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Fukuda N, Suwa Y, Uchida M, Kobashigawa Y, Yokoyama H, Morioka H. Role of the mobility of antigen binding site in high affinity antibody elucidated by surface plasmon resonance. J Biochem 2016; 161:37-43. [PMID: 27507818 DOI: 10.1093/jb/mvw050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/20/2016] [Indexed: 11/12/2022] Open
Abstract
Antibody is known to exhibit conformational change in the antigen recognition site after forming the initial complex. This structural change, which is widely known as "induced fit", is believed to be critical for high affinity (Kd of nM range) of antigen-antibody interaction. Elucidation of this 'induced fit' process is essential for rational design of high affinity antibody, while it is prevented by limitation of the available biophysical and biochemical data of the initial complex. Here, we performed kinetic and thermodynamic analysis of the interaction between single-chain variable fragment (denoted as scFv) of 64M5 antibody and a (6-4) photoproduct by using surface plasmon resonance (denoted as SPR). It revealed that the 64M5scFv associates the (6-4) photoproduct at initial step by hydrophobic interactions, and enthalpy-driving interactions, hydrogen bonds and van der Waals interactions, were formed by second step structural rearrangement. Furthermore, mutational analysis revealed that the mobility of the antigen-binding site is critical for the second step. It could be assumed that optimization of the mobility of the antigen recognition site is a clue for rational design of high affinity antibody.
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Affiliation(s)
- Natsuki Fukuda
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshiaki Suwa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Makiyo Uchida
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hideshi Yokoyama
- Labratory of Physical Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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Mitchell D, Brooks B. Antibodies and DNA Photoproducts: Applications, Milestones and Reference Guide. Photochem Photobiol 2010; 86:2-17. [DOI: 10.1111/j.1751-1097.2009.00673.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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3
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Kobayashi H, Sato K, Komatsu Y, Morioka H, Stewart JD, Tsurimoto T, Ohtsuka E. Effects of a High-Affinity Antibody Fragment on DNA Polymerase Reactions Near a (6-4) Photoproduct Site. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1999.tb03278.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Morioka H, Kurihara M, Kobayashi H, Satou K, Komatsu Y, Uchida M, Ohtsuka E, Torizawa T, Kato K, Shimada I, Matsunaga T, Nikaido O. DNA-binding properties of the antibody specific for the Dewar photoproduct of thymidylyl-(3-5')-thymidine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:667-79. [PMID: 16838854 DOI: 10.1080/15257770600686469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A monoclonal antibody (DEM-1) specific for the Dewar photoproduct is used for detection and quantification of photolesions in DNA. To help understand the molecular recognition of damaged DNA by the antibody protein, we have cloned and sequenced the variable region genes of DEM-1. We have also prepared Fab fragments of DEM-1 (DEM1Fab), and synthesized two kinds of 3'-biotinylated oligonucleotides of different lengths containing a central Dewar photoproduct of TpT to analyze the effects of the antigen size on the binding rates by means of surface plasmon resonance (SPR). Results obtained from SPR analyses suggest that DEM1Fab may recognize tetranucleotide unit as the epitope.
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Affiliation(s)
- Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan.
