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Ponomarenko N, Chatziefthimiou SD, Kurkova I, Mokrushina Y, Mokrushina Y, Stepanova A, Smirnov I, Avakyan M, Bobik T, Mamedov A, Mitkevich V, Belogurov A, Fedorova OS, Dubina M, Golovin A, Lamzin V, Friboulet A, Makarov AA, Wilmanns M, Gabibov A. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:708-19. [PMID: 24598740 PMCID: PMC3949517 DOI: 10.1107/s1399004713032446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022]
Abstract
The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.
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Affiliation(s)
- Natalia Ponomarenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Spyros D. Chatziefthimiou
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Inna Kurkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Anastasiya Stepanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Ivan Smirnov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Marat Avakyan
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Tatyana Bobik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Azad Mamedov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Alexey Belogurov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Michael Dubina
- St Petersburg Academic University, St Petersburg 194021, Russian Federation
| | - Andrey Golovin
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Victor Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alain Friboulet
- Université de Technologie de Compiègne, Unité Mixte de Recherche 6022, Centre National de la Recherche Scientifique, 60205 Compiègne, France
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Gabibov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
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Hsieh PC, Vaisvila R. Protein engineering: single or multiple site-directed mutagenesis. Methods Mol Biol 2013; 978:173-86. [PMID: 23423897 DOI: 10.1007/978-1-62703-293-3_13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Site-directed mutagenesis techniques are invaluable tools in molecular biology to study the structural and functional properties of a protein. To expedite the time required and simplify methods for mutagenesis, we recommend two protocols in this chapter. The first method for single site-directed mutagenesis, which includes point mutations, insertions, or deletions, can be achieved by an inverse PCR strategy with mutagenic primers and the high-fidelity Phusion(®) DNA Polymerase to introduce a site-directed mutation with exceptional efficiency. The second method is for engineering multiple mutations into a gene of interest. This can be completed in one step by PCR with mutagenic primers and by assembling all mutagenized PCR products using the Gibson Assembly™ Master Mix. This method allows multiple nucleotides to be changed simultaneously, which not only saves time but also reagents compared to traditional methods of mutagenesis.
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Smirnov I, Belogurov A, Friboulet A, Masson P, Gabibov A, Renard PY. Strategies for the selection of catalytic antibodies against organophosphorus nerve agents. Chem Biol Interact 2012; 203:196-201. [PMID: 23123255 DOI: 10.1016/j.cbi.2012.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/12/2012] [Accepted: 10/16/2012] [Indexed: 01/25/2023]
Abstract
Among the strategies aimed at biocompatible means for organophosphorus nerve agents neutralization, immunoglobulins have attracted attention in the 1990's and 2000's both for their ability to immobilize the toxicants, but also for their ability to be turned into enzymatically active antibodies known as catalytic antibodies or abzymes (antibodies--enzymes). We will present here a critical review of the successive strategies used for the selection of these nerve agent-hydrolyzing abzymes, based on hapten design, namely antibodies raised against a wide variety of transition state analogs, and eventually the strategies based on anti-idiotypic antibodies and reactibodies.
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Affiliation(s)
- Ivan Smirnov
- MM Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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Belogurov A, Smirnov I, Ponomarenko N, Gabibov A. Antibody-antigen pair probed by combinatorial approach and rational design: bringing together structural insights, directed evolution, and novel functionality. FEBS Lett 2012; 586:2966-73. [PMID: 22841717 DOI: 10.1016/j.febslet.2012.07.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/18/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022]
Abstract
The unique hypervariability of the immunoglobulin (Ig) superfamily provides a means to create both binding and catalytic antibodies with almost any desired specificity and activity. The diversity of antigens and concept of adaptive response suggest that it is possible to find an antigen pair to any raised Ig. In the current review we discuss combinatorial approaches, which makes it possible to obtain an antibody with predefined properties, followed by 3D structure-based rational design to enhance or dramatically change its characteristics. A similar strategy, but applied to the second partner of the antibody-antigen pair, may result in selection of complementary substrates to the chosen Ig. Finally, 2D screening may be performed solving the "Chicken and Egg" problem when neither antibody nor antigen is known.
