1
|
Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins. Int J Mol Sci 2014; 15:20321-38. [PMID: 25383676 PMCID: PMC4264169 DOI: 10.3390/ijms151120321] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 01/09/2023] Open
Abstract
Exposure to the ultraviolet component of sunlight causes DNA damage, which subsequently leads to mutations, cellular transformation, and cell death. DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts are more mutagenic than cyclobutane pyrimidine dimers. These lesions must be repaired because of the high mutagenic potential of (6-4) photoproducts. We here reviewed the structures of (6-4) photoproducts, particularly the detailed structures of the (6-4) lesion and (6-4) lesion-containing double-stranded DNA. We also focused on interactions with their binding proteins such as antibody Fabs, (6-4) photolyase, and nucleotide excision repair protein. The (6-4) photoproducts that bound to these proteins had common structural features: The 5'-side thymine and 3'-side pyrimidone bases of the T(6-4)T segment were in half-chair and planar conformations, respectively, and both bases were positioned nearly perpendicularly to each other. Interactions with binding proteins showed that the DNA helices flanking the T(6-4)T segment were largely kinked, and the flipped-out T(6-4)T segment was recognized by these proteins. These proteins had distinctive binding-site structures that were appropriate for their functions.
Collapse
|
2
|
Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O. Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:232-8. [PMID: 22349224 DOI: 10.1107/s0907444912000327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 01/04/2012] [Indexed: 11/10/2022]
Abstract
Pyrimidine (6-4) pyrimidone DNA photoproducts produced by ultraviolet light are highly mutagenic and carcinogenic. The crystal structure of the dTT(6-4)TT photoproduct in complex with the Fab fragment of the antibody 64M-2 that is specific for (6-4) photoproducts was determined at 2.4 Å resolution. The dT(6-4)T segment is fully accommodated in the concave binding pocket of the Fab, as observed in the complex of dT(6-4)T with the Fab. The pyrimidine and pyrimidone bases of the dT(6-4)T segment are positioned nearly perpendicularly to each other. The thymidine segments flanking both ends extend away from the dT(6-4)T segment. The 5'-side thymine base is parallel to the side chain of Tyr100iH of the antibody heavy chain and is also involved in electrostatic interactions with Asn30L, Tyr32L and Lys50L of the antibody light chain. The 5'-side and 3'-side phosphate groups exhibit electrostatic interactions with Asn28L and Ser58H, respectively. These interactions with the flanking nucleotides explain why longer oligonucleotides containing dT(6-4)T segments in the centre show higher antibody-binding affinities than the dT(6-4)T ligand.
Collapse
Affiliation(s)
- Hideshi Yokoyama
- School of Pharmaceutical Sciences, University of Shizuoka, Japan.
| | | | | | | | | | | | | |
Collapse
|
3
|
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]
|
4
|
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]
|
5
|
Wen X, Wang T, Wang Z, Li L, Zhao C. Preparation of konjac glucomannan hydrogels as DNA-controlled release matrix. Int J Biol Macromol 2007; 42:256-63. [PMID: 18190958 DOI: 10.1016/j.ijbiomac.2007.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2007] [Revised: 11/24/2007] [Accepted: 11/26/2007] [Indexed: 11/29/2022]
Abstract
In this study, hydrogels for DNA-controlled release was prepared with konjac glucomannan (KGM), a water-soluble non-ionic polysaccharide, by means of deacetylated reaction and physically cross-linking method under mild conditions. The properties of the KGM hydrogels were analyzed by FTIR spectra and scanning electron microscopy (SEM). The integrality of the released DNA was investigated by circular dichroism (CD). The DNA release kinetics was performed using the DNA-loaded KGM gels in buffer solutions of pH 7.4 at 37+/-0.5 degrees C. Peppas model and Higuchi model were used to analysis the DNA release mechanism; the data indicated that the DNA release can be controlled by changing the preparation conditions and the structure parameters of the gels. This study suggested that the KGM hydrogels have a potential use for advanced controlled release.
Collapse
Affiliation(s)
- Xian Wen
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610065, PR China
| | | | | | | | | |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Ueda T, Kato A, Kuramitsu S, Terasawa H, Shimada I. Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27. J Biol Chem 2005; 280:36237-43. [PMID: 16118222 DOI: 10.1074/jbc.m507972200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyases use light to repair CPDs. For efficient light absorption, CPD photolyases use a second chromophore. We purified Thermus thermophilus CPD photolyase with its second chromophore. UV-visible absorption spectra, reverse-phase HPLC, and NMR analyses of the chromophores revealed that the second chromophore of the enzyme is flavin mononucleotide (FMN). To clarify the role of FMN in the CPD repair reaction, the enzyme without FMN (Enz-FMN(-) and that with a stoichiometric amount of FMN (Enz-FMN(+)) were both successfully obtained. The CPD repair activity of Enz-FMN(+) was higher than that of Enz-FMN(-), and the CPD repair activity ratio of Enz-FMN(+) and Enz-FMN(-) was dependent on the wavelength of light. These results suggest that FMN increases the light absorption efficiency of the enzyme. NMR analyses of Enz-FMN(+) and Enz-FMN(-) revealed that the binding mode of FMN is similar to that of 7,8-didemethyl-8-hydroxy-5-deazariboflavin in Anacystis nidulans CPD photolyase, and thus a direct electron transfer between FMN and CPD is not likely to occur. Based on these results, we concluded that FMN acts as a highly efficient light harvester that gathers light and transfers the energy to FAD.
