Dynamical networks in tRNA: Protein complexes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 16, 2009, Pages 6620-6625

  Sethi, Anurag ^a   Eargle, John ^a   Black, Alexis A ^a   Luthey Schulten, Zaida ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Aminoacyl tRNA synthetase; Communication networks; Community; Suboptimal paths

Indexed keywords

MONOMER; NUCLEOTIDE; PROTEIN; TRANSFER RNA; AMINOACYL TRANSFER RNA; GLUTAMATE TRANSFER RNA LIGASE; LEUCINE TRANSFER RNA LIGASE; TRNA, GLUTAMIC ACID; TRNA, GLUTAMIC ACID-; TRNA, LEUCINE; TRNA, LEUCINE-;

ALLOSTERISM; ARTICLE; CATALYSIS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR SIZE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; AMINOACYLATION; ARCHAEBACTERIUM; BACTERIUM; COMPUTER SIMULATION; ENZYMOLOGY; METABOLISM; PROTEIN SECONDARY STRUCTURE;

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEA; BACTERIA; COMPUTER SIMULATION; GLUTAMATE-TRNA LIGASE; LEUCINE-TRNA LIGASE; PROTEIN STRUCTURE, SECONDARY; RNA, TRANSFER, AMINO ACYL; TRANSFER RNA AMINOACYLATION;

EID: 66149086947     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0810961106     Document Type: Article

References (31)

1. Ibba M, Francklyn C, Cusack S, eds (2005) The Aminoacyl-tRNA Synthetases (Landes Bioscience, Georgetown, TX).
2. Sekine S, et al. (2003) ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J 22:676-688.
3. Changeux J, Edelstein S (2005) Allosteric mechanisms of signal transduction. Science 308:1424-1428.
4. Miyashita O, Onuchic J, Wolynes P (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci USA 100:12570-12575.
5. Hyeon C, Lorimer G, Thirumalai D (2006) Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci USA 103:18939-18944.
6. Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 17:633-640.
7. Amaro RE, Sethi A, Myers RS, Davisson VJ, Luthey-Schulten ZA (2007) A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry 46:2156-2173.
8. Hammes-Schiffer S, Benkovic S (2006) Relating protein motion to catalysis. Annu Rev Biochem 75:519-541.
9. Aszó i A, Taylor W (1993) Connection topology of proteins. Comput Appl Biosci 9:523-529.
10. del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol 2:1-12.
11. Ghosh A, Vishveshwara S (2007) A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc Natl Acad Sci USA 104:15711-6.
12. Chennubhotla C, Bahar I (2006) Markov propagation of allosteric effects in biomolec-ular systems: Application to GroEL-GroES. Mol Syst Biol 2:36.
13. Girvan M, Newman M (2002) Community structure in social and biological networks. Proc Natl Acad Sci USA 99:7821-7826.
14. Palla G, Deré nyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814-818.
15. Frugier M, Florentz C, Giegé , R (1992) Anticodon-independent aminoacylation of an RNA minihelix with valine. Proc Natl Acad Sci USA 89:3990-3994.
16. Sekine S, et al. (1996) Major identity determinants in the ''augmented D helix'' of tRNAGlu from Escherichia coli. J Mol Biol 256:685-700.
17. Perona JJ, Rould MA, Steitz TA (1993) Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry 32:8758-8771.
18. Sekine S, Nureki O, Tateno M, Yokoyama S (1999) The identity determinants required for the discrimination between tRNAGlu and tRNAAsp by glutamyl-tRNA synthetase from Escherichia coli. Eur J Biochem 261:354-360.
19. Fukunaga R, Yokoyama S (2005) Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. J Mol Biol 346:57-71.
20. Cusack S, Yaremchuk A, Tukalo M (2000) The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J 19:2351-2361.
21. Eswar N, Eramian D, Webb B, Shen M, Sali A (2008) Protein structure modeling with MODELLER. Methods Mol Biol 426:145-159.
22. Foloppe N, MacKerrell AD, Jr (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21:86-104.
23. Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802.
24. Eargle J, Black AA, Sethi A, Trabuco LG, Luthey-Schulten Z (2008) Dynamics of recognition between tRNA and elongation factor Tu. J Mol Biol 377:1382-1405.
25. Glykos NM (2006) Software news and updates. CARMA: A molecular dynamics analysis program. J Comput Chem 27:1765-1768.
26. Sethi A, O'Donoghue P, Luthey-Schulten Z (2005) Evolutionary profiles from the QR factorization of multiple sequence alignments. Proc Natl Acad Sci USA 102:4045-4050.
27. Roberts E, Eargle J, Wright D, Luthey-Schulten Z (2006) MultiSeq: Unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics 7:382.
28. Humphrey W, Dalke A, Schulten K (1996) VMD - Visual molecular dynamics. J Mol Graphics 14:33-38.
29. Newman M, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E 69:026113.
30. Newman M (2006) Modularity and community structure in networks. Proc Natl Acad Sci USA 103:8577-8582.
31. Rosvall M, Bergstrom C (2008) Maps of random walks on complex networks reveal community structure. Proc Natl Acad Sci USA 105:1118-1123.