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Kobayashi H, Komatsu Y, Morioka H, Ohtsuka E. DNA Binding Mode of Antibody Fragments Specific for TT Photo-Dimers. PHOSPHORUS SULFUR 2002. [DOI: 10.1080/10426500212301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hiroyuki Kobayashi
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| | - Yasuo Komatsu
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| | - Hiroshi Morioka
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| | - Eiko Ohtsuka
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
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6
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Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O. Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation. J Mol Biol 2000; 299:711-23. [PMID: 10835279 DOI: 10.1006/jmbi.2000.3772] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation are implicated in mutagenesis and cancer, particularly skin cancer. The crystal structure of the Fab fragment of the murine 64M-2 antibody specific to DNA T(6-4)T photoproducts is determined as a complex with dT(6-4)T, a (6-4) pyrimidine-pyrimidone photodimer of dTpT, at 2.4 A resolution to a crystallographic R-factor of 0.199 and an R(free) value of 0.279. The 64M-2 Fab molecule is in an extended arrangement with an elbow angle of 174 degrees, and its five complementarity-determining regions, except L2, are involved in the ligand binding. The bound dT(6-4)T ligand adopting a ring structure with (6-4) linked 5' thymine-3' pyrimidone bases is fully accommodated in an antigen-binding pocket of about 15 Ax10 A. The 5'-thymine and 3'-pyrimidone bases are in half-chair and planar conformations, respectively, and are nearly perpendicular to each other. The 5'-thymine base is hydrogen-bonded to Arg95H and Ser96H, and is in van der Waals contact with Tyr100iH. The 3'-pyrimidone base is hydrogen-bonded to His35H, and is in contact with Trp33H. Three water molecules are located at the interface between the bases and the Fab residues. Hydrogen bonds involving these water molecules also contribute to Fab recognition of the dT(6-4)T bases. The sugar-phosphate backbone connecting the bases is surrounded by residues His27dL, Tyr32L, Ser92L, Trp33H, and Ser58H, but is not hydrogen-bonded to these residues.
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MESH Headings
- Animals
- Antibodies, Antinuclear/chemistry
- Antibodies, Antinuclear/immunology
- Antibody Specificity
- Binding Sites, Antibody
- Cattle
- Crystallography, X-Ray
- DNA/chemistry
- DNA/genetics
- DNA/immunology
- DNA/radiation effects
- DNA Damage/genetics
- DNA Damage/immunology
- DNA Damage/radiation effects
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/immunology
- DNA, Single-Stranded/radiation effects
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Epitopes/radiation effects
- Hydrogen Bonding
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/immunology
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation/radiation effects
- Nucleotides/chemistry
- Nucleotides/genetics
- Nucleotides/immunology
- Protein Conformation
- Pyrimidine Dimers/chemistry
- Pyrimidine Dimers/genetics
- Pyrimidine Dimers/immunology
- Pyrimidine Dimers/radiation effects
- Static Electricity
- Ultraviolet Rays
- Water/metabolism
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Affiliation(s)
- H Yokoyama
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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Torizawa T, Yamamoto N, Suzuki T, Nobuoka K, Komatsu Y, Morioka H, Nikaido O, Ohtsuka E, Kato K, Shimada I. DNA binding mode of the Fab fragment of a monoclonal antibody specific for cyclobutane pyrimidine dimer. Nucleic Acids Res 2000; 28:944-51. [PMID: 10648787 PMCID: PMC102577 DOI: 10.1093/nar/28.4.944] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Monoclonal antibodies specific for the cyclobutane pyrimidine dimer (CPD) are widely used for detection and quantification of DNA photolesions. However, the mechanisms of antigen binding by anti-CPD antibodies are little understood. Here we report NMR analyses of antigen recognition by TDM-2, which is a mouse monoclonal antibody specific for the cis - syn -cyclobutane thymine dimer (T[ c, s ]T). (31)P NMR and surface plasmon resonance data indicated that the epitope recognized by TDM-2 comprises hexadeoxynucleotides centered on the CPD. Chemical shift perturbations observed for TDM-2 Fab upon binding to d(T[ c, s ]T) and d(TAT[ c, s ]TAT) were examined in order to identify the binding sites for these antigen analogs. It was revealed that d(T[ c, s ]T) binds to the central part of the antibody-combining site, while the CPD-flanking nucleotides bind to the positively charged area of the V(H)domain via electrostatic interactions. By applying a novel NMR method utilizing a pair of spin-labeled DNA analogs, the orientation of DNA with respect to the antigen-binding site was determined: CPD-containing oligonucleotides bind to TDM-2 in a crooked form, draping the 3'-side of the nucleotides onto the H1 and H3 segments, with the 5'-side on the H2 and L3 segments. These data provide valuable information for antibody engineering of TDM-2.
