메뉴 건너뛰기




Volumn 7, Issue 1, 2012, Pages

A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; MESSENGER RNA; TRANSFER RNA;

EID: 84855301491     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029377     Document Type: Article
Times cited : (34)

References (41)
  • 1
    • 46049099976 scopus 로고    scopus 로고
    • Correlating ribosome function with high-resolution structures
    • Bashan A, Yonath A, (2008) Correlating ribosome function with high-resolution structures. Trends Microbiol 16: 326-335.
    • (2008) Trends Microbiol , vol.16 , pp. 326-335
    • Bashan, A.1    Yonath, A.2
  • 2
    • 39749138785 scopus 로고    scopus 로고
    • A structural understanding of the dynamic ribosome machine
    • Steitz TA, (2008) A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9: 242-253.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 242-253
    • Steitz, T.A.1
  • 3
    • 33646495214 scopus 로고    scopus 로고
    • Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps
    • Mitra K, Frank J, (2006) Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu Rev Biophys Biomol Struct 35: 299-317.
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , pp. 299-317
    • Mitra, K.1    Frank, J.2
  • 4
    • 49349091280 scopus 로고    scopus 로고
    • What we have learned from ribosome structures
    • Ramakrishnan V, (2008) What we have learned from ribosome structures. Biochem Soc Trans 36: 567-574.
    • (2008) Biochem Soc Trans , vol.36 , pp. 567-574
    • Ramakrishnan, V.1
  • 6
    • 0031028688 scopus 로고    scopus 로고
    • Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome
    • Rodnina MV, Savelsbergh A, Katunin VI, Wintermeyer W, (1997) Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385: 37-41.
    • (1997) Nature , vol.385 , pp. 37-41
    • Rodnina, M.V.1    Savelsbergh, A.2    Katunin, V.I.3    Wintermeyer, W.4
  • 7
    • 0014690239 scopus 로고
    • Studies on the formation of transfer ribonucleic acid-ribosome complexes. VI. Oligopeptide synthesis and translocation on ribosomes in the presence and absence of soluble transfer factors
    • Pestka S, (1969) Studies on the formation of transfer ribonucleic acid-ribosome complexes. VI. Oligopeptide synthesis and translocation on ribosomes in the presence and absence of soluble transfer factors. J Biol Chem 244: 1533-1539.
    • (1969) J Biol Chem , vol.244 , pp. 1533-1539
    • Pestka, S.1
  • 8
    • 84886634813 scopus 로고
    • Factor-free ("non-enzymic") and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes
    • Gavrilova LP, Kostiashkina OE, Koteliansky VE, Rutkevitch NM, Spirin AS, (1976) Factor-free ("non-enzymic") and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J Mol Biol 101: 537-552.
    • (1976) J Mol Biol , vol.101 , pp. 537-552
    • Gavrilova, L.P.1    Kostiashkina, O.E.2    Koteliansky, V.E.3    Rutkevitch, N.M.4    Spirin, A.S.5
  • 9
    • 34547111594 scopus 로고    scopus 로고
    • Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements
    • Kavran JM, Steitz TA, (2007) Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J Mol Biol 371: 1047-1059.
    • (2007) J Mol Biol , vol.371 , pp. 1047-1059
    • Kavran, J.M.1    Steitz, T.A.2
  • 10
    • 42949126723 scopus 로고    scopus 로고
    • Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation
    • Fei J, Kosuri P, MacDougall DD, Gonzalez RL Jr, (2008) Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell 30: 348-359.
    • (2008) Mol Cell , vol.30 , pp. 348-359
    • Fei, J.1    Kosuri, P.2    MacDougall, D.D.3    Gonzalez Jr., R.L.4
  • 12
    • 70349470607 scopus 로고    scopus 로고
    • Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation
    • Fei J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, et al. (2009) Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci U S A 106: 15702-15707.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 15702-15707
    • Fei, J.1    Bronson, J.E.2    Hofman, J.M.3    Srinivas, R.L.4    Wiggins, C.H.5
  • 13
    • 77952343336 scopus 로고    scopus 로고
    • Simulating activity of the bacterial ribosome
    • Trylska J, (2009) Simulating activity of the bacterial ribosome. Q Rev Biophys 42: 301-316.
    • (2009) Q Rev Biophys , vol.42 , pp. 301-316
    • Trylska, J.1
  • 14
    • 27644502679 scopus 로고    scopus 로고
    • Simulating movement of tRNA into the ribosome during decoding
    • Sanbonmatsu KY, Joseph S, Tung CS, (2005) Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A 102: 15854-15859.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15854-15859
    • Sanbonmatsu, K.Y.1    Joseph, S.2    Tung, C.S.3
  • 15
    • 24144478280 scopus 로고    scopus 로고
    • Exploring global motions and correlations in the ribosome
    • Trylska J, Tozzini V, McCammon JA, (2005) Exploring global motions and correlations in the ribosome. Biophys J 89: 1455-1463.
    • (2005) Biophys J , vol.89 , pp. 1455-1463
    • Trylska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 16
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • Tama F, Valle M, Frank J, Brooks CL 3rd, (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A 100: 9319-9323.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks III, C.L.4
