Dynamic correlation networks in human peroxisome proliferator-activated receptor-γ nuclear receptor protein

European Biophysics Journal

Volumn 39, Issue 11, 2010, Pages 1503-1512

  Fidelak, Jeremy ^a   Ferrer, Silvia ^a   Oberlin, Michael ^a   Moras, Dino ^a   Dejaegere, Annick ^a   Stote, Roland H ^a  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Allostery; Molecular dynamics; Normal mode; Nuclear receptor; Protein

Indexed keywords

2,4 THIAZOLIDINEDIONE DERIVATIVE; APOPROTEIN; LIGAND; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; ROSIGLITAZONE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECT; DRUG POTENTIATION; HUMAN; METABOLISM; MOVEMENT (PHYSIOLOGY); PROTEIN BINDING; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; VIBRATION;

APOPROTEINS; HUMANS; LIGANDS; MODELS, MOLECULAR; MOVEMENT; PPAR GAMMA; PROTEIN BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; THIAZOLIDINEDIONES; VIBRATION;

EID: 77957692443     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-010-0608-9     Document Type: Article

References (57)

1. Accelrys The QUANTA program, San Diego, CA, USA
2. AK Agarwal A Garg 2002 A novel heterozygous mutation in peroxisome proliferator-activated receptor-gamma gene in a patient with familial partial lipodystrophy J Clin Endocrinol Metab 87 408 411 1:CAS:528: DC%2BD38XntVyrug%3D%3D 10.1210/jc.87.1.408 11788685 (Pubitemid 34084723)
3. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The protein data bank Nucleic Acids Res 28 235 242 1:CAS:528:DC%2BD3cXhvVKjt7w%3D 10.1093/nar/28.1.235 10592235
4. FC Bernstein TF Koetzle GJ Williams EF Meyer Jr MD Brice JR Rodgers O Kennard T Shimanouchi M Tasumi 1977 The Protein Data Bank: a computer-based archival file for macromolecular structures J Mol Biol 112 535 542 1:CAS:528:DyaE2sXkvVert7o%3D 10.1016/S0022-2836(77)80200-3 875032
5. BH Besler KM Merz PA Kollman 1990 Atomic charges derived from semiempirical methods J Comput Chem 11 431 439 1:CAS:528:DyaK3cXkt12nu7k%3D 10.1002/jcc.540110404
6. Y Brelivet S Kammerer N Rochel O Poch D Moras 2004 Signature of the oligomeric behaviour of nuclear receptors at the sequence and structural level EMBO Rep 5 423 429 1:CAS:528:DC%2BD2cXis1Krtrw%3D 10.1038/sj.embor.7400119 15105832 (Pubitemid 38618287)
7. BR Brooks RE Bruccoleri BD Olafson DJ States S Swaminathan M Karplus 1983 CHARMM: a program for macromolecular energy minimization and dynamics calculations J Comp Chem 4 187 217 1:CAS:528:DyaL3sXit1aiu7w%3D 10.1002/jcc.540040211
8. BR Brooks D Janezic M Karplus 1995 Harmonic analysis of large systems. I. Methodology J Comp Chem 16 1522 1542 1:CAS:528:DyaK2MXpsVGmtbk%3D 10.1002/jcc.540161209
9. AT Brunger M Karplus 1988 Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison Proteins Struct Funct Gen 4 148 156 1:CAS:528:DyaL1cXmt1Khsbs%3D 10.1002/prot.340040208
10. JB Bruning MJ Chalmers S Prasad SA Busby TM Kamenecka Y He KW Nettles PR Griffin 2007 Partial agonists activate PPARgamma using a helix 12 independent mechanism Structure 15 1258 1271 1:CAS:528:DC%2BD2sXhtFKhsLzI 10.1016/j.str.2007.07.014 17937915 (Pubitemid 47539157)
11. Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F (2008) Structure of the intact PPAR-gamma-RXR-alpha nuclear receptor complex on DNA. Nature 350-356
12. A Cooper DT Dryden 1984 Allostery without conformational change. A plausible model Eur Biophys J 11 103 109 1:CAS:528:DyaL2MXktFOrtA%3D%3D 10.1007/BF00276625 6544679
13. P Cronet JF Petersen R Folmer N Blomberg K Sjoblom U Karlsson EL Lindstedt K Bamberg 2001 Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family Structure 9 699 706 1:CAS:528:DC%2BD3MXmtV2ku78%3D 10.1016/S0969-2126(01)00634-7 11587644 (Pubitemid 32772892)
