Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics

European Biophysics Journal

Volumn 38, Issue 1, 2008, Pages 25-35

  Li, Tong ^a   Froeyen, Matheus ^a   Herdewijn, Piet ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Aminoacyl tRNA synthetases; Hydrogen bond; KMSKS; Molecular dynamics; Tyrosyl tRNA synthetase

Indexed keywords

ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE; TYROSINE; TYROSINE TRANSFER RNA LIGASE;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME SUBSTRATE; HYDROGEN BOND; MOLECULAR DYNAMICS; NONHUMAN; RNA BINDING; STAPHYLOCOCCUS AUREUS;

CATALYSIS; COMPUTER SIMULATION; ENZYME ACTIVATION; ENZYME STABILITY; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; STAPHYLOCOCCUS AUREUS; SUBSTRATE SPECIFICITY; TYROSINE-TRNA LIGASE;

STAPHYLOCOCCUS AUREUS;

EID: 55349114344     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-008-0350-8     Document Type: Article

References (37)

1. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig 2000 The protein data bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235
2. TN Bhat DM Blow P Brick J Nyborg 1982 Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold J Mol Biol 158 699 709 10.1016/0022-2836(82)90255-8
3. tyr/TyrRS aminoacylation systems Biochimie 87 873 883 10.1016/j.biochi.2005.03.008
4. P Brick DM Blow 1987 Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine J Mol Biol 194 287 294 10.1016/0022-2836(87)90376-7
5. P Brick TN Bhat DM Blow 1989 Structure of tyrosyl-tRNA synthetase refined at 23 Å resolution. Interaction of the enzyme with the tyrosyl-adeylate intermediate. J Mol Biol 208 83 98 10.1016/0022-2836(89)90090-9
6. ME Budiman MH Knaggs JS Fetrow RW Alexander 2007 Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase Proteins 68 670 689 10.1002/prot.21426
7. Tyr interacts with both subunits Proc Natl Acad Sci USA 83 1189 1192 10.1073/pnas.83.5.1189
8. Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE et al (2006) AMBER 9. University of California, San Francisco
9. VM Dadarlat CB Post 2001 Insights into protein compressibility from molecular dynamics simulations J Phys Chem B 105 715 724 10.1021/jp0024118
10. T Darden D York L Pedersen 1993 Particle mesh Ewald: an NLog(N) method for Ewald sums in large systems J Chem Phys 98 10089 10092 10.1063/1.464397
11. Y Duan C Wu S Chowdhury MC Lee G Xiong W Zhang 2003 A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J Comput Chem 24 1999 2012 10.1002/jcc.10349
12. G Eriani M Delarue O Poch J Gangloff D Moras 1990 Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs Nature 347 203 206 10.1038/347203a0
13. AR Fersht JW Knill-Jones H Bedouelle G Winter 1988 Reconstruction by site-directed mutagenesis of the transition state for the activation of tyrosine by the tyrosyl-tRNA synthetase: a mobile loop envelopes the transition state in an induced-fit mechanism Biochemistry 27 1581 1587 10.1021/bi00405a028
14. H Gohlke LA Kuhn DA Case 2004 Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach Proteins 56 322 337 10.1002/prot.20116
15. C Hountondji P Dessen S Blanquet 1986 Sequence similarities among the family of aminoacyl-tRNA synthetases Biochimie 68 1071 1078 10.1016/S0300- 9084(86)80181-X
16. SJ Hughes JA Tanner AD Miller IR Gould 2006 Molecular dynamics simulations of LysRS: a asymmetric state Proteins 62 649 662 10.1002/prot.20609
17. M Ibba D Soll 2000 Aminoacyl-tRNA synthesis Annu Rev Biochem 69 617 650 10.1146/annurev.biochem.69.1.617
18. Jakalian A, Bush BL, Jack DB, Bayly CI (2000) Fast, efficient generation of high-quality atomic charges AM1-BCC model: I Method. J Comput Chem 21:132-146. doi:10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0. CO;2-P
19. WL Jorgensen 1982 Revised TIPS for simulations of liquid water and aqueous solutions J Chem Phys 77 4156 4163 10.1063/1.444325
20. WL Jorgensen J Chandrasekhar JD Madura RW Impey ML Klein 1983 Comparison of simple potential functions for simulating liquid water J Chem Phys 79 926 935 10.1063/1.445869
21. M Kapustina CW Carter 2006 Computational studies of Tryptophanyl-tRNA synthetase: activation of ATP by induced-fit J Mol Biol 362 1159 1180 10.1016/j.jmb.2006.06.078
22. T Kobayashi O Nureki R Ishitani A Yaremchuk M Tukalo S Cusack 2003 Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion Nat Struct Biol 10 425 429 10.1038/nsb934
23. T Kobayashi T Takimura R Sekine K Vincent K Kamata K Sakamoto 2005 Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase J Mol Biol 346 105 117 10.1016/j.jmb.2004. 11.034
24. M Kuratani H Sakai M Takahashi T Yanagisawa T Kobayashi K Murayama 2006 Crystal structures of tyrosyl-tRNA synthetases from Archaea J Mol Biol 355 395 408 10.1016/j.jmb.2005.10.073
25. McCammon JA, Harvey SC (1987) Dynamics of proteins and nucleic acids. Cambridge University Press, Cambridge
26. UA Ochsner X Sun T Jarvis I Critchley N Janjic 2007 Aminoacyl-trna synthetases: essential and still promising targets for new anti-infective agents Expert Opin Investig Drugs 16 573 593 10.1517/13543784.16.5.573
27. DA Pearlman DA Case JW Caldwell W Ross TE Cheatham III S DeBolt 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 Comput Phys Commun 91 1 41 10.1016/0010-4655(95)00041-D
28. EF Pettersen TD Goddard CC Huang GS Couch DM Greenblatt EC Meng 2004 UCSF chimera-a visualization system for exploratory research and analysis J Comput Chem 25 1605 1612 10.1002/jcc.20084
29. X Qiu CA Janson WW Smith SM Green P McDevitt K Johanson 2001 Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors Protein Sci 10 2008 2016 10.1110/ps.18001
30. P Retailleau Y Yin M Hu J Roach G Bricogne C Vonrhein 2001 High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5′AMP Acta Crystallogr D Biol Crystallogr 57 1595 1608 10.1107/S090744490101215X
31. JP Ryckaert G Ciccotti HJC Berendsen 1977 Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J Comput Phys 23 327 341 10.1016/0021-9991(77)90098-5
32. 2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions J Biol Chem 281 23792 23803 10.1074/jbc.M602870200
33. D Thompson P Plateau T Simonson 2006 Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase Chembiochem 7 337 344 10.1002/cbic.200500364
34. J Wang RM Wolf JW Caldwell PA Kollman DA Case 2004 Development and testing of a general amber force field J Comput Chem 25 1157 1174 10.1002/jcc.20035
35. G Winter GL Koch BS Hartley DG Barker 1983 The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus Eur J Biochem 132 383 387 10.1111/j.1432-1033.1983.tb07374.x
36. Tyr by tyrosyl-tRNA synthetase J Mol Biol 303 299 310 10.1006/jmbi.2000.4126
37. A Yaremchuk I Kriklivyi M Tukalo S Cusack 2002 Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition EMBO J 21 3829 3840 10.1093/emboj/cdf373