Dynamical regulations of protein-ligand bindings at single molecular level

Biochemical and Biophysical Research Communications

Volumn 355, Issue 3, 2007, Pages 770-775

  Sagawa, Takuma ^a   Azuma, Takachika ^b   Sasaki, Yuji C ^a,c  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b TOKYO UNIVERSITY OF SCIENCE   (Japan)

^c JAPAN SYNCHROTRON RADIATION RESEARCH INSTITUTE   (Japan)

Author keywords

Antigen antibody interaction; Binding affinity; Protein ligand interaction; Single molecular dynamics; Structural fluctuation; X ray

Indexed keywords

ANTIGEN ANTIBODY REACTION; ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; BIOMEDICINE; BIOTECHNOLOGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE; X RAY;

ANTIBODIES, MONOCLONAL; ANTIGEN-ANTIBODY REACTIONS; IMMUNOGLOBULIN FAB FRAGMENTS; LIGANDS; PROTEIN BINDING; PROTEINS; X-RAY DIFFRACTION;

EID: 33847308111     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.02.031     Document Type: Article

References (32)

1. Pabo C.O., and Sauer R.T. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61 (1992) 1053-1095
2. Kraut D.A., Carroll K.S., and Herschlag D. Challenges in enzyme mechanism and energetics. Annu. Rev. Biochem. 72 (2003) 517-571
3. Wiseman T., Willson S., Brands J.F., and NanLin L. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179 (1989) 131-137
4. Puglisi J.D., Tan R., Calnan B.J., Frankel A.D., and Williamson J.R. Conformation of the TAR RNA-Arginine complex by NMR spectroscopy. Science 257 (1992) 76-80
5. Torigoe H., Nakayama T., Imazato M., Shimada I., Arata Y., and Sarai A. The affinity maturation of anti-4-hydroxy-3-nitrophenylacetyl mouse monoclonal antibody. J. Biol. Chem. 270 (1995) 22218-22222
6. Wedmayer G.J., Patten P.A., Wang L.H., Schultz P.G., and Stevens R.C. Structural insights into the evolution of an antibody combining site. Science 276 (1997) 1665-1669
7. Oda M., Kozono H., Morii H., and Azuma T. Evidence of allosteric conformational changes in the antibody constant region upon antigen binding. Int. Immunol. 15 (2003) 417-426
8. Sagawa T., Oda M., Morii H., Takizawa H., Kozono H., and Azuma T. Conformational changes in the antibody constant domains upon hapten-binding. Mol. Immunol. 42 (2005) 9-18
9. Jones R.B., Gordus A., Krall J.A., and MacBeath G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439 (2006) 168-174
10. 1-ATP is a highly efficient molecular motor that rotates with discrete 120° steps. Cell 93 (1998) 1117-1124
11. 1-ATPase. Nature 410 (2001) 898-904
12. Sasaki Y.C., Suzuki Y., and Ishibashi T. Fluorescent X-ray interference from a protein monolayer. Science 263 (1994) 62-64
13. Sasaki Y.C., Suzuki Y., Yagi N., Adachi S., Ishibashi M., Suda H., Toyota K., and Yanagihara M. Tracking of individual nanocrystals using diffracted X-rays. Phys. Rev. E. 62 (2000) 3843-3847
14. Sasaki Y.C., Okumura Y., Adachi S., Suzuki Y., and Yagi N. Diffracted X-ray tracking: new system for single molecular detection with X-rays. Nucl. Instrum. Methods (2001) A467-A468
15. Sasaki Y.C., Okumura Y., Adachi S., Suda H., Taniguchi Y., and Yagi N. Picometer-scale dynamical X-ray imaging of single DNA molecules. Phys. Rev. Lett. 87 (2001) 248102 1-4
16. Sasaki Y.C., Okumura Y., Miyazaki T., and Higurashi T. Observations of X-ray radiation pressure force on individual gold nanocrystals. Appl. Phys. Lett. 89 (2006) 053121 1-3
17. Okumura Y., Oka T., Kataoka M., Taniguchi Y., and Sasaki Y.C. Picometer-scale dynamical observations of individual membrane proteins: The case of bacteriorhodopsin. Phys. Rev. E 70 (2004) 021917 1-7
18. Boutet S., and Robinson I.K. Radiation driven collapse of protein crystals. J. Synchrotron Radiat. 13 (2006) 1-7
19. Teng T., and Moffat K. Primary radiation damage of protein crystals by an intense synchrotron X-ray beam. J. Synchrotron Radiat. 7 (2000) 313-317
20. Henderson R. Cryo-protection of protein crystals against radiation damage in electron and X-ray diffraction. Proc. R. Soc. Lond. B 241 (1990) 6-8
21. Navea C., and Hill M.A. Will reduced radiation damage occur with very small crystals?. J. Synchrotron Radiat. 12 (2005) 299-303
22. Radmacher M., Fritz M., Hansma H.G., and Hansma P.K. Direct observation of enzyme activity with the atomic force microscope. Science 265 (1994) 1577-1579
23. Oda M., and Azuma T. Reevaluation of stoichiometry and affinity/avidity in interactions between anti-hapten antibodies and mono- or multi-valent antigens. Mol. Immunol. 37 (2000) 1111-1122
24. Brownstone A., Mitchison N.A., and Pitt-Rivers R. Chemical and serological studies with an iodine-containing synthetic immunological determinant 4-hydroxy-3-iodo-5-nitrophenyl acetic acid (NIP) and related compounds. Immunology 10 (1966) 465-479
25. Frauenfelder H., Sligar S.G., and Wolynes P.G. The energy landscapes and motions of proteins. Science 254 (1991) 1598-1603
26. Miller D.W., and Dill K.A. Ligand binding to proteins: the binding landscape model. Protein Sci. 6 (1997) 2166-2179
27. Kumar S., Ma B., Tsai C.-J., Sinha N., and Nussinov R. Folding and binding cascade: dynamic landscapes and population shifts. Protein Sci. 9 (2000) 10-19
28. Celej M.S., Montich G.G., and Fidelio G.D. Conformational flexibility of avidin: the influence of biotin binding. Biochem. Biophys. Res. Commun. 325 (2004) 922-927
29. Celej M.S., Dassie S.A., Freire E., Bianconi M.L., and Fidelio G.D. Ligand-induced thermostability in proteins: thermodynamic analysis of ANS-albumin interaction. Biochim. Biophys. Acta 1750 (2005) 122-133
30. Kusumi A., Sako Y., and Yamamoto M. Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells. Biophys. J. 65 (1993) 2021-2040
31. Furukawa K., Akasako-Furukawa A., Shirai H., Nakamura H., and Azuma T. Junctional amino acids determine the maturation pathway of an antibody. Immunity 11 (1999) 329-338
32. Sagawa T., Oda M., Ishimura M., Furukawa K., and Azuma T. Thermodynamic and kinetic aspects of antibody evolution during the immune response to hapten. Mol. Immunol. 39 (2003) 801-808