Dynamic communication between androgen and coactivator: Mutually induced conformational perturbations in androgen receptor ligand-binding domain

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 4, 2011, Pages 1154-1171

  Xu, Xue ^a,b   Yang, Wei ^a,b   Wang, Xia ^a   Li, Yan ^b   Wang, Yonghua ^a   Ai, Chunzhi ^c  

^a NORTHWEST A F UNIVERSITY   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^c DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

Author keywords

Androgen receptor; Coactivator; Dihydrotestosterone; Dynamic communication; Molecular dynamics; Thermodynamic analysis

Indexed keywords

ACTIVATION FUNCTION 2; ANDROGEN RECEPTOR; ANDROSTANOLONE; NUCLEAR RECEPTOR COACTIVATOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; GENETIC TRANSCRIPTION; LIGAND BINDING; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN QUATERNARY STRUCTURE; REGULATORY MECHANISM; SIGNAL TRANSDUCTION; SIMULATION; SRC HOMOLOGY DOMAIN; THERMODYNAMICS;

BINDING SITES; CATALYTIC DOMAIN; DIHYDROTESTOSTERONE; HUMANS; MOLECULAR DYNAMICS SIMULATION; NUCLEAR RECEPTOR COACTIVATORS; POISSON DISTRIBUTION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STABILITY; RECEPTORS, ANDROGEN; SIGNAL TRANSDUCTION; THERMODYNAMICS;

EID: 79952456642     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22951     Document Type: Article

References (56)