Collapse
Affiliation(s)
- Takumi Ueda
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | | | | |
Collapse
|
8
|
Liu W, Sun S, Cao Z, Zhang X, Yao K, Lu WW, Luk KDK. An investigation on the physicochemical properties of chitosan/DNA polyelectrolyte complexes. Biomaterials 2005; 26:2705-11. [PMID: 15585274 DOI: 10.1016/j.biomaterials.2004.07.038] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Accepted: 07/22/2004] [Indexed: 11/28/2022]
Abstract
In this work, to eliminate the effect of the hydrophobicity of N-acetyl groups in chitosan on the interaction between chitosan and DNA, a water soluble chitosan with molecular weight of 5000 and deacetylated degree of 99% was selected to complex with DNA at varied charged ratios. The physicochemical properties of chitoplexes were investigated by means of FTIR, circular dichroism (CD), static fluorescence spectroscopy, and atomic force microscopy (AFM). The results indicated that upon interacting with chitosan, the DNA molecules saved a B conformation, and the binding affinity of chitosan to DNA was dependent on pH of media. At pH 5.5, highly charged chitosan had a strong binding affinity with DNA; whereas in pH 12.0 medium, only weak interactions existed. The CD spectra of Hoechst 33258 competitive displacement revealed that chitosan was partially bound to the minor groove of DNA. The morphology of chitosan/DNA complexes was strongly dependent upon the charge ratios. At charge ratio (+/-) of 1:4, not all DNA could be entrapped in the complex; at ratio of 8:1, the spherical complexes with mean size of nanoscale were formed without free DNA, but no typical toroid patterns were observed, which might stem from the strong compact of DNA caused by highly charged chitosan. It was supposed that the strong interaction of chitosan with DNA possibly prevented gene unpacking from chitosan vector, consequently restraining gene expression in nucleus.
Collapse
Affiliation(s)
- Wenguang Liu
- Research Institute of Polymeric Materials, Tianjin University, Tianjin 300072, P.R. China.
| | | | | | | | | | | | | |
Collapse
|
9
|
Torizawa T, Ueda T, Kuramitsu S, Hitomi K, Todo T, Iwai S, Morikawa K, Shimada I. Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses. J Biol Chem 2004; 279:32950-6. [PMID: 15169780 DOI: 10.1074/jbc.m404536200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyclobutane pyrimidine dimer (CPD) is one of the major forms of DNA damage caused by irradiation with ultraviolet (UV) light. CPD photolyases recognize and repair UV-damaged DNA. The DNA recognition mechanism of the CPD photolyase has remained obscure because of a lack of structural information about DNA-CPD photolyase complexes. In order to elucidate the CPD photolyase DNA binding mode, we performed NMR analyses of the DNA-CPD photolyase complex. Based upon results from (31)P NMR measurements, in combination with site-directed mutagenesis, we have demonstrated the orientation of CPD-containing single-stranded DNA (ssDNA) on the CPD photolyase. In addition, chemical shift perturbation analyses, using stable isotope-labeled DNA, revealed that the CPD is buried in a cavity within CPD photolyase. Finally, NMR analyses of a double-stranded DNA (dsDNA)-CPD photolyase complex indicated that the CPD is flipped out of the dsDNA by the enzyme, to gain access to the active site.
Collapse
Affiliation(s)
- Takuya Torizawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Buchko GW, Tung CS, McAteer K, Isern NG, Spicer LD, Kennedy MA. DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA. Nucleic Acids Res 2001; 29:2635-43. [PMID: 11410673 PMCID: PMC55733 DOI: 10.1093/nar/29.12.2635] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent NMR-based, chemical shift mapping experiments with the minimal DNA-binding domain of XPA (XPA-MBD: M98-F219) suggest that a basic cleft located in the loop-rich subdomain plays a role in DNA-binding. Here, XPA-DNA interactions are further characterized by NMR spectroscopy from the vantage point of the DNA using a single-stranded DNA nonamer, dCCAATAACC (d9). Up to 2.5 molar equivalents of XPA-MBD was titrated into a solution of d9. A subset of (31)P resonances of d9 were observed to broaden and/or shift providing direct evidence that XPA-MBD binds d9 by a mechanism that perturbs the phosphodiester backbone of d9. The interior five residues of d9 broadened and/or shifted before (31)P resonances of phosphate groups at the termini, suggesting that when d9 is bound to XPA-MBD the internal residues assume a correlation time that is characteristic of the molecular weight of the complex while the residues at the termini undergo a fraying motion away from the surface of the protein on a timescale such that the line widths are more characteristic of the molecular weight of ssDNA. A molecular model of the XPA-MBD complex with d9 was calculated based on the (15)N (XPA-MBD) and (31)P (d9) chemical shift mapping studies and on the assumption that electrostatic interactions drive the complex formation. The model shows that a nine residue DNA oligomer fully covers the DNA-binding surface of XPA and that there may be an energetic advantage to binding DNA in the 3'-->5' direction rather than in the 5'-->3' direction (relative to XPA-MBD alpha-helix-3).
Collapse
Affiliation(s)
- G W Buchko
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | | | | | | | | |
Collapse
|
11
|
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.
Collapse
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
Collapse
Affiliation(s)
- H Yokoyama
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- T Torizawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
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.
Collapse
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
| | | | | | | | | |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- T Torizawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|