Multi-scale calculation and global-fit analysis of hydrodynamic properties of biological macromolecules: Determination of the overall conformation of antibody IgG molecules

European Biophysics Journal

Volumn 39, Issue 3, 2010, Pages 361-370

  Amoros D ^a   Ortega, A ^a   Harding, S E ^b   Garcia De La Torre J ^a  

^a UNIVERSITY OF MURCIA   (Spain)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Antibodies; Global fit analysis; Hydrofit; Hydrosub; Multisubunit structure

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT; IMMUNOGLOBULIN FC FRAGMENT; IMMUNOGLOBULIN G; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER; COMPUTER PROGRAM; GENETICS; MUTATION; PROTEIN CONFORMATION; VALIDATION STUDY;

COMPUTERS; IMMUNOGLOBULIN FAB FRAGMENTS; IMMUNOGLOBULIN FC FRAGMENTS; IMMUNOGLOBULIN G; MODELS, CHEMICAL; MUTATION; PROTEIN CONFORMATION; SOFTWARE; WATER;

EID: 77950592426     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-008-0388-7     Document Type: Conference Paper

References (36)

1. Bernado P, García de la Torre J, Pons M (2002) Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. J Biomol NMR 23:139-150. doi:10.1023/A:1016359412284 (Pubitemid 34778166)
2. Bloomfield VA, Dalton WO, Holde KEV (1967) Frictional coefficients of multisubunit structures I. Theory. Biopolymers 5:135-148. doi:10.1002/bip.1967. 360050202
3. Brady RL, Edwards DJ, Hubbard RE, Jiang JS, Lange G, Roberts SM, Todd RJ, Adair JR, Emtage JS, King DJ, Low DC (1992) Crystal structure of a chimeric Fab0 fragment of an antibody binding tumour cells. J Mol Biol 227:253-264. doi:10.1016/0022-2836(92)90695-G
4. Burton D (1987) Structure and function of antibodies, In: molecular genetics of immunoglobulin. Elsevier, New York
5. Byron O (2000) Hydrodynamic bead modelling of biological macromolecules. Methods Enzymol 321:278-304. doi:10.1016/S0076-6879(00)21199-3
6. Byron O (2008) Hydrodynamic modelling: the solution conformation of macromolecules and their complexes, In: Correia J, Detrich H (eds) "methods in cell biology, vol 84, biophysical tools for biologists, vol 1 in vitro techniques, of analytical ultracentrifuge data in biophysical techniques, pp 327-373
7. Carrasco B, García de la Torre J (1999) Hydrodynamic properties of rigid particles. Comparison of different modelling and computational procedures. Biophys J 76:3044-3057
8. Carrasco B, García de la Torre J, Byron O, King D, Walters C, Jones S, Harding SE (1999) Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab0 domain using SOLPRO and ELLIPS. Biophys J 77:2902-2910
9. Carrasco B, García de la Torre J, Davis KG, Jones S, Athwal D, Walters C, Burton DR, Harding SE (2001) Crystallohydrodynamics for solving the hydration problem for multi-domain proteins: open physiological conformations of human IgG. Biophys Chem 93:181-196. doi:10.1016/S0301-4622(01)00220-4 (Pubitemid 34142186)
10. Deisenhofer J (1981) Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9 A and 2.8 A resolution. Biochemistry 20:2361-2370. doi: 10.1021/bi00512a001 (Pubitemid 11089772)
11. Fernandes MX, Bernado P, Pons M, García de la Torre J (2001) An analytical solution to the problem of the orientation of rigid particles by planar obstacles. J Am Chem Soc 123:12037-12047. doi:10.1021/ja011361x (Pubitemid 33135035)
12. Fernandes MX, Ortega A, Martínez MCL, García de la Torre J (2002) Calculation of hydrodynamic properties of small nucleic acids from their atomic structures. Nucleic Acids Res 30:1782-1788. doi:10.1093/nar/30.8.1782
13. Furtado PB, Whitty PW, Robertson A, Eaton JT, Almogren A, Kerr MA, Wolf HM, Perkins SJ (2004) Solution structure determination of monomeric human IgA2 by X-ray and neutron scattering, analytical ultracentrifugation and constrained modelling: a comparison with monomeric human IgA1. J Mol Biol 338:921-941. doi:10.1016/j.jmb.2004.03.007 (Pubitemid 38542823)
14. García de la Torre J, Carrasco B (2002) Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits. Biopolymers 63:163-167. doi:10.1002/bip.10013 (Pubitemid 34150362)
15. García de la Torre J, Navarro S, Martínez MCL, Diaz FG, Lopez Cascales JJ (1994) HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. Biophys J 67:530-531
