Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1

PLoS Computational Biology

Volumn 9, Issue 6, 2013, Pages

  Dorosh, Lyudmyla ^a,b   Kharenko, Olesya A ^a   Rajagopalan, Nandhakishore ^a   Loewen, Michele C ^a,c   Stepanova, Maria ^a,b  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DIMERS; LIGANDS; PROTEINS; STABILITY;

ABSCISIC ACID; ABSCISIC ACID RESPONSE; ACID RECEPTORS; COMPETITIVE INTERACTIONS; DOWNSTREAM TARGET; HOMODIMERS; IN-VITRO; LIGAND BINDING; MOLECULAR MECHANISM; MONOMERICS;

MOLECULAR DYNAMICS;

ABSCISIC ACID; PHOSPHOPROTEIN PHOSPHATASE 2; PHOSPHOPROTEIN PHOSPHATASE 2C; PYRABACTIN RESISTANCE 1; RECEPTOR PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; COMPETITIVE INHIBITION; CONTROLLED STUDY; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REGULATORY MECHANISM; SEQUENCE HOMOLOGY;

EID: 84879544169     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003114     Document Type: Article

References (47)

1. Leung J, Giraudat J, (1998) Abscisic acid signal transduction. Annu Rev Plant Physiol Plant Mol Biol 49: 199-222.
2. Nambara E, Marion-Poll A, (2005) Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol 56: 165-185.
3. Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR, (2010) Abscisic acid: emergence of a core signaling network. Annu Rev Plant Biol 61: 651-679.
4. Hirayama T, Shinozaki K, (2007) Perception and transduction of abscisic acid signals: keys to the function of the versatile plant hormone ABA. Trends Plant Sci 12: 343-351.
5. Klingler JP, Batelli G, Zhu JK, (2010) ABA receptors: the START of a new paradigm in phytohormone signaling. J Exp Bot 61: 3199-3210.
6. Ma Y, Szostkiewicz I, Korte A, Moes D, Yang Y, et al. (2009) Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 324: 1064-1068.
7. Park SY, Fung P, Nishimura N, Jensen DR, Fuji H, et al. (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324: 1068-1071.
8. Santiago J, Dupeux F, Round A, Antoni R, Park SY, et al. (2009) The abscisic acid receptor PYR1 in complex with abscisic acid. Nature 462: 665-668.
9. Nishimura N, Hitomi K, Arvai AS, Rambo RP, Hitomi C, et al. (2009) Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 326: 1373-1379.
10. Peterson FC, Burgie ES, Park SY, Jensen DR, Weiner JJ, et al. (2010) Structural basis for selective activation of ABA receptors. Nat Struct Mol Biol 17: 1109-1113.
11. Melcher K, Ng LM, Zhou XE, Soon FF, Xu Y, et al. (2009) A gate-latch-lock mechanism for hormone signaling by abscisic acid receptors. Nature 462: 602-608.
12. Miyazono K, Miyukawa T, Sawano Y, Kubota K, Kang HJ, et al. (2009) Structural basis of abscisic acid signaling. Nature 462: 609-614.
13. Hubbard KE, Nishimura N, Hitomi K, Getzoff ED, Schroeder JI, (2010) Early abscisic acid signal transduction mechanisms: newly discovered components and newly emerging questions. Genes & Dev 24: 1695-1708.
14. Melcher K, Xu Y, Ng LM, Zhou XE, Soon FF, et al. (2010) Identification and mechanism of ABA receptor. Nat Struct Mol Biol 17: 1102-1108.
15. Hao Q, Yin P, Li W, Wang L, Yan C, et al. (2011) The molecular basis of ABA-independent inhibition of PP2C by a subclass of PYL proteins. Mol Cell 42: 662-672.
16. Dupeux F, Santiago J, Betz K, Twycross J, Park SY, et al. (2011) A thermodynamic switch modulates abscisic acid receptor sensitivity. EMBO J 30: 4171-4184.
17. Dupeux F, Antoni R, Betz K, Santiago J, Gonzalez-Guzman M, et al. (2011) Modulation of abscisic acid signaling in vivo by an engineered receptor-insensitive protein phosphatase type 2C allele. Plant Physiol 156: 106-116.
18. Mosquna A, Peterson FC, Park SY, Lozano-Juste J, Volkman BF, et al. (2012) Potent and selective activation of abscisic acid receptors in vivo by mutational stabilization of their agonist-bound conformation. Proc Nat Acad Sci USA 108: 20838-43.
19. Wieligmann K, Pineda De Castro LF, Zacharias M, (2002) Molecular dynamics simulations of the free and complexed N-terminal SH2 domain of SHP-2. In Silico Biol 2: 305-311.
