Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants

FEBS Open Bio

Volumn 4, Issue , 2014, Pages 496-509

  Dorosh, Lyudmyla ^a,b   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

Abscisic acid signaling; Constitutively active mutations; Essential collective dynamics analysis; Molecular dynamics simulations; Pyrabactin resistance

Indexed keywords

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

ARTICLE; IN VITRO STUDY; MOLECULAR DYNAMICS; MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; SIMULATION; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DIMERIZATION; ENZYME INHIBITION; GENE FREQUENCY; MOLECULAR INTERACTION; MUTANT; NONHUMAN; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SURFACE PROPERTY;

EID: 84902513708     PISSN: 22115463     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fob.2014.05.001     Document Type: Article

References (26)

1. Park S.Y., Fung P., Nishimura N., Jensen D.R., Fuji H., Zhao Y., Lumba S., Santiago J., Rodriguez A., Chow T.F., Alfred S.E., Bonetta D., Finkelstein R., Provart N.J., Desveaux D., Rodriguez P.L., McCourt P., Zhu J.K., Schroeder J.I., Volkman B.F., Cutler S.R. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 2009, 324:1068-1071.
2. Ma Y., Szostkiewicz I., Korte A., Moes D., Yang Y., Christmann A., Grill E. Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 2009, 324:1064-1068.
3. Santiago J., Dupeux F., Round A., Antoni R., Park S.Y., Jamin M., Cutler S.R., Rodriguez P.L., Marquez J.A. The abscisic acid receptor PYR1 in complex with abscisic acid. Nature 2009, 462:665-668.
4. Miyazono K., Miyukawa T., Sawano Y., Kubota K., Kang H.J., Asano A., Miyauchi Y., Takahashi M., Zhi Y., Fujita Y., Yoshida T., Kodaira K.S., Yamaquchi-Shinozaki K., Tanokura M. Structural basis of abscisic acid signaling. Nature 2009, 462:609-614.
5. Melcher K., Ng L.M., Zhou X.E., Soon F.F., Xu Y., Suino-Powell K.M., Park S.Y., Weiner J.J., Fujii H., Chinnusamy V., Kovach A., Li J., Wang Y., Li J., Peterson F.C., Jensen D.R., Young E.L., Volkman B.F., Cutler S.R., Zhu J.K., Xu H.E. A gate-latch-lock mechanism for hormone signaling by abscisic acid receptors. Nature 2009, 462:602-608.
6. Melcher K., Xu Y., Ng L.M., Zhou X.E., Soon F.F., Chinnusamy V., Suino-Powell K.M., Kovach A., Tham F.S., Cutler S.R., Li J., Yong E.L., Zhu J.K., Xu H.E. Identification and mechanism of ABA receptor. Nat. Struct. Mol. Biol. 2010, 17:1102-1108.
7. Hao Q., Yin P., Li W., Wang L., Yan C., Lin Z., Wu J.Z., Wang J., Yan S.F., Yan N. The molecular basis of ABA-independent inhibition of PP2C by a subclass of PYL proteins. Mol. Cell 2011, 42:662-672.
8. Mosquna A., Peterson F.C., Park S.Y., Lozano-Juste J., Volkman B.F., Cutler S.R. Potent and selective activation of abscisic acid receptors in vivo by mutational stabilization of their agonist-bound conformation. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:20838-20843.
9. Dupeux F., Santiago J., Betz K., Twycross J., Park S.Y., Rodriguez L., Gonzalez-Guzman M., Jensen M.R., Krasnogor N., Blackledge M., Holdsworth M., Cutler S.R., Rodriguez P.L., Marquez J.A. A thermodynamic switch modulates abscisic acid receptor sensitivity. EMBO J. 2011, 30:4171-4184.
10. Dorosh L., Kharenko O.A., Rajagopalan N., Loewen M.C., Stepanova M. Molecular mechanisms in the activation of abscisic acid receptor PYR1. PLoS Comput. Biol. 2013, 9(6):e1003114.
11. Stepanova M. Dynamics of essential collective motions in proteins: theory. Phys. Rev. E 2007, 76. 05191.
12. Blinov N., Berjanskii M., Wishart D.S., Stepanova M. Structural domains and main-chain flexibility in prion proteins. Biochemistry 2009, 48:1488-1497.
13. Potapov A., Stepanova M. Conformational modes in biomolecules: dynamics and approximate invariance. Phys. Rev. E 2012, 85. 020901(R).
14. Issack B.B., Berjanskii M., Wishart D.S., Stepanova M. Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers. Proteins Struct. Funct. Bioinf. 2012, 80:1847-1865.
15. Dupeux F., Antoni R., Betz K., Santiago J., Gonzalez-Guzman M., Rodriguez L., Rubio S., Park S.Y., Cutler S.R., Rodriguez P.L., Marquez J.A. Modulation of abscisic acid signaling in vivo by an engineered receptor-insensitive protein phosphatase type 2C allele. Plant Physiol. 2011, 156:106-116.
16. Peterson F.C., Burgie E.S., Park S.Y., Jensen D.R., Weiner J.J., Bingman C.A., Chang C.E., Cutler S.R., Phillips G.N., Volkman B.F. Structural basis for selective activation of ABA receptors. Nat. Struct. Mol. Biol. 2010, 17:1109-1113.
17. Nishimura N., Hitomi K., Arvai A.S., Rambo R.P., Hitomi C., Cutler S.R., Schroeder J.I., Getzoff E.D. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 2009, 326:1373-1379.
18. Yin P., Fan H., Hao Q., Yuan X., Wu D., Pang Y., Yan C., Li W., Wang J., Yan N. Structural insights into the mechanism of abscisic acid signaling by PYL proteins. Nat. Struct. Mol. Biol. 2009, 16:1230-1236.
19. Creighton T. Proteins 1984, Freeman, San-Francisco.
20. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 1977, 112:535-542.
21. Accelrys Software Inc. [Online]. (accessed May 26, 2011). http://www.accelrys.com/.
22. Berendsen H.J.C., van der Spoel D., van Drunen R. GROMACS - a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 1995, 91:43-56.
23. Santo K.P., Berjanskii M., Wishart D.S., Stepanova M. Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionary diverse prion proteins. Prion 2011, 5:188-200.
24. Barakat K., Issack B.B., Stepanova M., Tuszynski J. Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant. PLoS One 2011, 6:e27651.
25. Stueker O., Ortega V.A., Goss G.G., Stepanova M. Understanding interactions of functionalized nanoparticles with proteins: a case study on lactate dehydrogenase. Small 2014, 10:2006-2021.
26. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996, 14(33-8):27-28.