14. M Delarue YH Sanejouand 2002 Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model J Mol Biol 320 1011 1024 1:CAS:528:DC%2BD38Xlt1Ghsr0%3D 10.1016/S0022-2836(02)00562-4 12126621 (Pubitemid 34808821)
15. S Ebdrup I Pettersson HB Rasmussen HJ Deussen A Frost Jensen SB Mortensen J Fleckner L Pridal L Nygaard P Sauerberg 2003 Synthesis and biological and structural characterization of the dual-acting peroxisome proliferator-activated receptor alpha/gamma agonist ragaglitazar J Med Chem 46 1306 1317 1:CAS:528:DC%2BD3sXhsFGnsr4%3D 10.1021/jm021027r 12672231 (Pubitemid 36512696)
16. M Einstein TE Akiyama GA Castriota CF Wang B McKeever RT Mosley JW Becker DE Moller PT Meinke HB Wood JP Berger 2008 The differential interactions of peroxisome proliferator-activated receptor gamma ligands with Tyr473 is a physical basis for their unique biological activities Mol Pharmacol 73 62 74 1:CAS:528:DC%2BD1cXkslCktA%3D%3D 10.1124/mol.107.041202 17940191 (Pubitemid 350294197)
17. P Ferre 2004 The biology of peroxisome proliferator-activated receptors: relationship with lipid metabolism and insulin sensitivity Diabetes 53 Suppl 1 S43 S50 1:CAS:528:DC%2BD2cXhtlGqsb4%3D 10.2337/diabetes.53.2007.S43 14749265
18. H Frauenfelder GA Petsko D Tsernoglou 1979 Temperature-dependent X-ray diffraction as a probe of protein structural dynamics Nature 280 558 563 1:CAS:528:DyaL3cXjslahtA%3D%3D 10.1038/280558a0 460437
19. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC (1998) Gaussian 98, Revision A, 7. Gaussian Inc., Pittsburgh
20. T Gaillard E Martin E San Sebastian FP Cossio X Lopez A Dejaegere RH Stote 2007 Comparative normal mode analysis of LFA-1 integrin I-domains J Mol Biol 374 231 249 1:CAS:528:DC%2BD2sXht1ahtLzO 10.1016/j.jmb.2007.07.006 17919656 (Pubitemid 47610778)
21. RT Gampe Jr VG Montana MH Lambert GB Wisely MV Milburn HE Xu 2000 Structural basis for autorepression of retinoid X receptor by tetramer formation and the AF-2 helix Genes Dev 14 2229 2241 1:CAS:528:DC%2BD3cXmtlensro%3D 10.1101/gad.802300 10970886
22. AC Gee JA Katzenellenbogen 2001 Probing conformational changes in the estrogen receptor: evidence for a partially unfolded intermediate facilitating ligand binding and release Mol Endocrinol 15 421 428 1:CAS:528: DC%2BD3MXhvVChu7o%3D 10.1210/me.15.3.421 11222743 (Pubitemid 32221919)
23. Y Hamuro SJ Coales JA Morrow KS Molnar SJ Tuske MR Southern PR Griffin 2006 Hydrogen/deuterium-exchange (H/D-Ex) of PPARgamma LBD in the presence of various modulators Protein Sci 15 1883 1892 1:CAS:528:DC%2BD28XnvF2qs7k%3D 10.1110/ps.062103006 16823031 (Pubitemid 44141506)
24. SJ Hasstedt QF Ren K Teng SC Elbein 2001 Effect of the peroxisome proliferator-activated receptor-gamma 2 pro(12)ala variant on obesity, glucose homeostasis, and blood pressure in members of familial type 2 diabetic kindreds J Clin Endocrinol Metab 86 536 541 1:CAS:528:DC%2BD3MXht1KnsL4%3D 10.1210/jc.86.2.536 11158005 (Pubitemid 32207455)
25. Hayward S (2001) Normal mode analysis of biological molecules. In: Becker OM, Roux B, Watanabe M (eds) Computational biochemistry and biophysics. Marcel-Dekker, New York, pp 153-168
26. RA Hegele H Cao C Frankowski ST Mathews T Leff 2002 PPARG F388L, a transactivation-deficient mutant, in familial partial lipodystrophy Diabetes 51 3586 3590 1:CAS:528:DC%2BD38Xptl2msrs%3D 10.2337/diabetes.51.12.3586 12453919
27. Information P (1999) Avandia, rosiglitazone maleate. SmithKline Beecham Pharmaceuticals, Philadelphia
28. BA Johnson EM Wilson Y Li DE Moller RG Smith G Zhou 2000 Ligand-induced stabilization of PPARgamma monitored by NMR spectroscopy: implications for nuclear receptor activation J Mol Biol 298 187 194 1:CAS:528: DC%2BD3cXitl2ru78%3D 10.1006/jmbi.2000.3636 10764590
