Trp RNA-Binding Attenuation Protein: Modifying Symmetry and Stability of a Circular Oligomer

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Bayfield, Oliver W ^a   Chen, Chao Sheng ^a,c   Patterson, Andrea R ^b   Luan, Weisha ^a   Smits, Callum ^a   Gollnick, Paul ^b   Antson, Alfred A ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

^b UNIVERSITY AT BUFFALO   (United States)

^c NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR PROTEIN OLIGOMER; MUTANT PROTEIN; PROTEIN; TRYPTOPHAN; TRYPTOPHAN RNA BINDING ATTENUATION PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS; BACILLUS HALODURANS; BACILLUS SUBTILIS; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; FLUOROMETRY; GEOBACILLUS STEAROTHERMOPHILUS; MASS SPECTROMETRY; NANOBIOTECHNOLOGY; POINT MUTATION; PROTEIN STABILITY; PROTEIN STRUCTURE; RNA BINDING; THERMOSTABILITY;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; KINETICS; MASS SPECTROMETRY; MUTANT PROTEINS; PROTEIN BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; RNA-BINDING PROTEINS; TRANSCRIPTION FACTORS; TRANSITION TEMPERATURE; TRYPTOPHAN;

BACILLI (CLASS);

EID: 84866070607     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044309     Document Type: Article

References (30)

1. Minamino T, Imada K, Kinoshita M, Nakamura S, Morimoto YV, et al. (2011) Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor. PLoS Biology 9(5): e1000616.
2. Weber J, Senior AE, (2003) ATP synthesis driven by proton transport in F1F0-ATP synthase. Febs Letters 545(1): 61-70.
3. Rao VB, Feiss M, (2008) The Bacteriophage DNA Packaging Motor. Annual Review of Genetics 42: 647-81.
4. Casjens SR, (2011) The DNA-packaging nanomotor of tailed bacteriophages. Nature Reviews Microbiology 9(9): 647-57.
5. Lebedev AA, Krause MH, Isidro AL, Vagin AA, Orlova EV, et al. (2007) Structural framework for DNA translocation via the viral portal protein. Embo Journal 26(7): 1984-94.
6. Thomas DR, Francis NR, Xu C, DeRosier DJ, (2006) The three-dimensional structure of the flagellar rotor from a clockwise-locked mutant of Salmonella enterica serovar typhimurium. Journal of Bacteriology 188(20): 7039-48.
7. Wendell D, Jing P, Geng J, Subramaniam V, Lee TJ, et al. (2009) Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores. Nature Nanotechnology 4(11): 765-72.
8. Antson AA, Dodson EJ, Dodson G, Greaves RB, Chen XP, et al. (1999) Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401(6750): 235-42.
9. Chen C-S, Smits C, Dodson GG, Shevtsov MB, Merlino N, et al. (2011) How to Change the Oligomeric State of a Circular Protein Assembly: Switch from 11-Subunit to 12-Subunit TRAP Suggests a General Mechanism. PLoS ONE 6(10): e25296.
10. Gollnick P, Babitzke P, Antson A, Yanofsky C, (2005) Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annual Review of Genetics 39: 47-68.
11. Heddle JG, Fujiwara I, Yamadaki H, Yoshii S, Nishio K, et al. (2007) Using the ring-shaped protein TRAP to capture and confine gold nanodots on a surface. Small 3(11): 1950-6.
12. Miranda FF, Iwasaki K, Akashi S, Sumitomo K, Kobayashi M, et al. (2009) A Self-Assembled Protein Nanotube with High Aspect Ratio. Small 5(18): 2077-84.
13. McElroy CA, Manfredo A, Gollnick P, Foster MP, (2006) Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein. Biochemistry 45(25): 7844-53.
14. McElroy C, Manfredo A, Wendt A, Gollnick P, Foster M, (2002) TROSY-NMR studies of the 91 kDa TRAP protein reveal allosteric control of a gene regulatory protein by ligand-altered flexibility. Journal of Molecular Biology 323(3): 463-73.
15. Malay AD, Watanabe M, Heddle JG, Tame JRH, (2011) Crystal structure of unliganded TRAP: implications for dynamic allostery. Biochemical Journal 434: 427-34.
16. Ruotolo BT, Giles K, Campuzano I, Sandercock AM, Bateman RH, et al. (2005) Evidence for macromolecular protein rings in the absence of bulk water. Science 310(5754): 1658-61.
17. Chen XP, Antson AA, Yang M, Li P, Baumann C, et al. (1999) Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus. Journal of Molecular Biology 289(4): 1003-16.
18. Antson AA, Otridge J, Brzozowski AM, Dodson EJ, Dodson GG, et al. (1995) The structure of trp RNA-binding attenuation protein. Nature 374(6524): 693-700.
19. Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromolecular Crystallography, Pt A 276: 307-26.
20. Bailey S, (1994) The CCP4 Suite- programs for protein crystallography. Acta Crystallographica Section D-Biological Crystallography. 50: 760-3.
21. Vagin A, Teplyakov A, (2000) An approach to multi-copy search in molecular replacement. Acta Crystallographica Section D-Biological Crystallography 56: 1622-4.
22. Murshudov GN, Vagin AA, Lebedev A, Wilson KS, Dodson EJ, (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallographica Section D- Biological Crystallography 55: 247-55.
23. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallographica Section D- Biological Crystallography 60: 2126-32.
24. Lamzin VS, Wilson KS, (1993) Automated refinement of protein models. Acta Crystallographica Section D- Biological Crystallography 49: 129-47.
25. Esnouf RM, (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. Journal of Molecular Graphics & Modelling 15(2): 132-134.
26. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera- A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25(13): 1605-12.
27. Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, et al. (2004) Developments in the CCP4 molecular-graphics project. Acta Crystallographica Section D- Biological Crystallography 60: 2288-94.
28. Niesen FH, Berglund H, Vedadi M, (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nature Protocols 2(9): 2212-21.
29. Ericsson UB, Hallberg BM, DeTitta GT, Dekker N, Nordlund P, (2006) Thermofluor-based high-throughput stability optimization of proteins for structural studies. Analytical Biochemistry 357(2): 289-98.
30. Li PTX, Gollnick P, (2004) Characterization of a trp RNA-binding attenuation protein (TRAP) mutant with tryptophan independent RNA binding activity. Journal of Molecular Biology 335(3): 707-22.