Multiple molecular dynamics simulation of the isoforms of human translation elongation factor 1A reveals reversible fluctuations between "open" and "closed" conformations and suggests specific for eEF1A1 affinity for Ca2+-calmodulin

BMC Structural Biology

Volumn 8, Issue , 2008, Pages

  Kanibolotsky, Dmitry S ^a,b   Novosyl'na, Oleksandra V ^a   Abbott, Catherine M ^c   Negrutskii, Boris S ^a   El'skaya, Anna V ^a  

^a INSTITUTE OF MOLECULAR BIOLOGY AND GENETICS   (Ukraine)

^b TARAS SHEVCHENKO NATIONAL UNIVERSITY OF KYIV   (Ukraine)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASPARAGINE; CALCIUM; CALMODULIN; CALMODULIN BINDING PROTEIN; ELONGATION FACTOR 1A1; ELONGATION FACTOR 1A2; GLYCINE; ISOPROTEIN; TRANSFER RNA; EEF1A1 PROTEIN, HUMAN; EEF1A2 PROTEIN, HUMAN; ELONGATION FACTOR 1;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; ENZYME LINKED IMMUNOSORBENT ASSAY; HUMAN; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN VARIANT; SIMULATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

EUKARYOTA;

AMINO ACID SEQUENCE; BINDING SITES; CALCIUM; CALMODULIN; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE ELONGATION FACTOR 1; PROTEIN CONFORMATION; PROTEIN ISOFORMS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

EID: 43049101171     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-8-4     Document Type: Article

References (47)

