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Yokoyama H, Mizutani R, Noguchi S, Hayashida N. Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms. Acta Crystallogr F Struct Biol Commun 2019; 75:80-88. [PMID: 30713158 PMCID: PMC6360445 DOI: 10.1107/s2053230x18017661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts produced by ultraviolet light are mutagenic and carcinogenic. The crystal structures of the anti-(6-4) photoproduct antibody 64M-5 Fab and of its complex with dT(6-4)T were determined at 2.5 and 2.0 Å resolution, respectively. A comparison between the dT(6-4)T-liganded and unliganded structures indicates that the side chain of His93L is greatly rotated and shifted on binding to dT(6-4)T, leading to the formation of an electrostatic interaction with the phosphate moiety of dT(6-4)T, which shows a remarkable induced fit. Based on a comparison of the dT(6-4)T-liganded structures of the 64M-5 and 64M-2 Fabs, the electrostatic interaction between the side chain of His93L in 64M-5 and the phosphate moiety of dT(6-4)T is lost for Leu93L in 64M-2, while Arg90L in 64M-5 instead of Gln90L in 64M-2 stabilizes the conformation of complementarity-determining region (CDR) L3. These differences contribute to the higher affinity of 64M-5 for dT(6-4)T compared with that of 64M-2.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ryuta Mizutani
- Graduate School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Shuji Noguchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Naoki Hayashida
- Division of Molecular Gerontology and Anti-Ageing Medicine, Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
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2
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Domljanovic I, Rexen Ulven E, Ulven T, Thomsen RP, Okholm AH, Kjems J, Voss A, Taskova M, Astakhova K. Dihydropyridine Fluorophores Allow for Specific Detection of Human Antibodies in Serum. ACS OMEGA 2018; 3:7580-7586. [PMID: 30087918 PMCID: PMC6068599 DOI: 10.1021/acsomega.8b00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/26/2018] [Indexed: 05/14/2023]
Abstract
Antigen recognition by antibodies plays an important role in human biology and in the development of diseases. This interaction provides a basis for multiple diagnostic assays and is a guide for treatments. We have developed dihydropyridine-based fluorophores that form stable complexes with double-stranded DNA and upon recognition of the antibodies to DNA (anti-DNA) provide an optical response. The fluorophores described herein have advantageous optical properties compared to those of the currently available dyes making them valuable for research and clinical diagnostics. By studying a series of novel fluorophores, crucial parameters for the design were established, providing the required sensitivity and specificity in the detection of antibodies. Using these DNA-fluorophore complexes in a direct immunofluorescence assay, antibodies to DNA are specifically detected in 80 patients diagnosed with an autoimmune disease, systemic lupus erythematosus. Positivity indicated by emission change of α-(4'-O-methoxyphenyl)-2-furyl dihydropyridine strongly correlates with other disease biomarkers and autoimmune arthritis.
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Affiliation(s)
- Ivana Domljanovic
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Elisabeth Rexen Ulven
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Trond Ulven
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken
2, 2100 Copenhagen, Denmark
| | - Rasmus P. Thomsen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Anders H. Okholm
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jørgen Kjems
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- Department
of Molecular Biology and Genetics, Aarhus
University, C.F. Møllers
Allé 3, 8000 Aarhus C, Denmark
| | - Anne Voss
- Department
of Rheumatology, Odense University Hospital, J. B. Winsløws Vej 19, 2, 5000 Odense C, Denmark
| | - Maria Taskova
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
| | - Kira Astakhova
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
- E-mail:
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3
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Klecka M, Thybo C, Macaubas C, Solov'yov I, Simard J, Balboni IM, Fox E, Voss A, Mellins ED, Astakhova K. Autoantibody Profiling in Lupus Patients using Synthetic Nucleic Acids. Sci Rep 2018; 8:5554. [PMID: 29615791 PMCID: PMC5883037 DOI: 10.1038/s41598-018-23910-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/19/2018] [Indexed: 02/08/2023] Open
Abstract
Autoantibodies to nuclear components of cells (antinuclear antibodies, ANA), including DNA (a-DNA), are widely used in the diagnosis and subtyping of certain autoimmune diseases, including systemic lupus erythematosus (SLE). Despite clinical use over decades, precise, reproducible measurement of a-DNA titers remains difficult, likely due to the substantial sequence and length heterogeneity of DNA purified from natural sources. We designed and tested a panel of synthetic nucleic acid molecules composed of native deoxyribonucleotide units to measure a-DNA. ELISA assays using these antigens show specificity and reproducibility. Applying the ELISA tests to serological studies of pediatric and adult SLE, we identified novel clinical correlations. We also observed preferential recognition of a specific synthetic antigen by antibodies in SLE sera. We determined the probable basis for this finding using computational analyses, providing valuable structural information for future development of DNA antigens. Synthetic nucleic acid molecules offer the opportunity to standardize assays and to dissect antibody-antigen interactions.