29. BC Kallenberger JD Love VK Chatterjee JW Schwabe 2003 A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease Nat Struct Biol 10 136 140 1:CAS:528:DC%2BD3sXms1KjtA%3D%3D 10.1038/nsb892 12536206 (Pubitemid 36177095)
30. SA Kliewer SS Sundseth SA Jones PJ Brown GB Wisely CS Koble P Devchand W Wahli TM Willson JM Lenhard JM Lehmann 1997 Fatty acids and eicosanoids regulate gene expression through direct interactions with peroxisome proliferator-activated receptors alpha and gamma Proc Natl Acad Sci USA 94 4318 4323 1:CAS:528:DyaK2sXjtVyht7w%3D 10.1073/pnas.94.9.4318 9113987 (Pubitemid 27194239)
31. R Kostadinova W Wahli L Michalik 2005 PPARs in diseases: control mechanisms of inflammation Curr Med Chem 12 2995 3009 1:CAS:528: DC%2BD2MXht1Grt7nM 10.2174/092986705774462905 16378501 (Pubitemid 41672488)
32. Leach AR (1996) Molecular modelling: principles and applications. Harlow, UK
33. JM Lehmann LB Moore TA Smith-Oliver WO Wilkison TM Willson SA Kliewer 1995 An antidiabetic thiazolidinedione is a high affinity ligand for peroxisome proliferator-activated receptor gamma (PPAR gamma) J Biol Chem 270 12953 12956 1:CAS:528:DyaK2MXmtV2itr0%3D 10.1074/jbc.270.50.30221 7768881 (Pubitemid 26001700)
34. M Levitt C Sander PS Stern 1985 Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme J Mol Biol 181 423 447 1:CAS:528:DyaL2MXhvVWjsbs%3D 10.1016/0022-2836(85)90230-X 2580101
35. Y Li M Choi K Suino A Kovach J Daugherty SA Kliewer HE Xu 2005 Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner Proc Natl Acad Sci USA 102 9505 9510 1:CAS:528:DC%2BD2MXmsVaktr0%3D 10.1073/pnas.0501204102 15976031 (Pubitemid 40981711)
36. A Ludtke J Buettner HH Schmidt HJ Worman 2007 New PPARG mutation leads to lipodystrophy and loss of protein function that is partially restored by a synthetic ligand J Med Genet 44 e88 10.1136/jmg.2007.050567 17766367
37. J Ma M Karplus 1998 The allosteric mechanism of the chaperonin GroEL: a dynamic analysis Proc Natl Acad Sci USA 95 8502 8507 1:CAS:528: DyaK1cXkvFamurY%3D 10.1073/pnas.95.15.8502 9671707 (Pubitemid 28350517)
38. ADJ MacKerell D Bashford M Bellott RLJ Dunbrack JD Evanseck MJ Field S Fischer J Gao H Guo S Ha D Joseph-McCarthy L Kuchnir K Kuczera FTK Lau C Mattos S Michnick T Ngo DT Nguyen B Prodhom WEI Reiher B Roux M Schlenkrich JC Smith R Stote J Straub M Watanabe J Wiorkiewicz-Kuczera D Yin M Karplus 1998 All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem 102 3586 3616 1:CAS:528:DyaK1cXivVOlsb4%3D
39. JD Madura JM Briggs RC Wade ME Davis BA Luty A Ilin J Antosiewicz MK Gilson B Bagheri LR Scott JA McCammon 1995 Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program Comp Phys Commun 91 57 95 1:CAS:528:DyaK2MXps1Wrtro%3D 10.1016/0010-4655(95)00043-F
40. DJ Mangelsdorf C Thummel M Beato P Herrlich G Schutz K Umesono B Blumberg P Kastner M Mark P Chambon RM Evans 1995 The nuclear receptor superfamily: the second decade Cell 83 835 839 1:CAS:528:DyaK2MXhtVSnu7nJ 10.1016/0092-8674(95) 90199-X 8521507 (Pubitemid 26006525)
41. O Marques YH Sanejouand 1995 Hinge-bending motion in citrate synthase arising from normal mode calculations Proteins 23 557 560 1:CAS:528: DyaK28Xht1yltQ%3D%3D 10.1002/prot.340230410 8749851 (Pubitemid 26009518)
42. R Montanari F Saccoccia E Scotti M Crestani C Godio F Gilardi F Loiodice G Fracchiolla A Laghezza P Tortorella A Lavecchia E Novellino F Mazza M Aschi G Pochetti 2008 Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could be exploited for drug design J Med Chem 51 7768 7776 1:CAS:528:DC%2BD1cXhsVWisb7I 10.1021/jm800733h 19053776
43. L Mouawad D Perahia 1996 Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures J Mol Biol 258 393 410 1:CAS:528:DyaK28Xislajt7w%3D 10.1006/jmbi.1996.0257 8627633 (Pubitemid 26131739)
