Skip to main content
SpringerLink
Log in

Combinations with Other Methods

  • Chapter
Real-Time Analysis of Biomolecular Interactions

  • 375 Accesses

Abstract

The BIACORE system, differential titration calorimetry (DTC) and a stoppedflow instrument have been used for measurement of physico-chemical constants associated with antigen-antibody interactions. After mutations were systematically introduced into the complementarity-determining regions (CDRs) of antibody that correspond to its antigen-binding site, the effects of mutations on its antigen-binding activity were physico-chemically analyzed. Since antigen-antibody interactions are reversible as shown by the following equation,

$$ Ag + Ab \leftrightarrows Ag \cdot Ab $$

they must obey the rules of thermodynamics as well as the rules of kinetics. The following three equations show the relationships between rate constants (association rate constant k a, dissociation rate constant k d) and an equilibrium constant (affinity constant K A) as well as the relationships among thermodynamic parameters (∆G, ∆H, ∆S).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Wiseman T, Williston S, Brands J F, Llin L -N (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179: 131–137

    Article  PubMed  CAS  Google Scholar 

  2. Ito W, Iba Y, Kurosawa Y (1993) Effects of substititions of closely related amino acids at the contact surface in an antigen-antibody complex on thermodynamic parameters. J. Biol. Chem. 268: 16639–16647

    PubMed  CAS  Google Scholar 

  3. Tonomura B, Nakatani H, Ohnishi M, Yamaguchi-Ito J, Hiromi K (1978) Test reaction for a stopped-flow apparatus. Reactions of 2,6-dichlorophenolindophenol and potassium ferricyanide by L-ascorbic acid. Anal. Biochem. 84: 370–383

    Article  PubMed  CAS  Google Scholar 

  4. Ito W, Kurosawa Y (1993) Development of an artificial antibody system with multiple valency using an Fv fragment fused to a flagment of protein A. J. Biol. Chem. 268: 20668–20675

    PubMed  CAS  Google Scholar 

  5. Ito W, Yasui H, Kurosawa Y (1995) Mutations in the complementarity-determining regions do not caused differences in free energy during the process of formation of the activated complex between an antibody and the corresponding protein antigen. J. Mol. Biol. 248: 729–732

    Article  PubMed  CAS  Google Scholar 

  6. Glasstone S, Ladler K J, Eyring H (1941) In the Theory of Rate Processes. McGraw-Hill, New York

    Google Scholar 

  7. Hillenkamp F, Karas M, Beavis R, Chait B T (1991) Matrix-assisted laser desorption/ionization of biopolymers. Anal. Chem. 63: 1193A-1203A

    PubMed  CAS  Google Scholar 

  8. Beavis R C, Chait B T (1990) Rapid, sensitive analysis of protein mixtures by mass spectrometry. Proc. Natl Acad. Sci. USA 87: 6873–6877

    Article  PubMed  CAS  Google Scholar 

  9. Henzel W J, Billeci T M, Stults J T, Wong S C, Grimley C, Wantanabe C (1993) Identifying proteins from two-dimensional gel gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl Acad. Sci. USA 90: 5011–5015

    Article  PubMed  CAS  Google Scholar 

  10. James P, Quadroni M, Carafoli E, Gonnet G (1993) Protein Identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195: 58–64

    Article  PubMed  CAS  Google Scholar 

  11. Mann M, Talbo G (1996) Developments in matrix-assisted laser desorption ionisation peptide mass sequence tags. Curr. Opin. Biotechnol. 7: 11–19

    Article  PubMed  CAS  Google Scholar 

  12. Pappin D C J, Hojrup P, Bleasby A J (1993) Rapid identification of proteins by peptidemass fingerprinting. Curr. Biol. 3: 327–332

    Article  PubMed  CAS  Google Scholar 

  13. Yates J R III, Speicher S, Griffen P R, Hunkapiller T (1993) Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214: 397–408

    Article  PubMed  CAS  Google Scholar 

  14. Femnn J B, Mann M, Meng C K, Wong S F, Whitehouse C M (1990) Electrospray ionization-principles and practice. Mass Spectrom. Rev. 9: 37–70

    Article  Google Scholar 

  15. Busch K, Glish G L, McLuckey S A (1988) Mass Spectrometry/ Mass Spectrometry: Techniques and Applications of Tandem Mass Spectrometry. VCH, New York

