Motion and flexibility in human cytochrome P450 aromatase

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Jiang, Wenhua ^a   Ghosh, Debashis ^a  

^a SUNY UPSTATE MEDICAL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROSTENEDIONE; AROMATASE; EXEMESTANE; STEROID; CYTOCHROME P450; HEME;

ANALYTIC METHOD; ARTICLE; CATALYSIS; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENDOPLASMIC RETICULUM; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME KINETICS; ENZYME STRUCTURE; HINGE REGION; LIGAND BINDING; MEMBRANE BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NORMAL MODE ANALYSIS; PHYSICAL MODEL; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; BIOLOGY; CHEMISTRY; ENZYMOLOGY; FEMALE; HUMAN; LIPID BILAYER; METABOLISM; METHODOLOGY; MOTION; PLACENTA; PREGNANCY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

AROMATASE; CATALYSIS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; CYTOCHROME P-450 ENZYME SYSTEM; ENDOPLASMIC RETICULUM; FEMALE; HEME; HUMANS; LIPID BILAYERS; MOTION; PLACENTA; PREGNANCY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EID: 84857615120     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032565     Document Type: Article

References (36)

1. Ghosh D, Griswold J, Erman M, Pangborn W, (2009) Structural basis for androgen specificity and oestrogen synthesis in human aromatase. Nature 457: 219-223.
2. Ghosh D, Jiang W, Lo J, Egbuta C, (2011) Higher order organization of human placental aromatase. Steroids 76: 753-758.
3. Praporski S, Ng SM, Nguyen AD, Corbin CJ, Mechler A, Zheng J, Conley AJ, Martin LL, (2009) Organization of cytochrome P450 enzymes involved in sex steroid synthesis: protein-protein interactions in lipid membranes. J Bio Chem 284: 33224-33232.
4. Phan G, Benabdelhak H, Lascombe MB, Benas P, Rety S, et al. (2010) Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel. Structure 18: 507-517.
5. Tirion M, (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77: 1905-1908.
6. Go N, Noguti T, Nishikawa T, (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci USA 80: 3696-3700.
7. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M, (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4: 187-217.
8. Tama F, Gadea FX, Marques O, Sanejouand YH, (2000) Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 41: 1-7.
9. Taly A, Delarue M, Grutter T, Nilges M, Le Novere N, et al. (2005) Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys J 88: 3954-3965.
10. Bahar I, Atilgan AR, Erman B, (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2: 173-181.
11. Kovacs JA, Chacon P, Abagyan R, (2004) Predictions of protein flexibility: first-order measures. Proteins 56: 661-668.
12. Bahar I, Lezon TR, Bakan A, Shrivastava IH, (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 110: 1463-1497.
13. Dobbins SE, Lesk VI, Sternberg MJ, (2008) Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci U S A 105: 10390-10395.
14. Soheilifard R, Makarov DE, Rodin GJ, (2008) Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors. Phys Biol 5: 026008.
15. Ma J, (2004) New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci 5: 119-123.
16. Van Wynsberghe A, Li G, Cui Q, (2004) Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry 43: 13083-13096.
17. Tama F, Sanejouand YH, (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14: 1-6.
18. Brooks B, Karplus M, (1985) Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc Natl Acad Sci U S A 82: 4995-4999.
19. Ma J, Karplus M, (1998) The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc Natl Acad Sci U S A 95: 8502-8507.
20. Gohlke H, Kuhn LA, Case DA, (2004) Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 56: 322-337.
21. Steinberg IZ, Scheraga HA, (1963) Entropy changes accompanying association reactions of proteins. J Biol Chem 238: 172-181.
22. Forman-Kay JD, (1999) The 'dynamics' in the thermodynamics of binding. Nat Struct Biol 6: 1086-1087.
23. Catalano S, Barone I, Giordano C, Rizza P, Qi H, et al. (2009) Rapid estradiol/ERalpha signaling enhances aromatase enzymatic activity in breast cancer cells. Mol Endocrinol 23: 1634-1645.
24. Poulos TL, (2003) Cytochrome P450 flexibility. Proc Natl Acad Sci U S A 100: 13121-13122.
25. Scott EE, He YA, Wester MR, White MA, Chin CC, et al. (2003) An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution. Proc Natl Acad Sci U S A 100: 13196-13201.
26. Hong Y, Li H, Yuan YC, Chen S, (2010) Sequence-function correlation of aromatase and its interaction with reductase. The Journal of steroid biochemistry and molecular biology 118: 203-206.
27. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
28. Suhre K, Sanejouand YH, (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32: W610-614.
29. Zinser E, Sperka-Gottlieb CD, Fasch EV, Kohlwein SD, Paltauf F, et al. (1991) Phospholipid synthesis and lipid composition of subcellular membranes in the unicellular eukaryote Saccharomyces cerevisiae. J Bacteriol 173: 2026-2034.
30. Brown DJ, Dupont FM, (1989) Lipid Composition of Plasma Membranes and Endomembranes Prepared from Roots of Barley (Hordeum vulgare L.): Effects of Salt. Plant Physiol 90: 955-961.
31. Davison SC, Wills ED, (1974) Studies on the lipid composition of the rat liver endoplasmic reticulum after induction with phenobarbitone and 20-methylcholanthrene. Biochem J 140: 461-468.
32. Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38 27-38.
33. Chemical Computing Group (2009) Molecular Operating Environment. 2009.10 ed Montreal, Canada.
34. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041.
35. DeLano WL, (2002) The PyMOL molecular graphics system San Carlos, CA, USA DeLano Scientific.
36. Fogolari F, Brigo A, Molinari H, (2002) The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit 15: 377-392.