44. L Nagy JW Schwabe 2004 Mechanism of the nuclear receptor molecular switch Trends Biochem Sci 29 317 324 1:CAS:528:DC%2BD2cXlsFentb4%3D 10.1016/j.tibs.2004.04.006 15276186 (Pubitemid 38968764)
45. K Nam V Maiorov B Feuston S Kearsley 2006 Dynamic control of allosteric antagonism of leukocyte function antigen-1 and intercellular adhesion molecule-1 interaction Proteins 64 376 384 1:CAS:528:DC%2BD28Xms1WmurY%3D 10.1002/prot.20999 16705652 (Pubitemid 43993646)
46. KW Nettles J Sun JT Radek S Sheng AL Rodriguez JA Katzenellenbogen BS Katzenellenbogen GL Greene 2004 Allosteric control of ligand selectivity between estrogen receptors alpha and beta: implications for other nuclear receptors Mol Cell 13 317 327 1:CAS:528:DC%2BD2cXhs1Cgtrk%3D 10.1016/S1097-2765(04)00054-1 14967140 (Pubitemid 38229805)
47. RT Nolte GB Wisely S Westin JE Cobb MH Lambert R Kurokawa MG Rosenfeld TM Willson CK Glass MV Milburn 1998 Ligand binding and co-activator assembly of the peroxisome proliferator- activated receptor-gamma Nature 395 137 143 1:CAS:528:DyaK1cXmtVekt7k%3D 10.1038/25931 9744270 (Pubitemid 28425645)
48. T Ostberg S Svensson G Selen J Uppenberg M Thor M Sundbom M Sydow-Backman AL Gustavsson L Jendeberg 2004 A new class of peroxisome proliferator-activated receptor agonists with a novel binding epitope shows antidiabetic effects J Biol Chem 279 41124 41130 10.1074/jbc.M401552200 15258145 (Pubitemid 39287714)
49. JP Renaud D Moras 2000 Structural studies on nuclear receptors Cell Mol Life Sci 57 1748 1769 1:CAS:528:DC%2BD3MXhsFKgsQ%3D%3D 10.1007/PL00000656 11130180
50. P Sauerberg I Pettersson L Jeppesen PS Bury JP Mogensen K Wassermann CL Brand J Sturis HF Woldike J Fleckner AS Andersen SB Mortensen LA Svensson HB Rasmussen SV Lehmann Z Polivka K Sindelar V Panajotova L Ynddal EM Wulff 2002 Novel tricyclic-alpha-alkyloxyphenylpropionic acids: dual PPARalpha/gamma agonists with hypolipidemic and antidiabetic activity J Med Chem 45 789 804 1:CAS:528:DC%2BD38XlvFSitA%3D%3D 10.1021/jm010964g 11831892 (Pubitemid 34173932)
51. MSM Schaefer M Karplus 1997 pH-dependence of protein stability: absolute electrostatic free energy differences between conformations J Phys Chem B 101 1663 1683 1:CAS:528:DyaK2sXpslWgsA%3D%3D 10.1021/jp962972s
52. F Tama M Valle J Frank CL Brooks 3rd 2003 Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc Natl Acad Sci USA 100 9319 9323 1:CAS:528:DC%2BD3sXmtlykt7c%3D 10.1073/pnas.1632476100 12878726 (Pubitemid 37033926)
53. A Thomas MJ Field D Perahia 1996 Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes J Mol Biol 261 490 506 1:CAS:528:DyaK28XltlKisLs%3D 10.1006/jmbi.1996.0478 8780788 (Pubitemid 26335902)
54. CJ Tsai A del Sol R Nussinov 2008 Allostery: absence of a change in shape does not imply that allostery is not at play J Mol Biol 378 1 11 1:CAS:528:DC%2BD1cXktVKisbs%3D 10.1016/j.jmb.2008.02.034 18353365
55. J Uppenberg C Svensson M Jaki G Bertilsson L Jendeberg A Berkenstam 1998 Crystal structure of the ligand binding domain of the human nuclear receptor PPARgamma J Biol Chem 273 31108 31112 1:CAS:528:DyaK1cXns1egtbo%3D 10.1074/jbc.273.47.31108 9813012 (Pubitemid 28533120)
56. S Verma PE Szmitko 2006 The vascular biology of peroxisome proliferator-activated receptors: modulation of atherosclerosis Can J Cardiol 22 (Suppl B) 12B 17B 16498507
57. HE Xu MH Lambert VG Montana KD Plunket LB Moore JL Collins JA Oplinger SA Kliewer RT Gampe Jr DD McKee JT Moore TM Willson 2001 Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors Proc Natl Acad Sci USA 98 13919 13924 1:CAS:528:DC%2BD3MXovVyntbk%3D 10.1073/pnas.241410198 11698662 (Pubitemid 33115999)