20. Peters GH, Frimurer TM, Andersen JN, Olsen OH, (2000) Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. Substrate-enzyme interactions and dynamics. Biophys J 78: 2191-2200.
21. Ashokan K, (2010) Docking studies on abscisic acid receptor pyrabactin receptor 1 (PYR1) and pyrabactin-like receptor (PYL1). Int J Environm Studies 1: 314-322.
22. Noguti T, Go N, (1985) Efficient Monte Carlo method for simulation of fluctuating conformations of native protein. Biopolymers 24: 527-546.
23. Garcia A, (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68: 2696-2699.
24. Amadei A, Linssen AB, Berendsen HJ, (1993) Essential dynamics of proteins. Proteins Struct Funct Genetics 17: 412-425.
25. Emberly EG, Mukhopadhyay R, Wingreen NS, Tang C, (2003) Flexibility of alpha-helices: Results on a statistical analysis of database protein structures. J Mol Biol 327: 229-237.
26. Tozzini V, (2005) Coarse-grained models for proteins. Curr Opin Struct Biol 15: 144-150.
27. Yesylevskyy SO, Kharkyanen VN, Demchenko AP, (2006) Dynamic protein domains: identification, interdependence, and stability. Biophys J 91: 670-685.
28. Sakuraba S, Joti Y, Kitao A, (2010) Detecting coupled collective motions in protein by independent subspace analysis. J Chem Phys 133: 185102.
29. Zhuravlev PI, Papoian GA, (2010) Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Q Rev Biophys 43: 295-332.
30. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatam III TE, et al. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Comm 91: 1-41.
31. Stepanova M, (2007) Dynamics of essential collective motions in proteins: Theory. Phys Rev E 76: 051918-15.
32. Blinov N, Berjanskii M, Wishart DS, Stepanova M, (2009) Structural domains and main-chain flexibility in prion proteins. Biochemistry 48: 1488-1497.
33. Potapov A, Stepanova M, (2012) Conformational modes in biomolecules: Dynamics and approximate invariance. Phys Rev E 85: 020901-4.
34. Issack BB, Berjanskii M, Wishart DS, Stepanova M, (2012) Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers. Proteins Str Funct Bioinorm 80: 1847-65.
35. Santo KP, Berjanskii M, Wishart DS, Stepanova M, (2011) Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionary diverse prion proteins. Prion 5: 188-200.
36. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice Jr MD, et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 112: 535-542.
37. Halle B, (2002) Flexibility and packing in proteins. Proc Nat Acad Sci USA 99: 1274-1279.
38. Zhang X, Zhang Q, Xin Q, Yu L, Wang Z, et al. (2012) Complex structures of the abscisic acid receptor PYL3/RCAR13 reveal a unique regulatory mechanism. Structure 20: 780-790.
39. Antoni R, Gonzalez-Guzman M, Rodriguez L, Rodriguez A, Pizzio GA, et al. (2012) Selective inhibition of clade a phosphatases type 2C by PYR/PYL/RCAR abscisic acid receptors. Plant Physiol 158: 970-980.
40. Accelrys Discovery Studio, version 3.0.0.10321. Available: http://accelrys.com/. Accessed May 26, 2011.
41. Sousa Da Silva AW, Vranken WF, (2012) ACPYPE- AnteChamber PYthon Parser interface. BMC Res Notes 5: 1-8.
42. Ribeiro A, Horta B, de Alencastro R, (2008) MKTOP: A program for automatic construction of molecular topologies. J Braz Chem Soc 19: 1433-1435.
43. Berendsen HJC, van der Spoel D, van Drunen R, (1995) GROMACS- A message-passing parallel molecular dynamics implementation. Comp Phys Comm 91: 43-56.
44. Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, et al. (2010) AMBER 11. San Francisco: University of California.
45. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR, (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
46. Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-8, 27-8.
47. Barakat K, Issack BB, Stepanova M, Tuszynski J, (2011) Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant. PLoS One 6: e27651.