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Affiliation(s)
- Martin Klecka
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800, Kgs, Lyngby, Denmark
| | - Christina Thybo
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Claudia Macaubas
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California, 94305, USA
| | - Ilia Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Julia Simard
- Department of Health and Research Policy, Stanford University School of Medicine, 150 Governor's Lane, Stanford, California, 94305, USA
| | - Imelda Maria Balboni
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University, 700 Welch Rd. Suite 301, Stanford, California, 94304, USA
| | - Emily Fox
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University, 700 Welch Rd. Suite 301, Stanford, California, 94304, USA
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, J. B. Winsløws Vej 19, 2, 5000, Odense C, Denmark
| | - Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California, 94305, USA.
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800, Kgs, Lyngby, Denmark.
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4
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Haji-Ghassemi O, Müller-Loennies S, Rodriguez T, Brade L, Grimmecke HD, Brade H, Evans SV. The Combining Sites of Anti-lipid A Antibodies Reveal a Widely Utilized Motif Specific for Negatively Charged Groups. J Biol Chem 2016; 291:10104-18. [PMID: 26933033 DOI: 10.1074/jbc.m115.712448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/29/2023] Open
Abstract
Lipopolysaccharide dispersed in the blood by Gram-negative bacteria can be a potent inducer of septic shock. One research focus has been based on antibody sequestration of lipid A (the endotoxic principle of LPS); however, none have been successfully developed into a clinical treatment. Comparison of a panel of anti-lipid A antibodies reveals highly specific antibodies produced through distinct germ line precursors. The structures of antigen-binding fragments for two homologous mAbs specific for lipid A, S55-3 and S55-5, have been determined both in complex with lipid A disaccharide backbone and unliganded. These high resolution structures reveal a conserved positively charged pocket formed within the complementarity determining region H2 loops that binds the terminal phosphates of lipid A. Significantly, this motif occurs in unrelated antibodies where it mediates binding to negatively charged moieties through a range of epitopes, including phosphorylated peptides used in diagnostics and therapeutics. S55-3 and S55-5 have combining sites distinct from anti-lipid A antibodies previously described (as a result of their separate germ line origin), which are nevertheless complementary both in shape and charge to the antigen. S55-3 and S55-5 display similar avidity toward lipid A despite possessing a number of different amino acid residues in their combining sites. Binding of lipid A occurs independent of the acyl chains, although the GlcN-O6 attachment point for the core oligosaccharide is buried in the combining site, which explains their inability to recognize LPS. Despite their lack of therapeutic potential, the observed motif may have significant immunological implications as a tool for engineering recombinant antibodies.
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Affiliation(s)
- Omid Haji-Ghassemi
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Sven Müller-Loennies
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Teresa Rodriguez
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Lore Brade
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Hans-Dieter Grimmecke
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Helmut Brade
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Stephen V Evans
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
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5
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Ojima-Kato T, Fukui K, Yamamoto H, Hashimura D, Miyake S, Hirakawa Y, Yamasaki T, Kojima T, Nakano H. 'Zipbody' leucine zipper-fused Fab in E. coli in vitro and in vivo expression systems. Protein Eng Des Sel 2016; 29:149-57. [PMID: 26902097 DOI: 10.1093/protein/gzw001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 01/12/2016] [Indexed: 02/06/2023] Open
Abstract
A small antibody fragment, fragment of antigen binding (Fab), is favorable for various immunological assays. However, production efficiency of active Fab in microorganisms depends considerably on the clones. In this study, leucine zipper-peptide pairs that dimerize in parallel (ACID-p1 (LZA)/BASE-p1 (LZB) or c-Jun/c-Fos) were fused to the C-terminus of heavy chain (Hc, VH-CH1) and light chain (Lc, VL-CL), respectively, to accelerate the association of Hc and Lc to form Fab in Escherichia coli in vivo and in vitro expression systems. The leucine zipper-fused Fab named 'Zipbody' was constructed using anti-E. coli O157 monoclonal antibody obtained from mouse hybridoma and produced in both in vitro and in vivo expression systems in an active form, whereas Fab without the leucine zipper fusion was not. Similarly, Zipbody of rabbit monoclonal antibody produced in in vitro expression showed significant activity. The purified, mouse Zipbody produced in the E. coli strain Shuffle T7 Express had specificity toward the antigen; in bio-layer interferometry analysis, the KD value was measured to be 1.5-2.0 × 10(-8) M. These results indicate that leucine zipper fusion to Fab C-termini markedly enhances active Fab formation in E. coli.