16. García de la Torre J, Carrasco B, Harding SE (1997) SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles. Eur Biophys J 25:361-372. doi:10.1007/ s002490050049 (Pubitemid 27305853)
17. García de la Torre J, Huertas ML, Carrasco B (2000) Calculation of hydrodynamic properties of globular proteins from their atomiclevel structures. Biophys J 78:719-730
18. García de la Torre J, Llorca O, Carrascosa JL, Valpuesta JM (2001) HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy. Eur Biophys J 30:457-462. doi:10.1007/s002490100176 (Pubitemid 32999224)
19. García de la Torre J, Pérez Sánchez HE, Ortega A, Hernández Cifre JG, Fernandes MX, Baños FGD, Martínez MCL (2003) Calculation of the solution properties of flexible macromolecules: methods and applications. Eur Biophys J 32:477-486. doi: 10.1007/s00249-003- 0292-0 (Pubitemid 37055604)
20. García de la Torre J, Bernado P, Pons M (2005) Hydrodynamic models and computational methods for NMR relaxation. Methods Enzymol 394:419-430. doi:10.1016/S0076-6879(05)94017-2 (Pubitemid 40460926)
21. Gregory L, Davis KS, Sheth B, Boyd J, Jefferis R, Naves C, Burton D (1987) The solution conformation of the subclass of human IgG deduced from sedimentation and small-angle X-ray scattering. Mol Immunol 24:821-829. doi:10.1016/0161-5890(87)90184-2 (Pubitemid 17100159)
22. Harding SE (1995) On the hydrodynamic analysis of macromolecular conformation. Biophys Chem 55:69-93. doi:10.1016/0301-4622 (94)00143-148
23. Harding SE, Longman E, Carrasco B, Ortega A, García de la Torre J (2003) Studying antibody conformations by ultracentrifugation and hydrodynamic modeling methods in molecular biology, vol 248. Humana Press, Totowa, pp 93-113
24. Harris LJ, Larson SB, Skaletsky E,McPhersonA(1998a) Comparison of the conformations of two intact antibodies with hinges. Immunol Rev 163:35-43. doi:10.1111/j.1600-065X.1998.tb01186.x (Pubitemid 28327860)
25. Harris LJ, Skaletsky E, McPherson A (1998b) Crystallographic structure of an intact IgG1 monoclonal antibody. J Mol Biol 275:861-872. doi:10.1006/jmbi.1997.1508 (Pubitemid 28077701)
26. Harvey SH, García de la Torre J (1980) Coordinate systems for modelling the hydrodynamic resistance and diffusion coefficients of irregularly shaped rigid macromolecules. Macromolecules 13:960-964. doi:10.1021/ma60076a037
27. Longman E, Kreusel K, Tendler SB, Fiebig I, King K, Adiar J, O'Shea P, Ortega A, García de la Torre J (2003) Estimating domain orientation of two human antibody IgG4 chimeras by crystallohydrodynamics. Eur Biophys J 32:502-510. doi: 10.1007/s00249-003-0314-y (Pubitemid 37055606)
28. Lu Y, Harding S, Michaelsen T, Longman E, Davis KG, Ortega A, Grossman G, Sandlie I, García de la Torre J (2007) Solution conformation of wild type and mutant IgG3 and IgG4 immunoglobulins using crystallohydrodynamics: possible implications for complement activation. Biophys J 93:3733-3744. doi: 10.1529/biophysj.107.108993 (Pubitemid 350223792)
29. Nöllmann M, Stark WM, Byron O (2005) A global multi-technique approach to study low-resolution solution structures. J Appl Cryst 38:874-887. doi:10.1107/S0021889805026191 (Pubitemid 41796610)
30. Ortega A, García de la Torre J (2003) Hydrodynamic properties of rodlike and disklike particles in dilute solution. J Chem Phys 119:9914-9919. doi:10.1063/1.1615967
31. Ortega A, García de la Torre J (2005) Efficient, accurate calculation of rotational diffusion and NMR relaxation of globular proteins from atomic-level structures and approximate hydrodynamic calculations. J Am Chem Soc 127:12764-12765. doi:10.1021/ja053080l (Pubitemid 41339141)
32. Ortega A, García de la Torre J (2007) Equivalent radii and ratios of radii from solution properties as indicators of macromolecular shape, conformation and flexibility. Biomacromolecules 8:2464-2475. doi:10.1021/bm700473f (Pubitemid 47316987)
33. Perkins SJ, Bonner A (2008) Structure determinations of human and chimeric antibodies by solution scattering and constrained molecular modelling. Biochem Soc Trans 36:37-42. doi: 10.1042/BST0360037 (Pubitemid 351269617)
34. Tanford C (1961) Physical chemistry of macromolecules. Wiley, New York
35. Yamakawa H (1971) Modern theory of polymer solutions. Harper & Row, New York
36. Zipper P, Durchschlag H (2003) Modeling of protein solution structures. J Appl Cryst 36:509-514. doi:10.1107/S0021889803001870