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Affiliation(s)
- Alexey Belogurov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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A novel molecular analysis of genes encoding catalytic antibodies. Mol Immunol 2012; 50:160-8. [PMID: 22325472 DOI: 10.1016/j.molimm.2012.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/09/2012] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
Among the numerous questions remaining opened about catalytic antibodies (abzymes), the understanding of the origin of the genes encoding them is of vital significance. An original statistical analysis of genes encoding abzymes is described in the present report. Results suggested that these genes display a high conservation degree with their germline counterpart and a limited number of amino acid changes. Hence, on the contrary with high-affinity antibodies, maturation process by accumulation of somatic hypermutations is not required for the catalytic function. We demonstrated that despite a weak somatic mutation rate, the physicochemical properties of mutated amino acid (AA) are predominantly dissimilar with that of the germline AA. Further, we developed a novel approach in order to analyze the nature of genes encoding catalytic antibodies. For the first time, an unexpected and significant high level expression of rare gene subgroups was noticed and emphasized. The data described in this paper would lay the foundation for future studies about origin of genes encoding catalytic antibodies.
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Siva AB, Kameshwari DB, Singh V, Pavani K, Sundaram CS, Rangaraj N, Deenadayal M, Shivaji S. Proteomics-based study on asthenozoospermia: differential expression of proteasome alpha complex. Mol Hum Reprod 2010; 16:452-62. [PMID: 20304782 DOI: 10.1093/molehr/gaq009] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
With a view to understand the molecular basis of sperm motility, we have tried to establish the human sperm proteome by two-dimensional PAGE MALDI MS/MS analysis. We report identification of 75 different proteins in the human spermatozoa. Comparative proteome analysis was carried out for asthenozoospermic and normozoospermic patients to understand the molecular basis of sperm motility. Analysis revealed eight proteins (including one unidentified) with altered intensity between the groups. Differential proteins distributed into three functional groups: 'energy and metabolism' (triose-phosphate isomerase, glycerol kinase 2, testis specific isoform and succinyl-CoA:3-ketoacid co-enzyme A transferase 1, mitochondrial precursor); 'movement and organization' (tubulin beta 2C and tektin 1) and 'protein turnover, folding and stress response' (proteasome alpha 3 subunit and heat shock-related 70 kDa protein 2). It was interesting to note that although the proteins falling in the functional group of 'energy and metabolism' are higher in the asthenozoospermic patients, the other two functional groups contain proteins, which are higher in the normozoospermic samples. Validation of results carried out for proteasome alpha 3 subunit by immunoblotting and confocal microscopy, confirmed significant changes in intensity of proteasome alpha 3 subunit in asthenozoospermic samples when compared with normozoospermic controls. Significant positive correlation too was found between proteasome alpha 3 subunit levels and rapid, linear progressive motility of the spermatozoa. In our understanding, this data would contribute appreciably to the presently limited information available about the proteins implicated in human sperm motility.
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Clark RL, Johnston BF, Suckling CJ, Mackay SP. A modelling study of a non-concerted hydrolytic cycloaddition reaction by the catalytic antibody H11. Bioorg Med Chem 2006; 14:2674-83. [PMID: 16378728 DOI: 10.1016/j.bmc.2005.11.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 11/23/2005] [Accepted: 11/28/2005] [Indexed: 11/21/2022]
Abstract
H11 is the first antibody reported to have dual activity as a non-concerted, Diels-Alderase and hydrolytic catalyst. It was previously shown to catalyse the cycloaddition of acetoxybutadiene 1a to N-alkyl maleimides 2 to afford hydroxy-substituted bicyclic adducts 3 with a 30% ee of a major isomer. To better understand this mechanism and the partial stereospecificity, a homology model of H11 was constructed and used in docking studies to evaluate potential antibody-ligand complexes. The model suggested the hydrolytic nature of H11 was due to Glu 95H acting as a catalytic base, and evaluation of the shape complementarity of the proposed antibody-ligand complexes confirmed at a semi-quantitative level the observation that the major enantiomer is produced in a 30% ee.