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Affiliation(s)
- T Torizawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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Abstract
The utilization of optical biosensors to study molecular interactions continues to expand. In 1998, 384 articles relating to the use of commercial biosensors were published in 130 different journals. While significant strides in new applications and methodology were made, a majority of the biosensor literature is of rather poor quality. Basic information about experimental conditions is often not presented and many publications fail to display the experimental data, bringing into question the credibility of the results. This review provides suggestions on how to collect, analyze and report biosensor data.
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Affiliation(s)
- D G Myszka
- University of Utah, Salt Lake City, UT 84132, USA.
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Kobayashi H, Kato J, Morioka H, Stewart JD, Ohtsuka E. Tryptophan H33 plays an important role in pyrimidine (6-4) pyrimidone photoproduct binding by a high-affinity antibody. PROTEIN ENGINEERING 1999; 12:879-84. [PMID: 10556249 DOI: 10.1093/protein/12.10.879] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The importance of Trp H33 in antibody recognition of DNA containing a central pyrimidine (6-4) pyrimidone photoproduct was investigated. This residue was replaced by Tyr, Phe and Ala and the binding abilities of these mutants were determined by surface plasmon resonance and fluorescence spectroscopy. Conservative substitution of Trp H33 by Tyr or Phe resulted in moderate losses of binding affinity; however, replacement by Ala had a significantly larger impact. The fluorescence properties of DNA containing a (6-4) photoproduct were strongly affected by the identity of the H33 residue. DNA binding by both the wild-type and the W-H33-Y mutant was accompanied by a small degree of fluorescence quenching; by contrast, binding by the W-H33-F and W-H33-A mutants produced large fluorescence increases. Taken together, these variations in binding and fluorescence properties with the identity of the H33 residue are consistent with a role in photoproduct recognition by Trp H33 in the high-affinity antibody 64M5.
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Affiliation(s)
- H Kobayashi
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan and the University of Florida, Gainesville, FL 32611, USA
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10
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Torizawa T, Kato K, Kato J, Kobayashi H, Komatsu Y, Morioka H, Nikaido O, Ohtsuka E, Shimada I. Conformational multiplicity of the antibody combining site of a monoclonal antibody specific for a (6-4) photoproduct. J Mol Biol 1999; 290:731-40. [PMID: 10395826 DOI: 10.1006/jmbi.1999.2926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The antigen binding site of monoclonal antibody 64M5, which possesses a high degree of affinity for DNA containing pyrimidine (6-4) pyrimidone photoproducts, were investigated by use of stable-isotope-assisted NMR spectroscopy. A variety of 64M5 Fab fragments specifically labeled with 13C and 15N at backbone amide groups were prepared. Extensive assignments of amide resonances originating from the variable region of 64M5 were made by using 2D-HN(CO) measurements along with recombination of the heavy and light chains of 64M5. On the basis of chemical shift changes of the amide resonances caused upon addition of d(T[6-4]T) and d(GTAT[6-4]TATG), the binding sites of 64M5 Fab for the (6-4) photodimer and for the oligodeoxynucleotides flanking it were identified. It was revealed that the L1 and L3 segments, which are responsible for the binding to (6-4) photodimer, exhibit conformational multiplicities in the absence of antigens, and take different conformations between the d(T[6-4]T) and d(GTAT[6-4]TATG)-bound forms. On the basis of spectral comparison with another Fab fragment with a similarity in the amino acid sequence of the VL domain of 64M5, we suggest that the conformational multiplicities observed in the present study is caused by a substitution of an amino acid residue at the position of a key residue in L3 canonical structure, which leads to a preferable effect on the antigen binding, and by a specific combination of L1 and L3 canonical structures.
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Affiliation(s)
- T Torizawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
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