A dynamical study of antibody-antigen encounter reactions

Physical Biology

Volumn 4, Issue 3, 2007, Pages 172-180

  Bongini, Lorenzo ^a   Fanelli, Duccio ^b   Piazza, Francesco ^c   De Los Rios, Paolo ^c   Sanner, Michel ^d   Skoglund, Ulf ^e  

^a UNIVERSITY OF FLORENCE   (Italy)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c EPFL   (Switzerland)

^d SCRIPPS RESEARCH   (United States)

^e KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; ANTIGEN;

ANALYTIC METHOD; ANTIGEN ANTIBODY REACTION; ANTIGEN BINDING; ARTICLE; CONCEPTUAL FRAMEWORK; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION;

EID: 35248832523     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/4/3/004     Document Type: Article

References (36)

1. Raab A, Han W, Badt D, Smith-Gill S J, Lindsay S M, Schindler H and Hinterdorfer P 1999 Antibody recognition imaging by force microscopy Nat. Biotechnol. 17 902
2. Milenic D E, Brady E D and Brechbiel M W 2004 Antibody-targeted radiation cancer therapy Nat. Rev. Drug Discovery 3 488
3. Roux K 1999 Immunoglobulin structure and function as revealed by electron microscopy Int. Arch. Allergy Immunol. 120 85-99
4. Nezlin R 1990 Internal movements in immunoglobulin molecules Adv. Immunol. 48 1-40
5. McCammon J A and Karplus M 1977 Internal motions of antibody molecules Nature 268 765-6
6. Raman C S, Jemmerson R, Nall B T and Allen M J 1992 Diffusion-limited rates for monoclonal antibody binding to cytochrome c Biochemistry 31 10370-9
7. Brooks B R, Bruccoleri R E, Olafson B D, States D J, Swaminathan S and Karplus M 1983 CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217
8. van Gunsteren W F and Berendsen H J C 1990 Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry Angew. Chem. Int. Edn Engl. 29 992-1023
9. Pearlman D A, Case D A, Caldwell J W, Ross W R, Cheatham T E III, DeBolt S, Ferguson D, Seibel G and Kollman P 1995 AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules Comput. Phys. Commun. 91 1-41
10. Bongini L, Fanelli D, Piazza F, De Los Rios P, Sandin S and Skoglund U 2004 Freezing immunoglobulins to see them move Proc. Natl Acad. Sci. USA 101 6466-71
11. Bongini L, Fanelli D, Piazza F, De Los Rios P, Sandin S and Skoglund U 2005 Dynamics of antibodies from cryo-electron tomography Biophys. Chem. 115 235-40
12. Crothers D M and Metzger H 1972 The influence of polyvalency on the binding properties of antibodies Immunochemistry 9 341-57
13. Yang T, Baryshnikova O K, Mao H, Holden M H and Cremer P S 2003 Investigations of bivalent antibody binding on fluid-supported phospholipid membranes: the effect of hapten density J. Am. Chem. Soc. 125 4779-84
14. Carrasco B, De la Torre J G, Byron O, King D, Walters C, Jones S and Harding S 1999 Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS Biophys. J. 77 2902-10
15. von Smoluchowski M 1916 Drei Vortrage uber Diffusion, Brownsche Bewegung und Koagulation von Kolloidteilchen Phys. Z. 17 557-71
16. von Smoluchowski M 1916 Drei Vortrage uber Diffusion, Brownsche Bewegung und Koagulation von Kolloidteilchen Phys. Z. 17 585-99
17. Wilson I A and Stanfield R L 1993 Antibody-antigen interactions Curr. Opin. Struct. Biol. 3 113-8
18. Traytak S D 1995 Diffusion-controlled reaction rate to an active site Chem. Phys. 192 1-7
19. Barzykin A V and Shushin A I 2001 Effect of anisotropic reactivity on the rate of diffusion-controlled reactions: comparative analysis of the models of patches and hemisphere Biophys. J. 80 2062-73
20. Janin J 1997 The kinetics of protein-protein recognition Proteins: Structure, Function and Genetics 28 153-61
21. Piazza F, De Los Rios P, Fanelli D, Bongini L and Skoglund U 2005 Anticooperativity in diffusion-controlled reactions with pairs of partially absorbing domains: a model for the antigen-antibody encounter Eur. Biophys. J. 34 899-911
22. Carrasco B, De la Torre J G, Davis K G, Jones S, Athwal D, Walters C, Burton D R and Harding S 2001 Crystallohydrodynamics for solving the hydration problem for multi-domain proteins: open physiological conformations for human IgG Biophys. Chem. 93 181-96
23. http://www.biacore.com/lifesciences/index.html
24. Ligler F S and Rowe Taitt C A (ed) 2005 Optical Biosensor: Present and Future (Amsterdam: Elsevier)
25. Malmborg A C, Micaelsson A, Ohlin M, Jansson B and Borrebaeck C A K 1992 Real-time analysis of antibody antigen reaction kinetics Scand. J. Immunol. 35 643-50
26. George A J T, French R R and Glennie M J 1995 Measurement of kinetic binding constants of a panel of anti-saporin antibodies using a resonant mirror biosensor J. Immunol. Methods 183 51-63
27. Kaufman E N and Jain R K 1992 Effect of bivalent interaction upon apparent antibody affinity: experimental confirmation of theory using fluorescence photobleaching and implications for antibody binding assays Cancer Res. 52 4157-67
28. Berezhkovskii A M, Monine M I, Muratov C B and Shvartsman S Y 2006 Homogenization of boundary conditions for surfaces with regular arrays of traps J. Chem. Phys. 124 036103
29. Berezhkovskii A M, Makhnovskii Yu A, Monine M I, Zitserman V Y and Shvartsman S Y 2004 Boundary homogenization for trapping by patchy surfaces J. Chem. Phys. 121 11390-94
30. Skoglund U, Ofverstedt L G, Burnett R M and Bricogne G 1996 Maximum-entropy three-dimensional reconstruction with deconvolution of the contrast transfer function: a test application with adenovirus J. Struct. Biol. 117 173-88
31. Weiss S 2000 Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy Nat. Struct. Biol. 7 724-9
32. Berdnikov V M and Doktorov A B 1981 The steric factor in the elementary act in the liquid phase Theor. Eksp. Khim. 17 318
33. Temkin S I and Yakobson B I 1984 Diffusion-controlled reactions of chemically anisotropic molecules J. Phys. Chem. 88 2679-82
34. Lee S and Karplus M 1987 Kinetics of diffusion-influenced bimolecular reactions in solution: II. Effects of the gating mode and orientation-dependent reactivity J. Chem. Phys. 86 1904-21
35. Solc K and Stockmayer W H 1973 Kinetics of diffusion-controlled reaction between chemically asymmetric molecules. II. Approximate steady-state solution Int. Chem. Kinet. 5 733-52
36. Berg O G 1985 Orientation constraints in diffusion-limited macromolecular association. The role of surface diffusion as a rate-enhancing mechanism Biophys. J. 47 1-14