Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma

by: apryl
December 2, 2007
6583 views
URL
Embed
Share

Please describe the reason for abuse:



Linked profiles:
Rommie, SDSC
Article:
Peer-Reviewed Paper, View Original
Description:
RNA editing ligase 1 (TbREL1) is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei, the parasite... » More
Citation:
PLoS Negl Trop Dis. 2007 Nov 14; 1(2):e68
Authors:
Rommie e. Amaro, Robert v. Swift, J. andrew Mccammon

Loading comments
  1. .
  2. Cross GA (2005) Trypanosomes at the gates.. Science 309: 355.
  3. Fairlamb AH (2003) Chemotherapy of human African trypanosomiasis: current and future prospects.. Trends Parasitol 19: 488-494.
  4. Stuart K, Allen TE, Heidmann S, Seiwert SD (1997) RNA editing in kinetoplastid protozoa.. Microbiol Mol Biol Rev 61: 105-120.
  5. Stuart KD, Schnaufer A, Ernst NL, Panigrahi AK (2005) Complex management: RNA editing in trypanosomes.. Trends Biochem Sci 30: 97-105.
  6. Simpson L, Sbicego S, Aphasizhev R (2003) Urididine insertion/deletion RNA editing in trypanosome mitochondria: A complex business.. RNA 9: 265-276.
  7. Worthey EA, Schnaufer A, Mian IS, Stuart K, Salavati R (2003) Comparative analysis of editosome proteins in trypanosomatids.. Nucleic Acids Res 31: 6392-6408.
  8. Panigrahi AK, Ernst NL, Domingo GJ, Fleck M, Salavati R (2006) Compositionally and functionally distinct editosomes in Trypanosoma brucei.. Rna 12: 1038-1049.
  9. Blum B, Simpson L (1992) Formation of guide RNA/messenger RNA chimeric molecules in vitro, the initial step of RNA editing, is dependent on an anchor sequence.. Proc Natl Acad Sci U S A 89: 11944-11948.
  10. Seiwert SD, Heidmann S, Stuart K (1996) Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing.. Cell 84: 831-841.
  11. Schnaufer A, Panigrahi AK, Panicucci B, Igo RP, Wirtz E (2001) An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei.. Science 291: 2159-2162.
  12. Rusche LN, Huang CE, Piller KJ, Hemann M, Wirtz E (2001) The two RNA ligases of the Trypanosoma brucei RNA editing complex: cloning the essential band IV gene and identifying the band V gene.. Mol Cell Biol 21: 979-989.
  13. Schnaufer A, Ernst NL, Palazzo SS, O'Rear J, Salavati R (2003) Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex.. Mol Cell 12: 307-319.
  14. Deng J, Schnaufer A, Salavati R, Stuart KD, Hol WG (2004) High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1.. J Mol Biol 343: 601-613.
  15. Cherepanov AV, de Vries S (2002) Kinetic Mechanism of the Mg2+-dependent Nucleotidyl Transfer Catalyzed by T4 DNA and RNA Ligases.. J Biol Chem 277: 1695-1704.
  16. Ho CK, Shuman S (2002) Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains.. Proc Natl Acad Sci U S A 99: 12709-12714.
  17. Yin S, Ho CK, Shuman S (2003) Structure-function analysis of T4 RNA ligase 2.. J Biol Chem 278: 17601-17608.
  18. Ho CK, Wang LK, Lima CD, Shuman S (2004) Structure and mechanism of RNA ligase.. Structure 12: 327-339.
  19. Zhang L, Hermans J (1996) Hydrophilicity of cavities in proteins.. Proteins: Structure, Function, and Genetics 24: 433-438.
  20. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins.. J Phys Chem B 102: 3586-3616.
  21. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E (2005) Scalable molecular dynamics with NAMD.. J Comput Chem 26: 1781-1802.
  22. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water.. The Journal of Chemical Physics 79: 926-935.
  23. Feller S, Zhang Y, Pastor R, Brooks B (1995) Constant pressure molecular dynamics simulation: The Langevin piston method.. Journal of Chemical Physics 103: 4613.
  24. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems.. The Journal of Chemical Physics 98: 10089-10092.
  25. Shuman S, Lima CD (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases.. Curr Opin Struct Biol 14: 757-764.
  26. Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine kinase.. Science 289: 1938-1942.
  27. Noble ME, Endicott JA, Johnson LN (2004) Protein kinase inhibitors: insights into drug design from structure.. Science 303: 1800-1805.
  28. Suydam IT, Snow CD, Pande VS, Boxer SG (2006) Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory.. Science 313: 200-204.
  29. Huang CE, Cruz-Reyes J, Zhelonkina AG, O'Hearn S, Wirtz E (2001) Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair.. Embo J 20: 4694-4703.
  30. Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces.. Biopolymers 38: 305-320.