IgG-secreting murine myeloma P2X63 cell line, contained bovine mu-chain in one of the seven hybridomas obtained, and bovine light chain in two of them. All the cell lines secreted murine light- and gamma-chains.
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Abstract
The amino acid sequence of the Bence-Jones protein Weir has been determined. This lambda II protein is of the Mcg type. Since a mixed dinner of Weir and Mcg can be prepared in a form suitable for crystallographic analysis it was of interest to compare the sequences of these two lambda-chains. A total of 37 differences, which include one previously determined constant-region substitution, have been found.
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Kranz DM, Voss EW. Restricted reassociation of heavy and light chains from hapten-specific monoclonal antibodies. Proc Natl Acad Sci U S A 1981; 78:5807-11. [PMID: 6795637 PMCID: PMC348870 DOI: 10.1073/pnas.78.9.5807] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Six murine monoclonal antifluorescyl antibody clones encompassing a defined range of affinities and containing kappa light chains with IgG1 or IgG2 heavy chains were examined. As the fluorescence of the ligand is quenched greater than 90% when fluorescein is bound by antifluorescyl antibodies, fluorescence quenching was assayed to monitor polypeptide reconstitution and active site formation on mixing of resolved heavy (H) and light (L) chains. Of 36 possible experimental combinations of H- and L-chain reaction mixtures, only homologous H and L chains (derived from the same parental immunoglobulin molecule) bound fluorescein. Results from fluorescence polarization studies, conducted independently of fluorescence quenching, confirmed the findings. Competitive inhibition and molecular sieve experiments showed that, despite preferential association of homologous H and L chains, several heterologous H and L chains associated to form intact 7S molecules, although no active site was constituted. Thus, polypeptide recombination and formation of functional antigen binding sites are two processes that immunocytes must regulate during cell differentiation and generation of diversity. A mechanism and underlying the observed preferential reassociation of specific H and L chains and a means of generating affinity maturation, as exhibited by the antifluorescein system, is proposed.
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