1
|
Crystal structure of two anti-porphyrin antibodies with peroxidase activity. PLoS One 2012; 7:e51128. [PMID: 23240001 PMCID: PMC3519839 DOI: 10.1371/journal.pone.0051128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/30/2012] [Indexed: 01/07/2023] Open
Abstract
We report the crystal structures at 2.05 and 2.45 Å resolution of two antibodies, 13G10 and 14H7, directed against an iron(III)-αααβ-carboxyphenylporphyrin, which display some peroxidase activity. Although these two antibodies differ by only one amino acid in their variable λ-light chain and display 86% sequence identity in their variable heavy chain, their complementary determining regions (CDR) CDRH1 and CDRH3 adopt very different conformations. The presence of Met or Leu residues at positions preceding residue H101 in CDRH3 in 13G10 and 14H7, respectively, yields to shallow combining sites pockets with different shapes that are mainly hydrophobic. The hapten and other carboxyphenyl-derivatized iron(III)-porphyrins have been modeled in the active sites of both antibodies using protein ligand docking with the program GOLD. The hapten is maintained in the antibody pockets of 13G10 and 14H7 by a strong network of hydrogen bonds with two or three carboxylates of the carboxyphenyl substituents of the porphyrin, respectively, as well as numerous stacking and van der Waals interactions with the very hydrophobic CDRH3. However, no amino acid residue was found to chelate the iron. Modeling also allows us to rationalize the recognition of alternative porphyrinic cofactors by the 13G10 and 14H7 antibodies and the effect of imidazole binding on the peroxidase activity of the 13G10/porphyrin complexes.
Collapse
|
2
|
McKenzie KM, Mee JM, Rogers CJ, Hixon MS, Kaufmann GF, Janda KD. Identification and characterization of single chain anti-cocaine catalytic antibodies. J Mol Biol 2006; 365:722-31. [PMID: 17084858 PMCID: PMC1828637 DOI: 10.1016/j.jmb.2006.10.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2006] [Revised: 10/07/2006] [Accepted: 10/10/2006] [Indexed: 11/16/2022]
Abstract
Cocaine is a powerful and addictive stimulant whose abuse remains a prevalent health and societal crisis. Unfortunately, no pharmacological therapies exist and therefore alternative protein-based therapies have been examined. One such approach is immunopharmacotherapy, wherein antibodies are utilized to either bind or hydrolyze cocaine thereby blocking it from exerting its euphoric effect. Towards this end, antibodies capable of binding and hydrolyzing cocaine were identified by phage display from a biased single chain antibody library generated from the spleens of mice previously immunized with a cocaine phosphonate transition state analog hapten. Two classes of antibodies emerged based on sequence homology and mode of action. Alanine scanning mutagenesis and kinetic analysis revealed that residues H97, H99, and L96 are crucial for antibodies 3F5 and 3H9 to accelerate the hydrolysis of cocaine. Antibodies 3F1 through 3F4, which are similar to our previously identified 3A6 class of antibodies, catalyze hydrolysis through transition state stabilization by tyrosine or histidine residues H50 and L94. Mutation of either one or both tyrosine residues to histidine conferred hydrolytic activity on previously inactive antibody 3F4. Mutational analysis of residue H50 of antibody 3F3 resulted in a glutamine mutant with a rate enhancement three times greater than wild-type. A double mutant, containing glutamineH50 and lysineH52, showed a tenfold rate enhancement over wild-type. These results indicate the power of initial selection of catalytic antibodies from a biased antibody library in both rapid generation and screening of mutants for improved catalysis.