    Google Scholar 

  16. Louris J N, Cooks R G, Syka J E, Kelley P E, Stafford G C, Todd J F J (1987) Anal. Chem. 59: 1677

    Article  CAS  Google Scholar 

  17. Weber-Grabauy M, Kelley P, Syka J, Bradshaw S, Brodbelt J (1987) Proc. 35th ASMS Conf. Mass Spectrom. Allied Topics, Denver, CO

    Google Scholar 

  18. March R E, Hughes R J (1989) Quadrupole Storage Mass Spectrometry. Wiley, New York

    Google Scholar 

  19. Davis S, Aldrich T H, Jones P F, Acheson A, Compton D L, Jain V, Ryan T E, Bruno J, Radziejewski C, Maisonpierre P C, Yancopoulos G D (1996) Isolation of angiopoietin-1, a ligand for the TIE2 receptor, by secretion-trap expression cloning. Cell 87: 1161–1169

    Article  PubMed  CAS  Google Scholar 

  20. Sakano S, Serizawa R, Inada T, Iwama A, Itoh A, Kato C, Shimizu Y, Shinkai F, Shimizu R, Kondo S, Ohno M, Suda T (1996) Characterization of a ligand for receptor protein tyrosine kinase HTK expressed in immature hemopoietic cells. Oncogene 13: 813–822

    PubMed  CAS  Google Scholar 

  21. Lackmann M, Bucci T, Mann R J, Kravets L A, Viney E, Smith F, Moritz R L, Carter W, Simpson R J, Nicola N A, Mackwell K, Nice E C, Wilks A F, Boyd A W (1996) Purification of the EPH-like receptor HEK using a biosensor-based affinity detection approach. Proc. Natl Acad. Sci. USA 93: 2523–2527

    Article  PubMed  CAS  Google Scholar 

  22. Krone J, Nelson R, Drogruel D, Williams P, Granzow R (1997) BIA/MS: Interfacing Biomolecular Interaction Analysis with Mass Spectrometry. Anal. Biochem. 242: 124

    Article  Google Scholar 

  23. Nelson R W, Krone J R, Osten J (1997) Surface Plasmon Resonance Biomolecular Interaction Analysis Mass Spectrometry. 1. Chip-Based Analysis. Anal. Chem. 69: 4363–4368

    Article  PubMed  CAS  Google Scholar 

  24. Roepstorff P (1997) Mass spectrometry in protein studies from genome to function. Curr. Opin. Biotechnol. 8: 6–13

    Article  PubMed  CAS  Google Scholar 

  25. Nelson R W, Krone J R, Osten J (1997) Surface Plasmon Resonance Biomolecular Interaction Analysis Mass Spectrometry. 2. Fiber Optic-Based Analysis. Anal. Chem. 69: 4369–4374

    Article  PubMed  CAS  Google Scholar 

  26. Wüthrich K (1986) NMR of Proteins and Nucleic Acids. John Wiley & Sons

    Google Scholar 

  27. Kainosho M, Tsuji T ( 1982) Assignment of the three methionyl carbonyl carbon resonances in Streptomyces subtilisin inhibitor by a carbon-13 and nitrogen-15 double-labeling tech­nique. A new strategy for structural studies of proteins in solution. Biochemistry 21: 6273–6279

    Article  PubMed  CAS  Google Scholar 

  28. Gouda H, Torigoe H, Saito A, Sato M, Arata Y, Shimada I (1992) Three-dimensional Solu­tion Structure of the B Domain of Staphylococcal Protein A: Comparison of the Solution and Crystal Structures. Biochemistry 31: 9665–9672

    Article  PubMed  CAS  Google Scholar 

  29. Gouda H, Shiraishi M, Takahashi H, Kato K, Torigoe H, Arata Y, Shimada I (1998) NMR Study on the Interaction between the B Domain of Staphylococcal Protein A and the Fc Portion of Immunoglobulin G. Biochemistry 37: 129–136

    Article  PubMed  CAS  Google Scholar 

  30. Nakayama T, Arata A, Shimada I (1993) A Multinuclear NMR Study of the Affinity Matu­ration of Anti-NP Mouse Monoclonal Antibodies: Comparison of Antibody Combining Sites between Primary Response Antibody N1G9 and Secondary Response Antibody 3B62. Biochemistry 32: 13961–13968