1. Eukaryotic translation elongation factor 1 alpha: structure, expression, functions, and possible role in aminoacyl-tRNA channeling. BS Negrutskii AV El'skaya, Prog Nucleic Acid Res Mol Biol 1998 60 47 78 9594571
2. Novel complexes of mammalian translation elongation factor eEF1A.GDP with uncharged tRNA and aminoacyl-tRNA synthetase. Implications for tRNA channeling. ZM Petrushenko TV Budkevich VF Shalak BS Negrutskii AV El'skaya, Eur J Biochem 2002 269 4811 4818 10.1046/j.1432-1033.2002.03178.x 12354112
3. Not just for housekeeping: protein initiation and elongation factors in cell growth and tumorigenesis. S Thornton N Anand D Purcell J Lee, J Mol Med 2003 81 536 548 10.1007/s00109-003-0461-8 12898041
4. Moonlighting functions of polypeptide elongation factor 1: from actin bundling to zinc finger protein R1-associated nuclear localization. S Ejiri, Biosci Biotechnol Biochem 2002 66 1 21 10.1271/bbb.66.1 11866090
5. The elongation factor 1 A-2 isoform from rabbit: cloning of the cDNA and characterization of the protein. S Kahns A Lund P Kristensen CR Knudsen BF Clark J Cavallius WC Merrick, Nucleic Acids Res 1998 26 1884 1890 9518480 10.1093/nar/26.8.1884
6. The translation elongation factor 1A in tumorigenesis, signal transduction and apoptosis: review article. A Lamberti M Caraglia O Longo M Marra A Abbruzzese P Arcari, Amino Acids 2004 26 443 448 10.1007/s00726-004- 0088-2 15290352
7. Protein elongation factor EEF1A2 is a putative oncogene in ovarian cancer. N Anand S Murthy G Amann M Wernick LA Porter IH Cukier C Collins JW Gray J Diebold DJ Demetrick JM Lee, Nat Genet 2002 31 301 305 12053177
8. Translation elongation factor eEF1A2 is a potential oncoprotein that is overexpressed in two-thirds of breast tumours. VA Tomlinson HJ Newbery NR Wray J Jackson A Larionov WR Miller JM Dixon CM Abbott, BMC Cancer 2005 5 113 16156888 10.1186/1471-2407-5-113
9. Expression of protein elongation factor eEF1A2 predicts favorable outcome in breast cancer. G Kulkarni DA Turbin A Amiri S Jeganathan MA Andrade-Navarro TD Wu DG Huntsman JM Lee, Breast Cancer Res Treat 2007 102 31 41 10.1007/s10549-006-9315-8 16897428
10. Location of seven post-translational modifications in rabbit elongation factor 1 alpha including dimethyllysine, trimethyllysine, and glycerylphosphorylethanolamine. TE Dever CE Costello CL Owens TL Rosenberry WC Merrick, J Biol Chem 1989 264 20518 20525 2511205
11. Structural Basis for Nucleotide Exchange and Competition with tRNA in the Yeast Elongation Factor Complex Eef1A:Eef1Ba. GR Andersen L Pedersen L Valente I Chatterjee TG Kinzy M Kjeldgaard J Nyborg, Mol Cell 2000 6 1261 10.1016/S1097-2765(00)00122-2 11106763
12. Crystal Structures of Nucleotide Exchange Intermediates in the Eef1A-Eef1Balpha Complex. GR Andersen L Valente L Pedersen TG Kinzy J Nyborg, Nat Struct Biol 2001 8 531 534 10.1038/88598 11373622
13. Calculation of nucleic acid conformation. S Louise-May P Auffinger E Westhof, Curr Opin Struct Biol 1996 6 289 298 10.1016/S0959-440X(96)80046-7 8804831
14. Multiple molecular dynamics simulations of the anticodon loop of tRNAAsp in aqueous solution with counterions. P Auffinger S Louise-May E Westhof, J Am Chem Soc 1995 117 6720 6726 10.1021/ja00130a011
15. Molecular dynamics simulations of the anticodon hairpin of tRNAAsp: structuring effects of C-H⋯O hydrogen bonds and of long-range hydration forces. P Auffinger S Louise-May E Westhof, J Am Chem Soc 1996 118 1181 1189 10.1021/ja952494j
16. A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns. AC Vaiana E Westhof P Auffinger, Biochimie 2006 88 1061 1073 10.1016/j.biochi.2006.06.006 16824662
17. Extended conformation of mammalian translation elongation factor 1A in solution. TV Budkevich AA Timchenko EI Tiktopulo BS Negrutskii VF Shalak ZM Petrushenko VL Aksenov R Willumeit J Kohlbrecher IN Serdyuk AV El'skaya, Biochemistry 2002 41 15342 15349 10.1021/bi026495h 12484773
18. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. P Nissen M Kjeldgaard S Thirup G Polekhina L Reshetnikova BF Clark J Nyborg, Science 1995 270 1453 1454 10.1126/science.270.5241.1464 7491488
19. The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. P Nissen S Thirup M Kjeldgaard J Nyborg, Structure 1999 7 143 156 10.1016/S0969-2126(99)80021-5 10368282
20. Elongation factor-1alpha stabilizes microtubules in a calcium/calmodulin-dependent manner. RC Moore NA Durso RJ Cyr, Cell Motil Cytoskeleton 1998 41 168 180 10.1002/(SICI)1097-0169(1998)41:2<168::AID- CM7>3.0.CO;2-A 9786091