Collapse
Affiliation(s)
| | | | | | | | | | - Kim D. Janda
- *Corresponding author, Email addresses of the corresponding authors:
| |
Collapse
|
3
|
Golinelli-Pimpaneau B, Lüthi C, Christen P. Structural Basis for D-Amino Acid Transamination by the Pyridoxal 5′-Phosphate-dependent Catalytic Antibody 15A9. J Biol Chem 2006; 281:23969-77. [PMID: 16790434 DOI: 10.1074/jbc.m602184200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibody 15A9, raised with 5'-phosphopyridoxyl (PPL)-N(epsilon)-acetyl-L-lysine as hapten, catalyzes the reversible transamination of hydrophobic D-amino acids with pyridoxal 5'-phosphate (PLP). The crystal structures of the complexes of Fab 15A9 with PPL-L-alanine, PPL-D-alanine, and the hapten were determined at 2.3, 2.3, and 2.5A resolution, respectively, and served for modeling the complexes with the corresponding planar imine adducts. The conformation of the PLP-amino acid adduct and its interactions with 15A9 are similar to those occurring in PLP-dependent enzymes, except that the amino acid substrate is only weakly bound, and, due to the immunization and selection strategy, the lysine residue that covalently binds PLP in these enzymes is missing. However, the N-acetyl-L-lysine moiety of the hapten appears to have selected for aromatic residues in hypervariable loop H3 (Trp-H100e and Tyr-H100b), which, together with Lys-H96, create an anion-binding environment in the active site. The structural situation and mutagenesis experiments indicate that two catalytic residues facilitate the transamination reaction of the PLP-D-alanine aldimine. The space vacated by the absent L-lysine side chain of the hapten can be filled, in both PLP-alanine aldimine complexes, by mobile Tyr-H100b. This group can stabilize a hydroxide ion, which, however, abstracts the C alpha proton only from D-alanine. Together with the absence of any residue capable of deprotonating C alpha of L-alanine, Tyr-H100b thus underlies the enantiomeric selectivity of 15A9. The reprotonation of C4' of PLP, the rate-limiting step of 15A9-catalyzed transamination, is most likely performed by a water molecule that, assisted by Lys-H96, produces a hydroxide ion stabilized by the anion-binding environment.
Collapse
Affiliation(s)
- Béatrice Golinelli-Pimpaneau
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS Bât. 34, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.
| | | | | |
Collapse
|
4
|
Zhu X, Dickerson TJ, Rogers CJ, Kaufmann GF, Mee JM, McKenzie KM, Janda KD, Wilson IA. Complete reaction cycle of a cocaine catalytic antibody at atomic resolution. Structure 2006; 14:205-16. [PMID: 16472740 DOI: 10.1016/j.str.2005.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/27/2005] [Accepted: 10/04/2005] [Indexed: 11/30/2022]
Abstract
Antibody 7A1 hydrolyzes cocaine to produce nonpsychoactive metabolites ecgonine methyl ester and benzoic acid. Crystal structures of 7A1 Fab' and six complexes with substrate cocaine, the transition state analog, products ecgonine methyl ester and benzoic acid together and individually, as well as heptaethylene glycol have been analyzed at 1.5-2.3 angstroms resolution. Here, we present snapshots of the complete cycle of the cocaine hydrolytic reaction at atomic resolution. Significant structural rearrangements occur along the reaction pathway, but they are generally limited to the binding site, including the ligands themselves. Several interacting side chains either change their rotamers or alter their mobility to accommodate the different reaction steps. CDR loop movements (up to 2.3 angstroms) and substantial side chain rearrangements (up to 9 angstroms) alter the shape and size (approximately 320-500 angstroms3) of the antibody active site from "open" to "closed" to "open" for the substrate, transition state, and product states, respectively.
Collapse
Affiliation(s)
- Xueyong Zhu
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Greaves R, Warwicker J. Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts. J Mol Biol 2005; 349:547-57. [PMID: 15882869 DOI: 10.1016/j.jmb.2005.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 03/30/2005] [Accepted: 04/08/2005] [Indexed: 12/30/2022]
Abstract
Electrostatics calculations with proteins that are uniformly charged over volume can aid enzyme/non-enzyme discrimination. For known enzymes, such methods locate active sites to within 5% on the enzyme surface, in 77% of a test set. We now report that removing the dielectric boundary improves active site location to 80%, with optimal discrimination between enzymes and non-enzymes of around 80% specificity and 80% sensitivity. This calculation quantifies burial of solvent-accessible regions. Many of the true enzymes incorrectly assigned as non-enzymes have active sites at subunit boundaries. These are missed in monomer-based calculations. Catalytic and non-catalytic antibodies are studied in this context of active/binding site burial. Whilst catalytic antibodies, on average, have marginally higher active site burial than non-catalytic antibodies, these values are generally smaller than for non-antibody enzymes, possibly contributing to their relatively low turnover. Prediction of active site location improves further when sequence profile-based weights replace the uniform charge distribution, so that a combination of burial and amino acid conservation is assessed. Accuracy rises to 93% of active sites to within 5%, in the test set, for the optimal profile weights scheme. The equivalent value in a separate validation set is 89% to within 5%. Enzyme/non-enzyme and enzyme functional site predictions are made for structural genomics proteins, suggesting that a substantial majority of these are non-enzymes.