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Affiliation(s)
- Rachel L Clark
- Department of Pharmaceutical Sciences, University of Strathclyde, Glasgow G4 0NR, UK
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Gouverneur V, Reiter M. Biocatalytic Approaches to Hetero-Diels-Alder Adducts of Carbonyl Compounds. Chemistry 2005; 11:5806-15. [PMID: 16003810 DOI: 10.1002/chem.200500406] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Very little information is available on hetero-Diels-Alderases for the assembly of heterocyclic products despite the synthetic value of these [4+2] cycloadditions. Hetero-Diels-Alderase antibodies raised against a bicyclic transition state analogue have been generated for the cycloaddition of ethylglyoxylate with an all-carbon diene. More recently, a conceptually novel biocatalytic approach to hetero-Diels-Alder (HDA) adducts derived from carbonyl dienophiles has been developed mirroring a stepwise aldol Michael mechanism instead of a concerted pathway. In this approach, the two key steps are an antibody-mediated kinetic resolution of beta-hydroxyenones and a subsequent ring-closure process. An attractive feature of this methodology is the possibility to convert the enantioenriched aldol intermediates into tetrahydropyranones or dihydropyranones. This bioorganic route is best applied for the preparation of enantioenriched HDA adducts derived from poorly electrophilic acceptors, therefore complementing existing catalytic routes to these adducts based on the use of small organocatalysts or chiral Lewis acids.
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Affiliation(s)
- Véronique Gouverneur
- University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, OX1 3TA Oxford, UK.
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Bathe F, Hahlen K, Dombi R, Driller L, Schliwa M, Woehlke G. The complex interplay between the neck and hinge domains in kinesin-1 dimerization and motor activity. Mol Biol Cell 2005; 16:3529-37. [PMID: 15901834 PMCID: PMC1182295 DOI: 10.1091/mbc.e04-11-0957] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Kinesin-1 dimerizes via the coiled-coil neck domain. In contrast to animal kinesins, neck dimerization of the fungal kinesin-1 NcKin requires additional residues from the hinge. Using chimeric constructs containing or lacking fungal-specific elements, the proximal part of the hinge was shown to stabilize the neck coiled-coil conformation in a complex manner. The conserved fungal kinesin hinge residue W384 caused neck coiled-coil formation in a chimeric NcKin construct, including parts of the human kinesin-1 stalk. The stabilizing effect was retained in a NcKinW384F mutant, suggesting important pi-stacking interactions. Without the stalk, W384 was not sufficient to induce coiled-coil formation, indicating that W384 is part of a cluster of several residues required for neck coiled-coil folding. A W384-less chimera of NcKin and human kinesin possessed a non-coiled-coil neck conformation and showed inhibited activity that could be reactivated when artificial interstrand disulfide bonds were used to stabilize the neck coiled-coil conformation. On the basis of yeast two-hybrid data, we propose that the proximal hinge can bind kinesin's cargo-free tail domain and causes inactivation of kinesin by disrupting the neck coiled-coil conformation.
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Affiliation(s)
- Friederike Bathe
- Department of Cell Biology, Adolf-Butenandt-Institute, University of Munich, D-80336 Munich, Germany
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Zheng L, Baumann U, Reymond JL. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 2004; 32:e115. [PMID: 15304544 PMCID: PMC514394 DOI: 10.1093/nar/gnh110] [Citation(s) in RCA: 885] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have developed a new primer design method based on the QuickChange site-directed mutagenesis protocol, which significantly improves the PCR amplification efficiency. This design method minimizes primer dimerization and ensures the priority of primer-template annealing over primer self-pairing during the PCR. Several different multiple mutations (up to 7 bases) were successfully performed with this partial overlapping primer design in a variety of vectors ranging from 4 to 12 kb in length. In comparison, all attempts failed when using complete-overlapping primer pairs as recommended in the standard QuickChange protocol. Our protocol was further extended to site-saturation mutagenesis by introducing randomized codons. Our data indicated no specific sequence selection during library construction, with the randomized positions resulting in average occurrence of each base in each position. This method should be useful to facilitate the preparation of high-quality site saturation libraries.
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Affiliation(s)
- Lei Zheng
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
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