  • 17
    • 77952717308 scopus 로고    scopus 로고
    • Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
    • Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, et al. (2010) Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 16: 1196-1204.
    • (2010) RNA , vol.16 , pp. 1196-1204
    • Whitford, P.C.1    Geggier, P.2    Altman, R.B.3    Blanchard, S.C.4    Onuchic, J.N.5
  • 18
    • 39749132831 scopus 로고    scopus 로고
    • Full correlation analysis of conformational protein dynamics
    • Lange OF, Grubmuller H, (2008) Full correlation analysis of conformational protein dynamics. Proteins 70: 1294-1312.
    • (2008) Proteins , vol.70 , pp. 1294-1312
    • Lange, O.F.1    Grubmuller, H.2
  • 19
    • 62649113018 scopus 로고    scopus 로고
    • Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1
    • Kamberaj H, van der Vaart A, (2009) Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. Biophys J 96: 1307-1317.
    • (2009) Biophys J , vol.96 , pp. 1307-1317
    • Kamberaj, H.1    van der Vaart, A.2
  • 20
    • 33749354360 scopus 로고    scopus 로고
    • Structure of the 70S ribosome complexed with mRNA and tRNA
    • Selmer M, Dunham CM, Murphy FVt, Weixlbaumer A, Petry S, et al. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935-1942.
    • (2006) Science , vol.313 , pp. 1935-1942
    • Selmer, M.1    Dunham, C.M.2    Murphy, F.V.3    Weixlbaumer, A.4    Petry, S.5
  • 22
    • 33745628037 scopus 로고    scopus 로고
    • The geometry of the ribosomal polypeptide exit tunnel
    • Voss NR, Gerstein M, Steitz TA, Moore PB, (2006) The geometry of the ribosomal polypeptide exit tunnel. J Mol Biol 360: 893-906.
    • (2006) J Mol Biol , vol.360 , pp. 893-906
    • Voss, N.R.1    Gerstein, M.2    Steitz, T.A.3    Moore, P.B.4
  • 26
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin EJ, Pande VS, (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J 88: 2472-2493.
    • (2005) Biophys J , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 28
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N⊕log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N⊕log(N) method for Ewald sums in large systems. J Chem Physics 98.
    • (1993) J Chem Physics , vol.98
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 29
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess B, Bekker H, Berendsen HJC, Fraaije JGEM, (1997) LINCS: A linear constraint solver for molecular simulations. 1997 18: 1463-1472.
    • (1997) 1997 , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 30
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi G, Donadio D, Parrinello M, (2007) Canonical sampling through velocity rescaling. J Chem Phys 126: 014101.
    • (2007) J Chem Phys , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 33
    • 67649412163 scopus 로고    scopus 로고
    • All-atom contact model for understanding protein dynamics from crystallographic B-factors
    • Li DW, Bruschweiler R, (2009) All-atom contact model for understanding protein dynamics from crystallographic B-factors. Biophys J 96: 3074-3081.
    • (2009) Biophys J , vol.96 , pp. 3074-3081
    • Li, D.W.1    Bruschweiler, R.2
  • 34
    • 26844561217 scopus 로고    scopus 로고
    • Symmetry at the active site of the ribosome: structural and functional implications
    • Agmon I, Bashan A, Zarivach R, Yonath A, (2005) Symmetry at the active site of the ribosome: structural and functional implications. Biol Chem 386: 833-844.
    • (2005) Biol Chem , vol.386 , pp. 833-844
    • Agmon, I.1    Bashan, A.2    Zarivach, R.3    Yonath, A.4
  • 36
    • 0034127361 scopus 로고    scopus 로고
    • Collective protein dynamics in relation to function
    • Berendsen HJ, Hayward S, (2000) Collective protein dynamics in relation to function. Curr Opin Struct Biol 10: 165-169.
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 165-169
    • Berendsen, H.J.1    Hayward, S.2
  • 37
    • 27744512500 scopus 로고    scopus 로고
    • Comparison of tRNA motions in the free and ribosomal bound structures
    • Wang Y, Jernigan RL, (2005) Comparison of tRNA motions in the free and ribosomal bound structures. Biophys J 89: 3399-3409.
    • (2005) Biophys J , vol.89 , pp. 3399-3409
    • Wang, Y.1    Jernigan, R.L.2
  • 38
    • 0037184536 scopus 로고    scopus 로고
    • Selection of tRNA by the ribosome requires a transition from an open to a closed form
    • Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V, (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721-732.
    • (2002) Cell , vol.111 , pp. 721-732
    • Ogle, J.M.1    Murphy, F.V.2    Tarry, M.J.3    Ramakrishnan, V.4
  • 39
    • 0030582394 scopus 로고    scopus 로고
    • Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice
    • Lata KR, Agrawal RK, Penczek P, Grassucci R, Zhu J, et al. (1996) Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. J Mol Biol 262: 43-52.
    • (1996) J Mol Biol , vol.262 , pp. 43-52
    • Lata, K.R.1    Agrawal, R.K.2    Penczek, P.3    Grassucci, R.4    Zhu, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.