Collapse
Affiliation(s)
- Richard Greaves
- Faculty of Life Sciences, Jackson's Mill, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, UK
| | | |
Collapse
|
6
|
Benedetti F, Berti F, Brady K, Colombatti A, Pauletto A, Pucillo C, Thomas NR. An unprecedented catalytic motif revealed in the model structure of amide hydrolyzing antibody 312d6. Chembiochem 2004; 5:129-31. [PMID: 14695523 DOI: 10.1002/cbic.200300738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fabio Benedetti
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, Via Giorgieri 1, 34127 Trieste, Italy.
| | | | | | | | | | | | | |
Collapse
|
7
|
Sonkaria S, Boucher G, FLóREZ-ÁLVAREZ J, Said B, Hussain S, Ostler E, Gul S, Thomas E, Resmini M, Gallacher G, Brocklehurst K. Evidence for 'lock and key' character in an anti-phosphonate hydrolytic antibody catalytic site augmented by non-reaction centre recognition: variation in substrate selectivity between an anti-phosphonate antibody, an anti-phosphate antibody and two hydrolytic enzymes. Biochem J 2004; 381:125-30. [PMID: 15053743 PMCID: PMC1133769 DOI: 10.1042/bj20031966] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 02/11/2004] [Accepted: 03/31/2004] [Indexed: 11/17/2022]
Abstract
The substrate selectivities of an anti-phosphonate and an anti-phosphate kinetically homogeneous polyclonal catalytic antibody preparation and two hydrolytic enzymes were compared by using hapten-analogous and truncated carbonate and ester substrates each containing a 4-nitrophenolate leaving group. Syntheses of the truncated substrates devoid of recognition features in the non-leaving group parts of the substrates are reported. The relatively high kinetic selectivity of the more active anti-phosphonate antibody preparation is considered to depend on a relatively rigid catalytic site with substantial reaction centre specificity together with other important recognition interactions with the extended non-leaving group part of the substrate. In contrast, the less catalytically active, more flexible anti-phosphate antibody exhibits much lower kinetic selectivity for the substrate reaction centre comparable with that of the hydrolytic enzymes with activity much less dependent on recognition interactions with the non-leaving group part of the substrate. The ways in which haptenic flexibility and IgG architecture might contribute to the differential kinetic selectivities are indicated.
Collapse
Affiliation(s)
- Sanjiv Sonkaria
- *Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| | - Guillaume Boucher
- †Department of Biological Sciences, School of Pharmacy and Biomolecular Sciences, Cockcroft Building, Lewes Road, Moulsecoomb, Brighton BN2 4GJ, U.K
| | - José FLóREZ-ÁLVAREZ
- *Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| | - Bilal Said
- †Department of Biological Sciences, School of Pharmacy and Biomolecular Sciences, Cockcroft Building, Lewes Road, Moulsecoomb, Brighton BN2 4GJ, U.K
| | - Syeed Hussain
- *Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| | - Elizabeth L. Ostler
- †Department of Biological Sciences, School of Pharmacy and Biomolecular Sciences, Cockcroft Building, Lewes Road, Moulsecoomb, Brighton BN2 4GJ, U.K
| | - Sheraz Gul
- *Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| | - Emrys W. Thomas
- ‡Department of Biological Sciences, University of Salford, The Crescent, Salford M5 4JW, U.K
| | - Marina Resmini
- §Department of Chemistry, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
- To whom correspondence should be addressed (e-mail or )
| | - Gerard Gallacher
- †Department of Biological Sciences, School of Pharmacy and Biomolecular Sciences, Cockcroft Building, Lewes Road, Moulsecoomb, Brighton BN2 4GJ, U.K
| | - Keith Brocklehurst
- *Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
- To whom correspondence should be addressed (e-mail or )
| |
Collapse
|
8
|
Kawamura-Konishi Y, Sasaki R, Sugiyama M, Hashimoto H, Kamo T, Hosomi N, Yamazaki M, Tashiro H, Suzuki H. Key residue responsible for catalytic activities in the antibodies elicited against N-methyl mesoporphyrin. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(03)00134-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|