21. Identification of elongation factor-1alpha as a Ca2+/calmodulin-binding protein in Tetrahymena cilia. H Ueno K Gonda T Takeda O Numata, Cell Motil Cytoskeleton 2003 55 51 60 10.1002/cm.10111 12673598
22. The Calmodulin Target Database. http://calcium.uhnres.utoronto.ca/ctdb/ flash.htm
23. Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition. P Radivojac S Vucetic TR O'Connor VN Uversky Z Obradovic AK Dunker, Proteins: Struct Funct Bioinf 2006 63 398 410 10.1002/prot.20873
24. SWISS-MODEL: an automated protein homology-modeling server. T Schwede J Kopp N Guex MC Peitsch, Nucleic Acids Research 2003 31 3381 3385 12824332 10.1093/nar/gkg520
25. Swiss-Model. An Automated Comparative Protein Modelling Server. http://swissmodel.expasy.org//SWISS-MODEL.html
26. The Crystal Structure of Sulfolobus Solfataricus Elongation Factor 1 Alpha in Complex with Gdp Reveals Novel Features in Nucleotide Binding and Exchange. L Vitagliano M Masullo F Sica A Zagari V Bocchini, EMBO J 2001 20 5305 5311 11574461 10.1093/emboj/20.19.5305
27. Comparison of NMR and MD N-H bond order parameters: example of HIV-1 protease. DS Kanibolotsky OS Ivanova VV Lisnyak, Molecular Simulation 2006 32 1155 1163 10.1080/08927020601078489
28. GROMACS. 3.0: a package for molecular simulation and trajectory analysis. E Lindahl B Hess D van der Spoel, J Mol Mod 2001 7 306 317
29. GROMACS: Fast, Free and Flexible MD. http://www.gromacs.org
30. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. LD Schuler X Daura WF van Gunsteren, J Comput Chem 2001 22 1205 1218 10.1002/jcc.1078
31. PRODRG - a tool for high-throughput crystallography of protein-ligand complexes. AW Schuettelkopf DMF van Aalten, Acta Crystallographica D 2004 60 1355 1363
32. The Dundee PRODRG2 Server. http://davapc1.bioch.dundee.ac.uk/programs/ prodrg/prodrg.html
33. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. PH Hunenberger JA McCammon, Biophys Chem 1999 78 69 88 10.1016/S0301-4622(99)00007-1 10343384
34. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. W Weber PH Hunenberger JA McCammon, J Phys Chem B 2000 104 3668 3675 10.1021/jp9937757
35. Interaction models for water in relation to protein hydration. HJC Berendsen JPM Postma WF van Gunsteren J Hermans, Intermolecular Forces Dordrecht: D. Reidel Publishing Company, Pullman B, 1981 331 342
36. LINCS: A linear constraint solver for molecular simulations. B Hess H Bekker HJC Berendsen JGEM Fraaije, J Comp Chem 1997 18 1463 1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
37. A smooth particle mesh Ewald method. U Essman L Perela ML Berkowitz T Darden H Lee LG Pedersen, J Chem Phys 1995 103 8577 8592 10.1063/1.470117
38. Molecular dynamics with coupling to an external bath. HJC Berendsen JPM Postma A DiNola JR Haak, J Chem Phys 1984 81 3684 3690 10.1063/1.448118
39. Convergence of sampling in protein simulations. B Hess, Phys Rev E 2002 65 3 031910, 1 10 10.1103/PhysRevE.65.031910
40. VMD - Visual Molecular Dynamics. W Humphrey A Dalke K Schulten, J Molec Graphics 1996 14 33 38 10.1016/0263-7855(96)00018-5
41. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. N Guex MC Peitsch, Electrophoresis 1997 18 2714 2723 10.1002/elps.1150181505 9504803
42. A fast and effective method for purification of elongation factor 1+ from rabbit liver. VF Shalak TV Budkevich BS Negrutskii AV El'skaya, Ukr Biokhim Zh 1997 69 104 109 9463227
43. Biological characterization of various forms of elongation factor 1 from rabbit reticulocytes. MD Carvalho JF Carvalho WC Merrick, Arch Biochem Biophys 1984 234 603 611 10.1016/0003-9861(84)90310-2 6568109
44. Ca2+-induced hydrophobic site on calmodulin: Application for purification of calmodulin by phenyl-Sepharose affinity chromatography. R Gopalakrishna WB Anderson, Biochem Biophys Res Commun 1982 73 830 836
45. Domain and nucleotide dependence of the interaction between Saccharomyces cerevisiae translation elongation factors 3 and 1A. M Anand B Balar R Ulloque SR Gross TG Kinzy, J Biol Chem 2006 281 32318 32326 10.1074/jbc.M601899200 16954224
46. Instantaneous computations of applied and scientific problems. High-performance computing cluster. http://www.cluster.kiev.ua/eng/?about
47. Supercomputers of Institute of Cybernetics NAS of Ukraine. Rapid computations of any complexity tasks. https://cluster.icyb.kiev.ua