The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody

Journal of Molecular Biology

Volumn 291, Issue 1, 1999, Pages 117-134

  Nakasako, Masayoshi ^a   Takahashi, Hideo ^a   Shimba, Nobuhisa ^a   Shimada, Ichio ^a   Arata, Yoji ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b WATER RESEARCH INSTITUTE   (Japan)

Author keywords

CDRH3; Cryogenic X ray crystal structure analysis; Fv fragment; Hydration structure; NMR pH titration

Indexed keywords

DANSYL CHLORIDE; HISTIDINE; IMMUNOGLOBULIN G; MONOCLONAL ANTIBODY; WATER;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; HYDRATION; MOLECULAR INTERACTION; NUCLEAR MAGNETIC RESONANCE; PH; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTON TRANSPORT;

EID: 0344931795     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2931     Document Type: Article

References (43)

1. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Rodgers J. R. Jr, Kennard O., Shimanouchi O., Tasumi M. The Protein Data Bank: a computer based archival file for macromolecular structure. J. Mol. Biol. 112:1977;535-542.
2. Bhat T. N., Fishmann T. O., Boulot G., Poljak R. J. Structure of Fv and Fab fragments of antibody D1.3 show small rearrangements upon antigen binding. Nature. 347:1990;483-485.
3. Bhat T. N., Bentley G. A., Boulot G., Greene M. I., Tello D., Dall'Acqua W., Souchon H., Schwarz F. P., Mariuzza R. A., Poljak R. J. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc. Natl Acad. Sci. USA. 91:1994;1089-1093.
4. Braden B. C., Fields B. A., Ysern X., Goldbaum F. A., Dall'Acqua W., Schwarz F. P., Poljak R. J., Mariuzza R. A. Crystal structure of the complex of the variable domain of antibody D1.3 and turkey egg white lysozyme: a novel conformational change in antibody CDR-L3 selects for antigen. J. Mol. Biol. 257:1996;889-894.
5. Brünger A. T. Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta Crystallog. sect. A. 46:1990;46-57.
6. Brünger A. T. X-PLOR Version 3.1: a system for X-ray crystallography and NMR. 1992a;Yale University Press, New Haven.
7. Brünger A. T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992b;472-475.
8. Chothia C., Lesk A. M. Canonical structures for hypervariable regions of immunoglobulins. J. Mol. Biol. 196:1987;901-917.
9. Chothia C., Lesk A. M., Tramontano A., Levitt M., Smith-Gill S. J., Sheriff G. A., Padlan W. A., Davis D., Tulip W. R., Colman P. M., Spinelli S., Alzari P. M., Poljak R. J. Conformation of immunoglobulin hypervariable regions. Nature. 342:1989;877-883.
10. Colman P. M., Laver W. G., Varghese J. N., Baker A. T., Tulloch P. A., Air G. M., Webster R. G. Three-dimensional structure of a complex of antibody and with influenza virus neuraminidase. Nature. 326:1987;358-363.
11. Dall'Acqua W., Carter P. Antibody engineering. Curr. Opin. Struct. Biol. 8:1998;443-450.
12. Engh R. A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A. 47:1991;392-400.
13. Freund C., Ross A., Plückthun A., Holak T. A. Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy. Biochemistry. 33:1994;3296-3303.
14. Goldbaum F. A., Schwarz F. P., Eisenstein E., Cauerhff A., Mariuzza R. A., Poljak R. J. The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1. J. Mol. Recogn. 9:1996;6-12.
15. 15N-labeled in the VL domain only. J. Mol. Biol. 232:1993;15-22.
16. Guddat L. W., Shan L., Anchin J. M., Linthicum D. S., Edmundson A. B. Local and transmitted conformational changes on complexation of an anti-sweetener Fab. J. Mol. Biol. 236:1994;247-274.
17. Herron J. N., He X. M., Ballard D. W., Blier P. R., Pace P. E., Bothwell A. L. M., Voss E. W. Jr, Edmundson A. B. An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unligated Fab and a deoxynucleotide-Fab complex. Proteins: Struct. Funct. Genet. 11:1991;159-175.
18. H1 domain: protein sequencing and small-angle X-ray scattering studies. Biochemistry. 29:1990;5725-5733.
