Free Energy Simulations and MM-PBSA Analyses on the Affinity and Specificity of Steriod Binding to Antiestradiol Antibody

Proteins: Structure, Function and Genetics

Volumn 55, Issue 1, 2004, Pages 34-43

  Laitinen, Tuomo ^a   Kankare, Jussi A ^b   Peräkylä, Mikael ^a  

^a UNIVERSITY OF EASTERN FINLAND   (Finland)

^b UNIVERSITY OF TURKU   (Finland)

Author keywords

Antibody fab fragment; Free energy perturbation simulation; Molecular dynamics simulation; Molecular mechanics Poisson Boltzmann surface area (MAM PBSA) method; Mutagenesis; Steroid

Indexed keywords

17 DEOXYESTRADIOL; 17ALPHA ESTRADIOL; ALANINE; ESTRADIOL; ESTRADIOL ANTIBODY; ESTRIOL; ESTRONE; IMMUNOGLOBULIN F(AB) FRAGMENT; STEROID; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ANTIBODY SPECIFICITY; ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; BINDING SITE; CROSS REACTION; ENERGY; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; POISSON DISTRIBUTION; PRIORITY JOURNAL;

ANTIBODIES, MONOCLONAL; ANTIBODY AFFINITY; ANTIBODY SPECIFICITY; BINDING SITES, ANTIBODY; COMPUTER SIMULATION; ESTRADIOL; ESTROGENS; HYDROGEN BONDING; MODELS, MOLECULAR; MUTAGENESIS; PROGESTERONE; PROTEIN BINDING; TESTOSTERONE;

EID: 1442300070     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10399     Document Type: Article

References (44)