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Affiliation(s)
- Teruyo Ojima-Kato
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan Knowledge Hub Aichi, Aichi Science and Technology Foundation, Yakusa-cho, Toyota 470-0356, Japan
| | - Kansuke Fukui
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hiroaki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Dai Hashimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shiro Miyake
- Advanced Scientific Technology and Management Research Institute of Kyoto, Chudoji Minamimachi, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Yuki Hirakawa
- Advanced Scientific Technology and Management Research Institute of Kyoto, Chudoji Minamimachi, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Tomomi Yamasaki
- Advanced Scientific Technology and Management Research Institute of Kyoto, Chudoji Minamimachi, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hideo Nakano
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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6
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Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected]. Nat Protoc 2014; 9:2771-83. [PMID: 25375991 DOI: 10.1038/nprot.2014.189] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (∼10 min on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together.
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7
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Wheeler SE, Bloom JWG. Toward a more complete understanding of noncovalent interactions involving aromatic rings. J Phys Chem A 2014; 118:6133-47. [PMID: 24937084 DOI: 10.1021/jp504415p] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Noncovalent interactions involving aromatic rings, which include π-stacking interactions, anion-π interactions, and XH-π interactions, among others, are ubiquitous in chemical and biochemical systems. Despite dramatic advances in our understanding of these interactions over the past decade, many aspects of these noncovalent interactions have only recently been uncovered, with many questions remaining. We summarize our computational studies aimed at understanding the impact of substituents and heteroatoms on these noncovalent interactions. In particular, we discuss our local, direct interaction model of substituent effects in π-stacking interactions. In this model, substituent effects are dominated by electrostatic interactions of the local dipoles associated with the substituents and the electric field of the other ring. The implications of the local nature of substituent effects on π-stacking interactions in larger systems are discussed, with examples given for complexes with carbon nanotubes and a small graphene model, as well as model stacked discotic systems. We also discuss related issues involving the interpretation of electrostatic potential (ESP) maps. Although ESP maps are widely used in discussions of noncovalent interactions, they are often misinterpreted. Next, we provide an alternative explanation for the origin of anion-π interactions involving substituted benzenes and N-heterocycles, and show that these interactions are well-described by simple models based solely on charge-dipole interactions. Finally, we summarize our recent work on the physical nature of substituent effects in XH-π interactions. Together, these results paint a more complete picture of noncovalent interactions involving aromatic rings and provide a firm conceptual foundation for the rational exploitation of these interactions in a myriad of chemical contexts.
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Affiliation(s)
- Steven E Wheeler
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
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8
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An Y, Raju RK, Lu T, Wheeler SE. Aromatic interactions modulate the 5'-base selectivity of the DNA-binding autoantibody ED-10. J Phys Chem B 2014; 118:5653-9. [PMID: 24802982 DOI: 10.1021/jp502069a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present detailed computational analyses of the binding of four dinucleotides to a highly sequence-selective single-stranded DNA (ssDNA) binding antibody (ED-10) and selected point mutants. Anti-DNA antibodies are central to the pathogenesis of systemic lupus erythematosus (SLE), and a more complete understanding of the mode of binding of DNA and other ligands will be necessary to elucidate the role of anti-DNA antibodies in the kidney inflammation associated with SLE. Classical molecular mechanics based molecular dynamics simulations and density functional theory (DFT) computations were applied to pinpoint the origin of selectivity for the 5'-nucleotide. In particular, the strength of interactions between each nucleotide and the surrounding residues were computed using MMGBSA as well as DFT applied to a cluster model of the binding site. The results agree qualitatively with experimental binding free energies, and indicate that π-stacking, CH/π, NH/π, and hydrogen-bonding interactions all contribute to 5'-base selectivity in ED-10. Most importantly, the selectivity for dTdC over dAdC arises primarily from differences in the strength of π-stacking and XH/π interactions with the surrounding aromatic residues; hydrogen bonds play little role. These data suggest that a key Tyr residue, which is not present in other anti-DNA antibodies, plays a key role in the 5'-base selectivity, while we predict that the mutation of a single Trp residue can tune the selectivity for dTdC over dAdC.