19. Inbar D., Hochman J., Givol D. Localization of antibody-combining sites within the variable portions of heavy and light chains. Proc. Natl Acad. Sci. USA. 69:1972;2659-2662.
20. Kabat E. A., Wu T. T., Reid-Miller M., Perry H. M., Gottesman K. S. Sequence of Proteins of Immunological Interest. 1991;US Department of Health and Human Services, Public Health Service (NIH Publication no. 91-3242) National Institutes of Health, Bethesda.
21. Kim J. I., Nakano T., Higuchi T., Hirobe M., Shimada I., Arata Y. Conformation and stereoselective reduction of hapten side chain in the antibody combining site. J. Am. Chem. Soc. 113:1991;9392-9394.
22. Kossiakoff A. A., Randal M., Guenot J., Eigenbrot C. Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures. Proteins: Struct. Funct. Genet. 14:1992;65-74.
23. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
24. Lesk A. M., Chothia C. Evolution of proteins formed by β-sheets. II. The core of immunoglobulin domains. J. Mol. Biol. 160:1982;325-342.
25. Luzzati P. V. Traitment statistique des erreurs dans la determination des structures Cristallines. Acta Crystallog. 5:1951;802-810.
26. Morea V., Tramontano A., Rustici M., Chothia C., Lesk A. M. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J. Mol. Biol. 275:1998;269-294.
27. Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
28. Odaka A., Kim J. I., Takahashi H., Shimada I., Arata Y. Isotope-edited nuclear magnetic resonance study of Fv fragment of an anti-dansyl mouse monoclonal antibody: recognition of the dansyl hapten. Biochemistry. 31:1992;10686-10691.
29. Ostermeier C., Essen L. O., Michel H. Crystals of an antibody Fv fragment against an integral membrane protein diffracting to 1.28 Å resolution. Proteins: Struct. Funct. Genet. 21:1995;74-77.
30. Otwinowski Z., Minor W. DENZO. A Film Processing Program for Macromolecular Crystallography. 1993;Yale University, New Haven.
31. Ramachandran G. N., Sasisekharan V. Conformation of polypeptides and proteins. Advan. Protein Chem. 23:1968;283-438.
32. 13C for heteronuclear NMR spectroscopy. FEBS Letters. 287:1991;185-188.
33. Rini J. M., Sculze-Gahman U., Wilson I. A. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science. 255:1992;959-965.
34. Stanfield R. L., Fisher T. M., Lerner R. A., Wilson I. A. Crystal structure of an antibody to a peptide and its complex with peptide antigen at 2.8 Å Science. 248:1990;712-719.
35. Stanfield R. L., Takimoto-Kamimura M., Rini J. M., Profy A. T., Wilson I. A. Major antigen-induced domain rearrangements in an antibody. Structure. 1:1993;83-93.
36. 1H NMR analyses of antigen-antibody interactions. Biochemistry. 30:1991a;2840-2847.
37. Takahashi H., Odaka A., Kawaminami S., Matsunaga C., Kato K., Shimada I., Arata Y. Multinuclear NMR study of the structure of the Fv fragment of anti-dansyl mouse IgG2a antibody. Biochemistry. 30:1991b;6611-6619.
38. 15N shift correlation NMR spectroscopy. Biochemistry. 31:1992;2464-2468.
39. 15N shift correlation NMR spectroscopy of the Fv and Fab fragments of antidansyl mouse monoclonal antibody. J. Mol. Biol. 243:1994;494-503.
40. Williams D. C., Rule G. S., Poljak R. J., Benjamin D. C. Reduction in the amide hydrogen exchange rates of an anti-lysozyme Fv fragment due to formation of the Fv-lysozyme complex. J. Mol. Biol. 270:1997;751-762.
41. Wilson I. A., Stanfield R. L. Antigen-induced conformational changes in antibodies: a protein structural prediction and design. Trends Biotechnol. 12:1994a;275-279.
42. Wilson I. A., Stanfield R. L. Antibody-antigen interactions: new structures and new conformational changes. Curr. Opin. Struct. Biol. 4:1994b;857-867.
43. Ysern X., Fields B. A., Bhat T. N., Goldbaum F. A., Dall'Acqua W., Schwarz F. P., Poljak R. J., Mariuzza R. A. Solvent rearrangement in an antigen-antibody interface introduced by site-directed mutagenesis of the antibody combining site. J. Mol. Biol. 238:1994;496-500.