1. Kuiper GG, Carlson B, Grandien K, Enmark E, Haggblad J, Nilsson S, Gustafsson JA. Comparison of the ligand binding specificity and transcript tissue distribution of estrogen receptors alpha and beta. Endocrinology 1997;138:863-870.
2. Thomas L, editor. Clinical Laboratory Diagnostics. Use and Assessment of Clinical Laboratory Results. Frankfurt/Main, Germany: TH-Books, Verlagsgesellschaft mbH; 1998.
3. Hulley S, Grady D, Bush T, Furberg C, Herrington D, Riggs B, Vittinghoff E. Cardiovascular disease outcomes during 6.8 years of hormone therepy: heart and estrogen/progestin replacement study follow-up (HERS II). JAMA 1998;280:605-613.
4. Viscoli CM, Brass LM, Kernan WN, Sarrel PM, Suissa S, Horwitz RI. A clinical trial of estrogen-replacement therapy after ischemic stroke. N Engl J Med 2001;345:1243-1249.
5. Grady D, Herrington D, Bittner V, Blumenthal R, Davidson M, Hlatky M, Hsia J, Hulley S, Herd A, Khan S, Newby LK, Waters D, Vittinghoff E, Wenger N. Cardiovascular disease outcomes during 6.8 years of hormone therapy: heart and estrogen/progestin replacement study follow-up (HERS II). JAMA 2002;288:49-57.
6. Writing group for the Women's Health Initiative Investigators. Risks and benefits of estrogen plus progestin in healthy postmenopausal women. JAMA 2002;288:321-333.
7. Pajunen M, Saviranta P, Jauria P, Karp M, Pettersson K, Mäntsälä P, Lövgren T. Cloning, sequencing, expression and characterization of three anti-estradiol-17β fab fragments. Biochem Biophys Acta 1997:1351;192-202.
8. Lamminmäki U, Villoutreix BO, Jauria P, Saviranta P, Vihinen M, Nilsson L, Teleman O, Lövgren T. Structural analysis of an anti-estradiol antibody. Mol Immunol 1997;34:1215-1226.
9. Lamminmäki U, Kankare J. Crystal structure of a recombinant anti-estradiol fab fragment in complex with 17β-estradiol. J Biol Chem 2001;276:36687-36694.
10. Jayaram B, Sprous D, Young MA, Beveridge DL. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J Am Chem Soc 1998;120:10629-10633.
11. Vorobjev YN, Almagro JC, Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum models. Proteins 1998;32:399-413.
12. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE III. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889-897.
13. Kuhn B, Kollman PA. A ligand that is predicted to bind better to avidin than biotin: insights from computational fluorine scanning. J Am Chem Soc 2000;122:3909-3916.
14. Kuhn B, Kollman PA. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem 2000;43:3786-3791.
15. Peräkylä M, Nordman N. Energetic analysis of binding of progesterone and 5β-androstane-3, 17-dione to anti-progesterone antibody DB3 using molecular dynamics and free energy calculations. Protein Eng 2001;14:753-758.
16. Nordman N, Valjakka J, Peräkylä M. Analysis of the binding energies of testosterone, 5α-dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an anti-testosterone antibody. Proteins 2003;50:135-143.
17. Chong LT, Duan Y, Wang L, Massova I, Kollman PA. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci. USA 1999;96:14330-14335.
18. Kollman P. Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
19. Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J Comput Chem 2002;23:15-27.
20. Reyes CM, Kollman PA. Investigating the binding specificity of U1A-RNA by computational mutagenesis. J Mol Biol 2000;295:1-6.
21. Reyes CM, Kollman PA. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol 2000;297:1145-1158.
22. Arevalo JH, Taussig MJ, Wilson IA. Molecular basis of crossreactivity and limits of antibody-antigen complementarity. Nature 1993;365:859-863.
23. Arevalo JH, Hassig CA, Stura EA, Sims MJ, Taussig MJ, Wilson IA. Structural analysis of antibody specificity. Detailed comparison of five Fab'-steroid complexes. J Mol Biol 1994;241:663-690.
24. Valjakka J, Takkinen K, Teerinen T, Söderlund H, Rouvinen J. Structural insights into steroid hormone binding. The crystal structure of a recombinant anti-testosterone Fab fragment in free and testosterone-bound forms. J Biol Chem 2002;277:4183-4190.
25. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Peterson GA, Ayala PY, Cui G, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA. Gaussian 98, Revision A.7. Pittsburgh, PA: Gaussian Inc.; 1998.
26. Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 1993;97:10269-10280.
27. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
28. Case DA, Pearlman DA, Caldwell JW, Cheatham TE III, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Ferguson DM, Radmer RJ, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER 6.0. San Francisco: University of California; 1997.
29. Jorgensen WL, Chandrasekhar J, Madura J, Impley RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
30. Schafmeister CEAF, Ross WS, Romanovski V. Leap, San Francisco: University of California; 1995.
31. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola AD, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
32. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J Comput Phys 1977;23:327-341.
33. Evans SV. Setor: hardware-lighted three-dimensional solid model representations of macromolecules. J Mol Graph 1993;11:134-138.
34. Nicholls A, Sharp KA, Honig B. Delphi. NY: Department of Biochemistry and Molecular Biophysics, Columbia University; 1990.
35. Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
36. Sanner MF, Olson AJ, Spehner JC. Reduced surface-an efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320.
37. Pearlman DA, Kollman PA. The overlooked bond-stretching contribution in free energy perturbation calculations. J Chem Phys 1991;94:4532-4545.
38. Chanbers CC, Hawkins GD, Cramer CJ, Truhlar DG. Model for aqueous solvation based on class IV atomic charges and first solvation shell effects. J Phys Chem 1996;100:16385-16398.
39. Jeffrey PD, Strong RK, Sieker LC, Chang CYY, Campbell RL, Petsko GA, Haber E, Margolies MN, Sheriff S. 26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity. Proc Natl Acad Sci USA 1993;90:10310-10314.
40. Fersht, A. Structure and Mechanism in Protein Science. A Guide to Enzyme Catalysis and Protein Engineering. New York: W.H. Freeman and Co.; 1999.
41. Miyamoto S, Kollman PA. What determines the strength of noncovalent association of ligands to proteins in aqueous solution. Proc Natl Acad Sci USA 1993;90:8402-8406.
42. Ohno S, Mori N, Matsunaga T. Antigen-binding specificities of antibodies are primarily determined by seven residues of VH. Proc Natl Acad Sci USA 1985;82:2945-2949.
43. Davies DR, Chacko S. Antibody structure. Acc Chem Res 1993;26:421-427.
44. Vargas-Madrazo E, Lara-Ochoa F, Almagro JC. Canonical structures repertoire of the antigen-binding site of immunoglobulins suggest strong geometrical restrictions associated to the mechanism of immune recognition. J Mol Biol 1995;254:497-504.