1. Nettles KW, Greene GL. Ligand control of coregulator recruitment to nuclear receptors. Annu Rev Physiol 2005; 67: 309-333.
2. He B, Gampe RT, Jr, Kole AJ, Hnat AT, Stanley TB, An G, Stewart EL, Kalman RI, Minges JT, Wilson EM. Structural basis for androgen receptor interdomain and coactivator interactions suggests a transition in nuclear receptor activation function dominance. Mol Cell 2004; 16: 425-438.
3. Xu X, Yang W, Li Y, Wang Y. Discovery of estrogen receptor modulators: a review of virtual screening and SAR efforts. Expert Opin Drug Discovery 2010; 5: 21-31.
4. Taplin M. Drug insight: role of the androgen receptor in the development and progression of prostate cancer. Oncology 2007; 4: 236-244.
5. Askew EB, Gampe RT, Stanley TB, Faggart JL, Wilson EM. Modulation of androgen receptor activation function 2 by testosterone and dihydrotestosterone. J Biol Chem 2007; 282: 25801-25816.
6. Gregory CW, He B, Johnson RT, Ford OH, Mohler JL, French FS, Wilson EM. A mechanism for androgen receptor-mediated prostate cancer recurrence after androgen deprivation therapy. Cancer Res 2001; 61: 4315-4319.
7. He B, Gampe RT, Faggart JL, Minges JT, French FS, Wilson EM. Probing the functional link between androgen receptor coactivator and ligand-binding sites in prostate cancer and androgen insensitivity. J Biol Chem 2006; 281: 6648-6663.
8. Danielian PS, White R, Lees JA, Parker MG. Identification of a conserved region required for hormone dependent transcriptional activation by steroid hormone receptors. EMBO J 1992; 11: 1025-1033.
9. Powell SM, Christiaens V, Voulgaraki D, Waxman J, Claessens F, Bevan CL. Mechanisms of androgen receptor signalling via steroid receptor coactivator-1 in prostate. Endocr Relat Cancer 2004; 11: 117-130.
10. Lee HJ, Chang C. Recent advances in androgen receptor action. Cell Mol Life Sci 2003; 60: 1613-1622.
11. Feng W, Ribeiro RC, Wagner RL, Nguyen H, Apriletti JW, Fletterick RJ, Baxter JD, Kushner PJ, West BL. Hormone-dependent coactivator binding to a hydrophobic cleft on nuclear receptors. Science 1998; 280: 1747-1749.
12. Moras D, Gronemeyer H. The nuclear receptor ligand-binding domain: structure and function. Curr Opin Cell Biol 1998; 10: 384-391.
13. Shiau AK, Barstad D, Radek JT, Meyers MJ, Nettles KW, Katzenellenbogen BS, Katzenellenbogen JA, Agard DA, Greene GL. Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism. Nat Struct Biol 2002; 9: 359-364.
14. Wilson EM. Functional Motifs of the Androgen Receptor. Androgen Action in Prostate Cancer 2009; 3: 241-267.
15. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Hornak V, Cui G, Beroza P, Schafmeister C, Kollman PA. AMBER 10. San Francisco, CA: University of California; 2008.
16. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee TA. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003; 24: 1999-2012.
17. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case D. Development and testing of a general amber force field. J Am Chem Soc 2004; 25: 1157-1174.
18. Jakalian A, Bush BL, Jack DB, Bayly CI. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J Comput Chem 2000; 21: 132-146.
19. Jakalian A, Jack DB, Bayly CI. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 2002; 23: 1623-1641.
20. Jorgensen WL, Chandrasekhar J, Madura J, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926-935.
21. Darden T, York D, Pederson L. Particle mesh Ewald: an N* log (N) method for computing Ewald sums. J Chem Phys 1993; 98: 10089-10092.
22. Ryckaert JP, Cicotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977; 23: 327-341.
23. Andrea TA, Swope WC, Andersen HC. The role of long range forces in determining the structure and properties of liquid water. J Chem Phys 1983; 79: 4576-4584.
24. Ichiye T, Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991; 11: 205-217.
25. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 2006; 34: 116-118.
26. Yamaguchi H, Aalten DMV, Pinak M, Furukawa A, Osman R. Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion. Nucleic Acids Res 1998; 26: 1939-1946.
27. Kitao A, Hayward S, Go N. Energy landscape of a native protein: jumping-among-minima model. Proteins 1998; 33: 425-437.
28. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart W, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998; 19: 1639-1662.
29. Mehler EL, Solmajer T. Electrostatic effects in proteins: comparison of dielectric and charge models. Protein Eng 1991; 4: 903-910.
30. Stouten PFW, Frommel C, Nakamura H, Sander C. An effective solvation term based on atomic occupancies for use in protein simulations. Mol Simul 1993; 10: 97-120.
31. 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. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000; 33: 889-897.
32. Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000; 39: 178-194.
33. Kuhn B, Donini O, Huo S, Wang JM, Kollman PA. MM-PBSA applied to computer-assisted ligand design. In: Reddy MR, Erion MD, editors. Free energy calculations in rational drug design. New York: Kluwer Academic/Plenum Publishers; 2001. pp 243-251.
34. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem 2005; 26: 1668-1688.
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. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. J Comput Chem 2002; 23: 128-137.
37. Honig B, Sharp K, Yang AS. Macroscopic models of aqueous solutions: biological and chemical applications. J Phys Chem 1993; 97: 1101-1109.
38. 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.
39. Ichiye T, Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991; 11: 205-217.
40. Bradley MJ, Chivers PT, Baker NA. Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. J Mol Biol 2008; 378: 1155-1173.
41. Matias PM, Donner P, Coelho R, Thomaz M, Peixoto C, Macedo S, Otto N, Joschko S, Scholz P, Wegg A, Basler S, Schafer M, Egner U, Carrondo MA. Structural evidence for ligand specificity in the binding domain of the human androgen receptor. J Biol Chem 2000; 275: 26164-26171.
42. Yarbrough WG, Quarmby VE, Simental JA, Joseph DR, Sar M, Lubahn DB, Olsen KL, French FS, Wilson EM. A single base mutation in the androgen receptor gene causes androgen insensitivity in the testicular feminized rat. J Biol Chem 1990; 265: 8893-8900.
43. Kemppainen JA, Lane MV, Sar M, Wilson EM. A single base mutation in the androgen receptor gene causes androgen insensitivity in the testicular feminized rat. Androgen receptor phosphorylation, turnover, nuclear transport, and transcriptional activation. Specificity for steroids and antihormones. J Biol Chem 1992; 267: 968-974.
44. Heinlein CA, Chang C. Androgen receptor (AR) coregulators: an overview. Endocr Rev 2002; 23: 175-200.
45. Duff J, McEwan IJ. Mutation of histidine 874 in the androgen receptor ligand-binding domain leads to promiscuous ligand activation and altered p160 coactivator interactions. Mol Endocrinol 2005; 19: 2943-2954.
46. Burd CJ, Morey LM, Knudsen KE. Androgen receptor corepressors and prostate cancer. Endocr Relat Cancer 2006; 13: 979-994.
47. Estébanez-Perpiňá E, Moore JMR, Mar E, Delgado-Rodrigues E, Nguyen P, Baxter JD, Buehrer BM, Webb P, Fletterick RJ, Guy RK. The molecular mechanisms of coactivator utilization in ligand-dependent transactivation by the androgen receptor. J Biol Chem 2005; 280: 8060-8068.
48. Kemppainen JA, Langley E, Wong C, Bobseine K, Kelce W, Wilson E. Distinguishing androgen receptor agonists and antagonists: distinct mechanisms of activation by medroxyprogesterone acetate and dihydrotestosterone. Mol Endocr 1999; 13: 440-454.
49. Obiol-Pardo C, Rubio-Martinez J. Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP- peptide complexes. J Chem Inf Model 2007; 47: 134-142.
50. Buchanan G, Yang M, Harris HM, Nahm HS, Han G, Moore N, Bentel JM, Matusik RJ, Horsfall DJ, Marshall VR, Greenberg NM, Tilley WD. Mutations at the boundary of the hinge and ligand binding domain of the androgen receptor confer increased transactivation function. Mol Endocrinol 2001; 15: 46-56.
51. Lonard DM, O'Malley BW. The expanding cosmos of nuclear receptor coactivators. Cell 2006; 125: 411-414.
52. Chang CY, Abdo J, Hartney T, McDonnell DP. Development of peptide antagonists for the androgen receptor using combinatorial peptide phage display. Mol Endocrinol 2005; 19: 2478-2490.
53. Huang DM, Chandler D. The Hydrophobic Effect and the Influence of Solute-Solvent Attractions. J Phys Chem B 2002; 106: 2047-2053.
54. Chandler D. Interfaces and the driving force of hydrophobic assembly. Nature 2005; 437: 9640-9647.
55. Black BE, Vitto MJ, Gioeli D, Spencer A, Afshar N, Conaway MR, Weber MJ, Paschal BM. Transient, ligand-dependent arrest of the androgen receptor in subnuclear foci alters phosphorylation and coactivator interactions. Mol Endocrinol 2004; 18: 834-850.
56. Gao W, Bohl CE, Dalton JT. Chemistry and structural biology of androgen receptor. Chem Rev 2005; 105: 3352-3370.