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Affiliation(s)
- Yi An
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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9
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Mikita CP, Padlan EA. Can we use DNA triple helices as treatment for systemic lupus erythematosus? Med Hypotheses 2014; 82:457-9. [DOI: 10.1016/j.mehy.2014.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/16/2014] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
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10
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Crystal structure determination of anti-DNA Fab A52. Proteins 2014; 82:1674-8. [DOI: 10.1002/prot.24514] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/19/2013] [Accepted: 01/06/2014] [Indexed: 11/07/2022]
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11
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Jefferis R. The antibody paradigm: present and future development as a scaffold for biopharmaceutical drugs. Biotechnol Genet Eng Rev 2011; 26:1-42. [PMID: 21415874 DOI: 10.5661/bger-26-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early studies of the humoral immune response revealed an apparent paradox: an infinite diversity of antibody specificities encoded within a finite genome. In consequence antibodies became a focus of interest for biochemists and geneticists. It resulted in the elucidation of the basic structural unit, the immunoglobulin (Ig) domain, comprised of ~ 100 amino acid residues that generate the characteristic "immunoglobulin (Ig) fold". The Ig fold has an anti-parallel ß-pleated sheet (barrel) structure that affords structural stability whilst the ß-bends allow for essentially infinite structural variation and functional diversity. This versatility is reflected in the Ig domain being the most widely utilised structural unit within the proteome. Human antibodies are comprised of multiple Ig domains and their structural diversity may be enhanced through the attachment of oligosaccharides. This review summarizes our current understanding of the immunoglobulin structure/function relationships and the application of protein and oligosaccharide engineering to further develop the Ig domain as a scaffold for the generation of new and novel antibody based therapeutics.
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Affiliation(s)
- Roy Jefferis
- School of Immunity and Infection, The College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.
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12
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Ou Z, Bottoms CA, Henzl MT, Tanner JJ. Impact of DNA hairpin folding energetics on antibody-ssDNA association. J Mol Biol 2007; 374:1029-40. [PMID: 18028946 DOI: 10.1016/j.jmb.2007.09.084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 09/25/2007] [Accepted: 09/27/2007] [Indexed: 10/22/2022]
Abstract
Deposition of anti-DNA antibodies in the kidney contributes to the pathogenesis of the autoimmune disease, systemic lupus erythematosus. Antibodies that bind to hairpin-forming DNA ligands may be particularly prone to deposition. Here we report the first structure of a Fab complexed with hairpin-forming DNA. The ligand used for co-crystallization is 5'-d [CTG(CCTT)CAG]-3', which has a predicted hairpin structure consisting of a four-nucleotide loop (CCTT) and a stem of three base-pairs. The 1.95 A resolution crystal structure of Fab DNA-1 complexed with this ligand shows that the conformation of the bound ligand differs radically from the predicted hairpin conformation. The three base-pairs in the stem are absent in the bound form. The protein binds to the last six nucleotides at the 3' end of the ligand. These nucleotides form a loop (TTCA) closed by a G:C base-pair in the bound state. Stacking of aromatic side-chains against DNA bases is the dominant interaction in the complex. Interactions with the DNA backbone are conspicuously absent. Thermodynamics of binding are examined using isothermal titration calorimetry. The apparent dissociation constant is 4 microM, and binding is enthalpically favorable and entropically unfavorable. Increasing the number of base-pairs in the DNA stem from three to six decreases binding affinity. These data suggest a conformational selection binding mechanism in which the Fab binds preferentially to the unstructured state of the ligand. In this interpretation, the ligand binding and ligand folding equilibria are coupled, with lower hairpin stability leading to greater effective binding affinity. Thus, pre-organization of the DNA loop into the preferred binding conformation does not play a major role in complexation. Rather, it is argued that the stem of the hairpin serves to reduce the degrees of freedom in the free DNA ligand, thereby limiting the entropic cost attendant to complexation with the Fab.
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Affiliation(s)
- Zhonghui Ou
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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