    Article  PubMed  CAS  Google Scholar 

  31. Mizutani R, Miura K, Nakayama T, Shimada I, Arata Y, Satow Y (1995) Three-dimensinal Structures of Fab Fragment and Its (4-Hydroxy-3-Nitrophenyl) Acetate Complex of Mu­rine N1G9 Antibody from Primary Immune Response. J. Mol. Biol. 254: 208–222

    Article  PubMed  CAS  Google Scholar 

  32. Stafford W T H I (1992) Boundary Analysis in Sedimentation Transport Experiment: A Procedure for Obtaining Sedimentation Coefficient Distributions Using the Time Deriva­tive of the Concentration Profile. Anal. Biochem. 203: 295–301

    Article  PubMed  CAS  Google Scholar 

  33. Ralston G (1993) Introduction to Analytical Ultracentrifugation. Beckman Instruments, Fullerton

    Google Scholar 

  34. Laue T, Philo J, Hays D. SEDNTERP: available on rasmb ftp site.

    Google Scholar 

  35. Dong F, Gogol E P, von Hippel P H (1995) The Phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate. J. Biol. Chem. 270: 7462–7473

    Article  PubMed  CAS  Google Scholar 

  36. Pintar A, Hennsmann M, Jumel K, Pitkeathly M, Harding S E, Campbell ID (1996) Solu­tion studies of the SH2 domain from the fyn tyrosine kinase: secondary structure, backbone dynamics and protein association. Eur. Biophys. J. 24: 371–380

    Article  PubMed  CAS  Google Scholar 

  37. Gonzalez L Jr, Plecs J J, Alber T (1996) An engineered allosteric switch in leucine-zipper oligomerization. Nature Struct. Biol. 3: 510–515

    Article  PubMed  CAS  Google Scholar 

  38. Cantor C R, Schimmel P R (1980) Biophysical Chemistry Part II. Techniques for the study of biological structure and function, pp.555–570, 610–612

    Google Scholar 

  39. Hansley P (1996) Defining the structure and stability of macromolecular assemblies in solution: the re-emergence of analytical ultracentrifugation as a practical tool. Structure 4: 367–373

    Article  Google Scholar 

  40. Matsui T, Riniviene B, Goldberg E, Tsugita A, Tanaka N, Arisaka F (1997) Isolation and Characterization of a Molecular Chaperone, gp 57A, of Bacteriopahge T4. J. Bacteriol. 179: 1846–1851

    PubMed  CAS  Google Scholar 

  41. McRorie D K, Voelker P J (1993) Self-Associating Systems in the Analytical Ultracentri-fuge. Beckman Instruments, Fullerton

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakukakubo, Kutukake-cho, Toyoake, 470-1101, Japan

    Yoshikazu Kurosawa

  2. Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Ichio Shimada & Ichio Shimada

  3. Millennium Pharmaceuticals, 40 Memorial Drive, Cambridge, MA, 02139, USA

    Christopher Williams

  4. Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagasuta-cho, Midori-ku, Yokohama, 226-8501, Japan

    Fumio Arisaka

Authors
  1. Yoshikazu Kurosawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ichio Shimada
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Christopher Williams
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ichio Shimada
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fumio Arisaka
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho Shogoin, 606-8507, Sakyo-ku, Kyoto, Japan

    Kazuhiro Nagata

  2. Frontier Collaborative Research Center, Tokyo Institute of Technology, 4259 Nagatsuta-cho, 226-8503, Midori-ku, Yokonhama, Japan

    Hiroshi Handa

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Springer Japan

About this chapter

Cite this chapter

Kurosawa, Y., Shimada, I., Williams, C., Shimada, I., Arisaka, F. (2000). Combinations with Other Methods. In: Nagata, K., Handa, H. (eds) Real-Time Analysis of Biomolecular Interactions. Springer, Tokyo. https://doi.org/10.1007/978-4-431-66970-8_20

Download citation

  • DOI: https://doi.org/10.1007/978-4-431-66970-8_20

  • Publisher Name: Springer, Tokyo

  • Print ISBN: 978-4-431-66972-2

  • Online ISBN: 978-4-431-66970-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation