-
1
-
-
84864453599
-
-
Springer, Wien, New York
-
Rodnina, M.V., Wintermeyer, W. and Green, R. (2011) Ribosomes. Structure, Function, and Dynamics. Springer, Wien, New York.
-
(2011)
Ribosomes. Structure, Function, and Dynamics
-
-
Rodnina, M.V.1
Wintermeyer, W.2
Green, R.3
-
2
-
-
57549112237
-
Structural dynamics of the ribosome
-
Korostelev, A., Ermolenko, D.N. and Noller, H.F. (2008) Structural dynamics of the ribosome. Curr. Opin. Chem. Biol., 12, 674-683.
-
(2008)
Curr. Opin. Chem. Biol
, vol.12
, pp. 674-683
-
-
Korostelev, A.1
Ermolenko, D.N.2
Noller, H.F.3
-
3
-
-
70350654363
-
What recent ribosome structures have revealed about the mechanism of translation
-
Schmeing, T.M. and Ramakrishnan, V. (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature, 461, 1234-1242.
-
(2009)
Nature
, vol.461
, pp. 1234-1242
-
-
Schmeing, T.M.1
Ramakrishnan, V.2
-
4
-
-
60349097663
-
Single-molecule observations of ribosome function
-
Blanchard, S.C. (2009) Single-molecule observations of ribosome function. Curr. Opin. Struct. Biol., 19, 103-109.
-
(2009)
Curr. Opin. Struct. Biol
, vol.19
, pp. 103-109
-
-
Blanchard, S.C.1
-
5
-
-
77449133028
-
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-TU
-
Agirrezabala, X. and Frank, J. (2009) Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-TU. Q. Rev. Biophys., 42, 159-200.
-
(2009)
Q. Rev. Biophys
, vol.42
, pp. 159-200
-
-
Agirrezabala, X.1
Frank, J.2
-
6
-
-
77952928661
-
Ribosome structure and dynamics during translocation and termination
-
Dunkle, J.A. and Cate, J.H.D. (2010) Ribosome structure and dynamics during translocation and termination. Annu. Rev. Biophys., 39, 227-244.
-
(2010)
Annu. Rev. Biophys
, vol.39
, pp. 227-244
-
-
Dunkle, J.A.1
Cate, J.H.D.2
-
7
-
-
85027942948
-
From DNA to proteins via the ribosome: Structural insights into the workings of the translation machinery
-
Agirrezabala, X. and Frank, J. (2010) From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery. Hum. Genomics, 4, 226-237.
-
(2010)
Hum. Genomics
, vol.4
, pp. 226-237
-
-
Agirrezabala, X.1
Frank, J.2
-
8
-
-
77952693978
-
Single ribosome dynamics and the mechanism of translation
-
Aitken, C.E., Petrov, A. and Puglisi, J.D. (2010) Single ribosome dynamics and the mechanism of translation. Annu. Rev. Biophys., 39, 491-513.
-
(2010)
Annu. Rev. Biophys
, vol.39
, pp. 491-513
-
-
Aitken, C.E.1
Petrov, A.2
Puglisi, J.D.3
-
9
-
-
77953625418
-
Structure and dynamics of a processive Brownian motor: The translating ribosome
-
Frank, J. and Gonzalez, R.L. Jr (2010) Structure and dynamics of a processive Brownian motor: the translating ribosome. Annu. Rev. Biochem., 79, 381-412.
-
(2010)
Annu. Rev. Biochem
, vol.79
, pp. 381-412
-
-
Frank, J.1
Gonzalez Jr., R.L.2
-
10
-
-
79551680953
-
Dynamics of the translational machinery
-
Petrov, A., Kornberg, G., O'Leary, S., Tsai, A., Uemura, S. and Puglisi, J.D. (2011) Dynamics of the translational machinery. Curr. Opin. Struct. Biol., 21, 137-145.
-
(2011)
Curr. Opin. Struct. Biol
, vol.21
, pp. 137-145
-
-
Petrov, A.1
Kornberg, G.2
O'Leary, S.3
Tsai, A.4
Uemura, S.5
Puglisi, J.D.6
-
11
-
-
0034691576
-
A ratchet-like inter-subunit reorganization of the ribosome during translocation
-
Frank, J. and Agrawal, R.K. (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature, 406, 318-322.
-
(2000)
Nature
, vol.406
, pp. 318-322
-
-
Frank, J.1
Agrawal, R.K.2
-
12
-
-
0038275890
-
Study of the structural dynamics of the E. Coli 70s ribosome using real-space refinement
-
Gao, H., Sengupta, J., Valle, M., Korostelev, A., Eswar, N., Stagg, S.M., Van Roey, P., Agrawal, R.K., Harvey, S.C., Sali, A. et al. (2003) Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell, 113, 789-801.
-
(2003)
Cell
, vol.113
, pp. 789-801
-
-
Gao, H.1
Sengupta, J.2
Valle, M.3
Korostelev, A.4
Eswar, N.5
Stagg, S.M.6
Van Roey, P.7
Agrawal, R.K.8
Harvey, S.C.9
Sali, A.10
-
13
-
-
0037963475
-
Locking and unlocking of ribosomal motions
-
Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M. and Frank, J. (2003) Locking and unlocking of ribosomal motions. Cell, 114, 123-134.
-
(2003)
Cell
, vol.114
, pp. 123-134
-
-
Valle, M.1
Zavialov, A.2
Sengupta, J.3
Rawat, U.4
Ehrenberg, M.5
Frank, J.6
-
14
-
-
38049178477
-
The process of mRNA-tRNA translocation
-
Frank, J., Gao, H., Sengupta, J., Gao, N. and Taylor, D.J. (2007) The process of mRNA-tRNA translocation. Proc. Natl. Acad. Sci. USA, 104, 19671-19678.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 19671-19678
-
-
Frank, J.1
Gao, H.2
Sengupta, J.3
Gao, N.4
Taylor, D.J.5
-
15
-
-
54049116765
-
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome
-
Agirrezabala, X., Lei, J., Brunelle, J.L., Ortiz-Meoz, R.F., Green, R. and Frank, J. (2008) Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell, 32, 190-197.
-
(2008)
Mol. Cell
, vol.32
, pp. 190-197
-
-
Agirrezabala, X.1
Lei, J.2
Brunelle, J.L.3
Ortiz-Meoz, R.F.4
Green, R.5
Frank, J.6
-
16
-
-
55949134736
-
Structure of ratcheted ribosomes with tRNAs in hybrid states
-
Julian, P., Konevega, A.L., Scheres, S.H., Lazaro, M., Gil, D., Wintermeyer, W., Rodnina, M.V. and Valle, M. (2008) Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc. Natl Acad. Sci. USA, 105, 16924-16927.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 16924-16927
-
-
Julian, P.1
Konevega, A.L.2
Scheres, S.H.3
Lazaro, M.4
Gil, D.5
Wintermeyer, W.6
Rodnina, M.V.7
Valle, M.8
-
17
-
-
77954650144
-
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy
-
Fischer, N., Konevega, A.L., Wintermeyer, W., Rodnina, M.V. and Stark, H. (2010) Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature, 466, 329-333.
-
(2010)
Nature
, vol.466
, pp. 329-333
-
-
Fischer, N.1
Konevega, A.L.2
Wintermeyer, W.3
Rodnina, M.V.4
Stark, H.5
-
18
-
-
79953216748
-
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation
-
Fu, J., Munro, J.B., Blanchard, S.C. and Frank, J. (2011) Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation. Proc. Natl Acad. Sci. USA, 108, 4817-4821.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4817-4821
-
-
Fu, J.1
Munro, J.B.2
Blanchard, S.C.3
Frank, J.4
-
19
-
-
33748582906
-
Crystal structure of a 70s ribosome-tRNA complex reveals functional interactions and rearrangements
-
Korostelev, A., Trakhanov, S., Laurberg, M. and Noller, H.F. (2006) Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell, 126, 1065-1077.
-
(2006)
Cell
, vol.126
, pp. 1065-1077
-
-
Korostelev, A.1
Trakhanov, S.2
Laurberg, M.3
Noller, H.F.4
-
20
-
-
33749354360
-
Structure of the 70s ribosome complexed with mRNA and tRNA
-
Selmer, M., Dunham, C.M., Murphy, F.V. IV, Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R. and Ramakrishnan, V. (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 IV, F.V.3
Weixlbaumer, A.4
Petry, S.5
Kelley, A.C.6
Weir, J.R.7
Ramakrishnan, V.8
-
21
-
-
36749068384
-
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome
-
Korostelev, A., Trakhanov, S., Asahara, H., Laurberg, M., Lancaster, L. and Noller, H.F. (2007) Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome. Proc. Natl Acad. Sci. USA, 104, 16840-16843.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 16840-16843
-
-
Korostelev, A.1
Trakhanov, S.2
Asahara, H.3
Laurberg, M.4
Lancaster, L.5
Noller, H.F.6
-
22
-
-
69249118597
-
Formation of the first peptide bond: The structure of EF-P bound to the 70s ribosome
-
Blaha, G., Stanley, R.E. and Steitz, T.A. (2009) Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science, 325, 966-970.
-
(2009)
Science
, vol.325
, pp. 966-970
-
-
Blaha, G.1
Stanley, R.E.2
Steitz, T.A.3
-
23
-
-
69249112231
-
Structures of the ribosome in intermediate states of ratcheting
-
Zhang, W., Dunkle, J.A. and Cate, J.H.D. (2009) Structures of the ribosome in intermediate states of ratcheting. Science, 325, 1014-1017.
-
(2009)
Science
, vol.325
, pp. 1014-1017
-
-
Zhang, W.1
Dunkle, J.A.2
Cate, J.H.D.3
-
24
-
-
33847051154
-
Identification of two distinct hybrid state intermediates on the ribosome
-
Munro, J.B., Altman, R.B., O'Connor, N. and Blanchard, S.C. (2007) Identification of two distinct hybrid state intermediates on the ribosome. Mol. Cell, 25, 505-517.
-
(2007)
Mol. Cell
, vol.25
, pp. 505-517
-
-
Munro, J.B.1
Altman, R.B.2
O'Connor, N.3
Blanchard, S.C.4
-
25
-
-
42949126723
-
Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation
-
Fei, J., Kosuri, P., MacDougall, D.D. and Gonzalez, R.L. 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
-
26
-
-
44449125068
-
Spontaneous intersubunit rotation in single ribosomes
-
Cornish, P.V., Ermolenko, D.N., Noller, H.F. and Ha, T. (2008) Spontaneous intersubunit rotation in single ribosomes. Mol. Cell, 30, 578-588.
-
(2008)
Mol. Cell
, vol.30
, pp. 578-588
-
-
Cornish, P.V.1
Ermolenko, D.N.2
Noller, H.F.3
Ha, T.4
-
27
-
-
62449216538
-
Following movement of the L1 stalk between three functional states in single ribosomes
-
Cornish, P.V., Ermolenko, D.N., Staple, D.W., Hoang, L., Hickerson, R.P., Noller, H.F. and Ha, T. (2009) Following movement of the L1 stalk between three functional states in single ribosomes. Proc. Natl Acad. Sci. USA, 106, 2571-2576.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 2571-2576
-
-
Cornish, P.V.1
Ermolenko, D.N.2
Staple, D.W.3
Hoang, L.4
Hickerson, R.P.5
Noller, H.F.6
Ha, T.7
-
28
-
-
68249151083
-
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling
-
Sternberg, S.H., Fei, J., Prywes, N., McGrath, K.A. and Gonzalez, R.L. Jr (2009) Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat. Struct. Mol. Biol., 16, 861-868.
-
(2009)
Nat. Struct. Mol. Biol
, vol.16
, pp. 861-868
-
-
Sternberg, S.H.1
Fei, J.2
Prywes, N.3
McGrath, K.A.4
Gonzalez Jr., R.L.5
-
29
-
-
70349470607
-
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation
-
Fei, J., Bronson, J.E., Hofman, J.M., Srinivas, R.L., Wiggins, C.H. and Gonzalez, R.L. Jr (2009) Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc. Natl Acad. Sci. USA, 106, 15702-15707.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 15702-15707
-
-
Fei, J.1
Bronson, J.E.2
Hofman, J.M.3
Srinivas, R.L.4
Wiggins, C.H.5
Gonzalez Jr., R.L.6
-
30
-
-
76249114762
-
Spontaneous formation of the unlocked state on the ribosome is a multistep process
-
Munro, J.B., Altman, R.B., Tung, C.S., Cate, J.H., Sanbonmatsu, K.Y. and Blanchard, S.C. (2010) Spontaneous formation of the unlocked state on the ribosome is a multistep process. Proc. Natl Acad. Sci. USA, 107, 709-714.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 709-714
-
-
Munro, J.B.1
Altman, R.B.2
Tung, C.S.3
Cate, J.H.4
Sanbonmatsu, K.Y.5
Blanchard, S.C.6
-
31
-
-
77954383845
-
Following the intersubunit conformation of the ribosome during translation in real time
-
Aitken, C.E. and Puglisi, J.D. (2010) Following the intersubunit conformation of the ribosome during translation in real time. Nat. Struct. Mol. Biol., 17, 793-800.
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 793-800
-
-
Aitken, C.E.1
Puglisi, J.D.2
-
32
-
-
78649830457
-
Correlated conformational events in EF-G and the ribosome regulate translocation
-
Munro, J.B., Wasserman, M.R., Altman, R.B., Wang, L. and Blanchard, S.C. (2010) Correlated conformational events in EF-G and the ribosome regulate translocation. Nat. Struct. Mol. Biol., 17, 1470-1477.
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 1470-1477
-
-
Munro, J.B.1
Wasserman, M.R.2
Altman, R.B.3
Wang, L.4
Blanchard, S.C.5
-
33
-
-
80052446046
-
Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis
-
Fei, J., Richard, A.C., Bronson, J.E. and Gonzalez, R.L. Jr (2011) Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat. Struct. Mol. Biol., 18, 1043-1051.
-
(2011)
Nat. Struct. Mol. Biol
, vol.18
, pp. 1043-1051
-
-
Fei, J.1
Richard, A.C.2
Bronson, J.E.3
Gonzalez Jr., R.L.4
-
34
-
-
33845228894
-
An arc of unpaired 'hinge bases' facilitates information exchange among functional centers of the ribosome
-
Rakauskaite, R. and Dinman, J.D. (2006) An arc of unpaired 'hinge bases' facilitates information exchange among functional centers of the ribosome. Mol. Cell. Biol., 26, 8992-9002.
-
(2006)
Mol. Cell. Biol
, vol.26
, pp. 8992-9002
-
-
Rakauskaite, R.1
Dinman, J.D.2
-
35
-
-
33845958586
-
The A-site finger in 23 S rRNA acts as a functional attenuator for translocation
-
Komoda, T., Sato, N.S., Phelps, S.S., Namba, N., Joseph, S. and Suzuki, T. (2006) The A-site finger in 23 S rRNA acts as a functional attenuator for translocation. J. Biol. Chem., 281, 32303-32309.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 32303-32309
-
-
Komoda, T.1
Sato, N.S.2
Phelps, S.S.3
Namba, N.4
Joseph, S.5
Suzuki, T.6
-
36
-
-
25144497020
-
The conserved A-site finger of the 23 S rRNA: Just one of the intersubunit bridges or a part of the allosteric communication pathway?
-
Sergiev, P.V., Kiparisov, S.V., Burakovsky, D.E., Lesnyak, D.V., Leonov, A.A., Bogdanov, A.A. and Dontsova, O.A. (2005) The conserved A-site finger of the 23 S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway? J. Mol. Biol., 353, 116-123.
-
(2005)
J. Mol. Biol
, vol.353
, pp. 116-123
-
-
Sergiev, P.V.1
Kiparisov, S.V.2
Burakovsky, D.E.3
Lesnyak, D.V.4
Leonov, A.A.5
Bogdanov, A.A.6
Dontsova, O.A.7
-
37
-
-
67651178174
-
The ribosome as a conveying thermal ratchet machine
-
Spirin, A.S. (2009) The ribosome as a conveying thermal ratchet machine. J. Biol. Chem., 284, 21103-21119.
-
(2009)
J. Biol. Chem
, vol.284
, pp. 21103-21119
-
-
Spirin, A.S.1
-
38
-
-
79956268777
-
An extensive network of information flow through the B1b/c intersubunit bridge of the yeast ribosome
-
Rhodin, M.H. and Dinman, J.D. (2011) An extensive network of information flow through the B1b/c intersubunit bridge of the yeast ribosome. PLoS One, 6, e20048.
-
(2011)
PLoS One
, vol.6
-
-
Rhodin, M.H.1
Dinman, J.D.2
-
39
-
-
33747889715
-
Multiple stages in codon-anticodon recognition: Double-trigger mechanisms and geometric constraints
-
Ninio, J. (2006) Multiple stages in codon-anticodon recognition: double-trigger mechanisms and geometric constraints. Biochimie, 88, 963-992.
-
(2006)
Biochimie
, vol.88
, pp. 963-992
-
-
Ninio, J.1
-
40
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama, F., Valle, M., Frank, J. and Brooks, C.L. III (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl Acad. Sci. USA, 100, 9319-9323.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks III, C.L.4
-
41
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang, Y., Rader, A.J., Bahar, I. and Jernigan, R.L. (2004) Global ribosome motions revealed with elastic network model. J. Struct. Biol., 147, 302-314.
-
(2004)
J. Struct. Biol
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.J.2
Bahar, I.3
Jernigan, R.L.4
-
42
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
Trylska, J., Tozzini, V. and McCammon, J.A. (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
-
43
-
-
77956935085
-
The role of L1 stalk-tRNA interaction in the ribosome elongation cycle
-
Trabuco, L.G., Schreiner, E., Eargle, J., Cornish, P., Ha, T., Luthey-Schulten, Z. and Schulten, K. (2010) The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J. Mol. Biol., 402, 741-760.
-
(2010)
J. Mol. Biol
, vol.402
, pp. 741-760
-
-
Trabuco, L.G.1
Schreiner, E.2
Eargle, J.3
Cornish, P.4
Ha, T.5
Luthey-Schulten, Z.6
Schulten, K.7
-
44
-
-
80054966329
-
Key intermolecular interactions in the E. Coli 70s ribosome revealed by coarse-grained analysis
-
Zhang, Z., Sanbonmatsu, K.Y. and Voth, G.A. (2011) Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. J. Am. Chem. Soc., 133, 16828-16838.
-
(2011)
J. Am. Chem. Soc
, vol.133
, pp. 16828-16838
-
-
Zhang, Z.1
Sanbonmatsu, K.Y.2
Voth, G.A.3
-
45
-
-
82755187769
-
Excited states of ribosome translocation revealed through integrative molecular modeling
-
Whitford, P.C., Ahmed, A., Yu, Y., Hennelly, S.P., Tama, F., Spahn, C.M., Onuchic, J.N. and Sanbonmatsu, K.Y. (2011) Excited states of ribosome translocation revealed through integrative molecular modeling. Proc. Natl Acad. Sci. USA, 108, 18943-18948.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 18943-18948
-
-
Whitford, P.C.1
Ahmed, A.2
Yu, Y.3
Hennelly, S.P.4
Tama, F.5
Spahn, C.M.6
Onuchic, J.N.7
Sanbonmatsu, K.Y.8
-
46
-
-
17844375121
-
Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases
-
Razga, F., Koca, J., Sponer, J. and Leontis, N.B. (2005) Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases. Biophys. J., 88, 3466-3485.
-
(2005)
Biophys. J
, vol.88
, pp. 3466-3485
-
-
Razga, F.1
Koca, J.2
Sponer, J.3
Leontis, N.B.4
-
47
-
-
33746388359
-
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations
-
Relova, K., Lankas, F., Razga, F., Krasovska, M.V., Koca, J. and Sponer, J. (2006) Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers, 82, 504-520.
-
(2006)
Biopolymers
, vol.82
, pp. 504-520
-
-
Relova, K.1
Lankas, F.2
Razga, F.3
Krasovska, M.V.4
Koca, J.5
Sponer, J.6
-
48
-
-
77950366458
-
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and cryo-EM
-
Reblova, K., Razga, F., Li, W., Gao, H., Frank, J. and Sponer, J. (2009) Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and cryo-EM. Nucleic Acids Res., 38, 1325-1340.
-
(2009)
Nucleic Acids Res
, vol.38
, pp. 1325-1340
-
-
Reblova, K.1
Razga, F.2
Li, W.3
Gao, H.4
Frank, J.5
Sponer, J.6
-
49
-
-
77950141432
-
An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 50-UAA/50-GAN internal loops studied by molecular dynamics methods
-
Reblova, K., Strelcova, Z., Kulhanek, P., Besseova, I., Mathews, D.H., Van Nostrand, K., Yildirim, I., Turner, D.H. and Sponer, J. (2010) An RNA molecular switch: intrinsic flexibility of 23S rRNA helices 40 and 68 50-UAA/50-GAN internal loops studied by molecular dynamics methods. J. Chem. Theor. Comput., 6, 910-929.
-
(2010)
J. Chem. Theor. Comput
, vol.6
, pp. 910-929
-
-
Reblova, K.1
Strelcova, Z.2
Kulhanek, P.3
Besseova, I.4
Mathews, D.H.5
Van Nostrand, K.6
Yildirim, I.7
Turner, D.H.8
Sponer, J.9
-
50
-
-
78049420557
-
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome
-
Besseova, I., Relova, K., Leontis, N.B. and Sponer, J. (2010) Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res., 38, 6247-6264.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 6247-6264
-
-
Besseova, I.1
Relova, K.2
Leontis, N.B.3
Sponer, J.4
-
51
-
-
80052800450
-
Understanding RNA flexibility using explicit solvent simulations: The ribosomal and group i intron reverse kink-turn motifs
-
Sklenovsky, P., Florova, P., Banas, P., Reblova, K., Lankas, F., Otyepka, M. and Sponer, J. (2011) Understanding RNA flexibility using explicit solvent simulations: the ribosomal and group I intron reverse kink-turn motifs. J. Chem. Theor. Comput., 7, 2963-2980.
-
(2011)
J. Chem. Theor. Comput
, vol.7
, pp. 2963-2980
-
-
Sklenovsky, P.1
Florova, P.2
Banas, P.3
Reblova, K.4
Lankas, F.5
Otyepka, M.6
Sponer, J.7
-
52
-
-
60549112849
-
A hierarchical model for evolution of 23s ribosomal RNA
-
Bokov, K. and Steinberg, S.V. (2009) A hierarchical model for evolution of 23S ribosomal RNA. Nature, 457, 977-980.
-
(2009)
Nature
, vol.457
, pp. 977-980
-
-
Bokov, K.1
Steinberg, S.V.2
-
53
-
-
1842576803
-
Domain movements of elongation factor eef2 and the eukaryotic 80s ribosome facilitate tRNA translocation
-
Spahn, C.M., Gez-Lorenzo, M.G., Grassucci, R.A., Jorgensen, R., Andersen, G.R., Beckmann, R., Penczek, P.A., Ballesta, J.P.G. and Frank, J. (2004) Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J., 23, 1008-1019.
-
(2004)
EMBO J
, vol.23
, pp. 1008-1019
-
-
Spahn, C.M.1
Gez-Lorenzo, M.G.2
Grassucci, R.A.3
Jorgensen, R.4
Andersen, G.R.5
Beckmann, R.6
Penczek, P.A.7
Ballesta, J.P.G.8
Frank, J.9
-
54
-
-
71049158443
-
Comprehensive molecular structure of the eukaryotic ribosome
-
Taylor, D.J., Devkota, B., Huang, A.D., Topf, M., Narayanan, E., Sali, A., Harvey, S.C. and Frank, J. (2009) Comprehensive molecular structure of the eukaryotic ribosome. Structure, 17, 1591-1604.
-
(2009)
Structure
, vol.17
, pp. 1591-1604
-
-
Taylor, D.J.1
Devkota, B.2
Huang, A.D.3
Topf, M.4
Narayanan, E.5
Sali, A.6
Harvey, S.C.7
Frank, J.8
-
55
-
-
78650546283
-
Cryo-EM structure and rRNA model of a translating eukaryotic 80s ribosome at 5.5 - A resolution
-
Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S. et al. (2010) Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5 - A resolution. Proc. Natl Acad. Sci. USA, 107, 19748-19753.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 19748-19753
-
-
Armache, J.P.1
Jarasch, A.2
Anger, A.M.3
Villa, E.4
Becker, T.5
Bhushan, S.6
Jossinet, F.7
Habeck, M.8
Dindar, G.9
Franckenberg, S.10
-
56
-
-
78649426085
-
Crystal structure of the eukaryotic ribosome
-
Ben-Shem, A., Jenner, L., Yusupova, G. and Yusupov, M. (2010) Crystal structure of the eukaryotic ribosome. Science, 330, 1203-1209.
-
(2010)
Science
, vol.330
, pp. 1203-1209
-
-
Ben-Shem, A.1
Jenner, L.2
Yusupova, G.3
Yusupov, M.4
-
57
-
-
81755173676
-
Structure and dynamics of the mammalian ribosomal pretranslocation complex
-
Budkevich, T., Giesebrecht, J., Altman, R.B., Munro, J.B., Mielke, T., Nierhaus, K.H., Blanchard, S.C. and Spahn, C.M.T. (2011) Structure and dynamics of the mammalian ribosomal pretranslocation complex. Mol. Cell, 44, 214-224.
-
(2011)
Mol. Cell
, vol.44
, pp. 214-224
-
-
Budkevich, T.1
Giesebrecht, J.2
Altman, R.B.3
Munro, J.B.4
Mielke, T.5
Nierhaus, K.H.6
Blanchard, S.C.7
Spahn, C.M.T.8
-
58
-
-
81555219350
-
Crystal structure of the eukaryotic 60s ribosomal subunit in complex with initiation factor 6
-
Klinge, S., Voigts-Hoffmann, F., Leibundgut, M., Arpagaus, S. and Ban, N. (2011) Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science, 334, 941-948.
-
(2011)
Science
, vol.334
, pp. 941-948
-
-
Klinge, S.1
Voigts-Hoffmann, F.2
Leibundgut, M.3
Arpagaus, S.4
Ban, N.5
-
59
-
-
79951479408
-
The eukaryotic ribosome
-
Ramakrishnan, V. (2011) The eukaryotic ribosome. Science, 331, 681-682.
-
(2011)
Science
, vol.331
, pp. 681-682
-
-
Ramakrishnan, V.1
-
60
-
-
75449112058
-
Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in
-
Ditzler, M.A., Otyepka, M., Sponer, J. and Walter, N.G. (2010) Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc. Chem. Res., 43, 40-47.
-
(2010)
Acc. Chem. Res
, vol.43
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Sponer, J.3
Walter, N.G.4
-
61
-
-
42949089487
-
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
-
Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and Schulten, K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16, 673-683.
-
(2008)
Structure
, vol.16
, pp. 673-683
-
-
Trabuco, L.G.1
Villa, E.2
Mitra, K.3
Frank, J.4
Schulten, K.5
-
62
-
-
77952717308
-
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
-
Whitford, P.C., Geggier, P., Altman, R.B., Blanchard, S.C., Onuchic, J.N. and Sanbonmatsu, K.Y. (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
Sanbonmatsu, K.Y.6
-
63
-
-
27644502679
-
Simulating movement of tRNA into the ribosome during decoding
-
Sanbonmatsu, K.Y., Joseph, S. and Tung, C.-S. (2005) Simulating movement of tRNA into the ribosome during decoding. Proc. Natl Acad. Sci. USA, 102, 15854-15859.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15854-15859
-
-
Sanbonmatsu, K.Y.1
Joseph, S.2
Tung, C.-S.3
-
64
-
-
59849110790
-
Stochastic gating and drug-ribosome interactions
-
Vaiana, A.C. and Sanbonmatsu, K.Y. (2009) Stochastic gating and drug-ribosome interactions. J. Mol. Biol., 386, 648-661.
-
(2009)
J. Mol. Biol
, vol.386
, pp. 648-661
-
-
Vaiana, A.C.1
Sanbonmatsu, K.Y.2
-
65
-
-
59049096394
-
Ribosome-induced changes in elongation factor tu conformation control GTP hydrolysis
-
Villa, E., Sengupta, J., Trabuco, L.G., LeBarron, J., Baxter, W.T., Shaikh, T.R., Grassucci, R.A., Nissen, P., Ehrenberg, M., Schulten, K. et al. (2009) Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc. Natl Acad. Sci. USA, 106, 1063-1068.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 1063-1068
-
-
Villa, E.1
Sengupta, J.2
Trabuco, L.G.3
LeBarron, J.4
Baxter, W.T.5
Shaikh, T.R.6
Grassucci, R.A.7
Nissen, P.8
Ehrenberg, M.9
Schulten, K.10
-
66
-
-
78149461723
-
Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome
-
Trylska, J. (2010) Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome. J. Phys. Condens. Matter, 22, 453101.
-
(2010)
J. Phys. Condens. Matter
, vol.22
, pp. 453101
-
-
Trylska, J.1
-
67
-
-
33744807172
-
The building blocks and motifs of RNA architecture
-
Leontis, N.B., Lescoute, A. and Westhof, E. (2006) The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol., 16, 279-287.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 279-287
-
-
Leontis, N.B.1
Lescoute, A.2
Westhof, E.3
-
68
-
-
0035863772
-
Tectorna: Modular assembly units for the construction of RNA nano-objects
-
Jaeger, L., Westhof, E. and Leontis, N.B. (2001) TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res., 29, 455-463.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 455-463
-
-
Jaeger, L.1
Westhof, E.2
Leontis, N.B.3
-
69
-
-
33746655784
-
The architectonics of programmable RNA and DNA nanostructures
-
Jaeger, L. and Chworos, A. (2006) The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol., 16, 531-543.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 531-543
-
-
Jaeger, L.1
Chworos, A.2
-
70
-
-
79954588306
-
Engineering cooperative tecto-RNA complexes having programmable stoichiometries
-
Novikova, I.V., Hassan, B.H., Mirzoyan, M.G. and Leontis, N.B. (2010) Engineering cooperative tecto-RNA complexes having programmable stoichiometries. Nucleic Acids Res., 39, 2903-2917.
-
(2010)
Nucleic Acids Res
, vol.39
, pp. 2903-2917
-
-
Novikova, I.V.1
Hassan, B.H.2
Mirzoyan, M.G.3
Leontis, N.B.4
-
71
-
-
34547629747
-
Elastic properties of ribosomal RNA building blocks: Molecular dynamics of the GTPase-associated center rRNA
-
Razga, F., Koca, J., Mokdad, A. and Sponer, J. (2007) Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Res., 35, 4007-4017.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4007-4017
-
-
Razga, F.1
Koca, J.2
Mokdad, A.3
Sponer, J.4
-
72
-
-
70350003679
-
Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations
-
Curuksu, J., Sponer, J. and Zacharias, M. (2009) Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations. Biophys. J., 97, 2004-2013.
-
(2009)
Biophys. J
, vol.97
, pp. 2004-2013
-
-
Curuksu, J.1
Sponer, J.2
Zacharias, M.3
-
73
-
-
0034625311
-
Sequence-dependent elastic properties of DNA
-
Lankas, F., Sponer, J., Hobza, P. and Langowski, J. (2000) Sequence-dependent elastic properties of DNA. J. Mol. Biol., 299, 695-709.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 695-709
-
-
Lankas, F.1
Sponer, J.2
Hobza, P.3
Langowski, J.4
-
74
-
-
0035595722
-
Extracting parameters for base-pair level models of DNA from molecular dynamics simulations
-
Gonzalez, O. and Maddocks, J.H. (2001) Extracting parameters for base-pair level models of DNA from molecular dynamics simulations. Theor. Chem. Acc., 106, 76-82.
-
(2001)
Theor. Chem. Acc
, vol.106
, pp. 76-82
-
-
Gonzalez, O.1
Maddocks, J.H.2
-
75
-
-
70450267492
-
On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations
-
Lankas, F., Gonzalez, O., Heffler, L.M., Stoll, G., Moakher, M. and Maddocks, J.H. (2009) On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations. Phys. Chem. Chem. Phys., 11, 10565-10588.
-
(2009)
Phys. Chem. Chem. Phys
, vol.11
, pp. 10565-10588
-
-
Lankas, F.1
Gonzalez, O.2
Heffler, L.M.3
Stoll, G.4
Moakher, M.5
Maddocks, J.H.6
-
76
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
Lankas, F., Sponer, J., Langowski, J. and Cheatham, T.E. III (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J., 85, 2872-2883.
-
(2003)
Biophys. J
, vol.85
, pp. 2872-2883
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham III, T.E.4
-
77
-
-
1842607449
-
DNA deformability at the base pair level
-
Lankas, F., Sponer, J., Langowski, J. and Cheatham, T.E. III (2004) DNA deformability at the base pair level. J. Am. Chem. Soc., 126, 4124-4125.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 4124-4125
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham Iii, T.E.4
-
78
-
-
34548187754
-
From rigid base pairs to semifexible polymers: Coarse-graining DNA
-
Becker, N. and Everaers, R. (2007) From rigid base pairs to semiFexible polymers: coarse-graining DNA. Phys. Rev. E, Stat. Nonlin, Soft. Mather. Phys., 76, 021923.
-
(2007)
Phys. Rev. E, stat. Nonlin. Soft. Mather. Phys
, vol.76
, pp. 021923
-
-
Becker, N.1
Everaers, R.2
-
79
-
-
33751003527
-
Indirect readout: Detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials
-
Becker, N.B., Wolff, L. and Everaers, R. (2006) Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials. Nucleic Acids Res., 34, 5638-5649.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5638-5649
-
-
Becker, N.B.1
Wolff, L.2
Everaers, R.3
-
80
-
-
4744350893
-
Relative flexibility of DNA and RNA: A molecular dynamics study
-
Noy, A., Peez, A., Lankas, F., Luque, F. and Orozco, M. (2004) Relative flexibility of DNA and RNA: a molecular dynamics study. J. Mol. Biol., 343, 627-638.
-
(2004)
J. Mol. Biol
, vol.343
, pp. 627-638
-
-
Noy, A.1
Peez, A.2
Lankas, F.3
Luque, F.4
Orozco, M.5
-
81
-
-
77957350921
-
Toward a consensus view of duplex RNA flexibility
-
Faustino, I., Peez, A. and Orozco, M. (2010) Toward a consensus view of duplex RNA flexibility. Biophys. J., 99, 1876-1885.
-
(2010)
Biophys. J
, vol.99
, pp. 1876-1885
-
-
Faustino, I.1
Peez, A.2
Orozco, M.3
-
82
-
-
27644491082
-
Structures of the bacterial ribosome at 3.5 A resolution
-
Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M. and Cate, J.H.D. (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science, 310, 827-834.
-
(2005)
Science
, vol.310
, pp. 827-834
-
-
Schuwirth, B.S.1
Borovinskaya, M.A.2
Hau, C.W.3
Zhang, W.4
Vila-Sanjurjo, A.5
Holton, J.M.6
Cate, J.H.D.7
-
83
-
-
41549163979
-
Translational regulation via L11: Molecular switches on the ribosome turned on and off by thiostrepton and micrococcin
-
Harms, J.M., Wilson, D.N., Schluenzen, F., Connell, S.R., Stachelhaus, T., Zaborowska, Z., Spahn, C.M.T. and Fucini, P. (2008) Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Mol. Cell, 30, 26-38.
-
(2008)
Mol. Cell
, vol.30
, pp. 26-38
-
-
Harms, J.M.1
Wilson, D.N.2
Schluenzen, F.3
Connell, S.R.4
Stachelhaus, T.5
Zaborowska, Z.6
Spahn, C.M.T.7
Fucini, P.8
-
84
-
-
2942615089
-
The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
-
Klein, D.J., Moore, P.B. and Steitz, T.A. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol., 340, 141-177.
-
(2004)
J. Mol. Biol
, vol.340
, pp. 141-177
-
-
Klein, D.J.1
Moore, P.B.2
Steitz, T.A.3
-
85
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M. et al. (2002) The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Muller, K.M.10
-
86
-
-
33748661254
-
Ribostral: An RNA 3D alignment analyzer and viewer based on basepair isostericities
-
Mokdad, A. and Leontis, N.B. (2006) Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities. Bioinformatics, 22, 2168-2170.
-
(2006)
Bioinformatics
, vol.22
, pp. 2168-2170
-
-
Mokdad, A.1
Leontis, N.B.2
-
87
-
-
0029011701
-
A second generation force field for the simulation of proteins. Nucleic acids, and organic molecules
-
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc., 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
88
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang, J.M., Cieplak, P. and Kollman, P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049-1074.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
89
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Peez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J
, vol.92
, pp. 3817-3829
-
-
Peez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
90
-
-
36849057065
-
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics
-
Relova, K., Fadrna, E., Sarzynska, J., Kulinski, T., Kulhanek, P., Ennifar, E., Koca, J. and Sponer, J. (2007) Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophys. J., 93, 3932-3949.
-
(2007)
Biophys. J
, vol.93
, pp. 3932-3949
-
-
Relova, K.1
Fadrna, E.2
Sarzynska, J.3
Kulinski, T.4
Kulhanek, P.5
Ennifar, E.6
Koca, J.7
Sponer, J.8
-
91
-
-
77952472539
-
Extensive molecular dynamics simulations showing that canonical G8 and protonated a38h+ forms are most consistent with crystal structures of hairpin ribozyme
-
Mlynsky, V., Banas, P., Hollas, D., Relova, K., Walter, N.G., Sponer, J. and Otyepka, M. (2010) Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J. Phys. Chem. B, 114, 6642-6652.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 6642-6652
-
-
Mlynsky, V.1
Banas, P.2
Hollas, D.3
Relova, K.4
Walter, N.G.5
Sponer, J.6
Otyepka, M.7
-
92
-
-
78651294111
-
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
-
Banas, P., Hollas, D., Zgarbova, M., Jurecka, P., Orozco, M., Cheatham, T.E. III, Sponer, J. and Otyepka, M. (2010) Performance of molecular mechanics force fields for RNA simulations: stability of UUCG and GNRA hairpins. J. Chem. Theory Comput., 6, 3836-3849.
-
(2010)
J. Chem. Theory Comput
, vol.6
, pp. 3836-3849
-
-
Banas, P.1
Hollas, D.2
Zgarbova, M.3
Jurecka, P.4
Orozco, M.5
Cheatham Iii, T.E.6
Sponer, J.7
Otyepka, M.8
-
93
-
-
80052820313
-
Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
-
Zgarbova, M., Otyepka, M., Sponer, J., Mladek, A., Banas, P., Cheatham, T.E. III and Jurecka, P. (2011) Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput., 7, 2886-2902.
-
(2011)
J. Chem. Theory Comput
, vol.7
, pp. 2886-2902
-
-
Zgarbova, M.1
Otyepka, M.2
Sponer, J.3
Mladek, A.4
Banas, P.5
Cheatham Iii, T.E.6
Jurecka, P.7
-
94
-
-
70549103338
-
Dependence of A-RNA simulations on the choice of the force field and salt strength
-
Besseova, I., Otyepka, M., Reblova, K. and Sponer, J. (2009) Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11, 10701-10711.
-
(2009)
Phys. Chem. Chem. Phys
, vol.11
, pp. 10701-10711
-
-
Besseova, I.1
Otyepka, M.2
Reblova, K.3
Sponer, J.4
-
95
-
-
81855169786
-
A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis
-
Relova, K., Sponer, J.E., Spackova, N., Besseova, I. and Sponer, J. (2011) A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis. J. Phys. Chem. B, 115, 13897-13910.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 13897-13910
-
-
Relova, K.1
Sponer, J.E.2
Spackova, N.3
Besseova, I.4
Sponer, J.5
-
96
-
-
0242396923
-
3Dna: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu, X.-J. and Olson, W.K. (2003) 3Dna: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5108-5121
-
-
Lu, X.-J.1
Olson, W.K.2
-
98
-
-
33750488430
-
Structural basis for mRNA and tRNA positioning on the ribosome
-
Berk, V., Zhang, W., Pai, R.D. and Cate, J.H.D. (2006) Structural basis for mRNA and tRNA positioning on the ribosome. Proc. Natl Acad. Sci. USA, 103, 15830-15834.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 15830-15834
-
-
Berk, V.1
Zhang, W.2
Pai, R.D.3
Cate, J.H.D.4
-
99
-
-
11444267252
-
The relative flexibility of B-DNA and A-RNA duplexes: Database analysis
-
Peez, A., Noy, A., Lankas, F., Luque, F.J. and Orozco, M. (2004) The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res., 32, 6144-6151.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6144-6151
-
-
Peez, A.1
Noy, A.2
Lankas, F.3
Luque, F.J.4
Orozco, M.5
-
101
-
-
0030845405
-
Structure of the acceptor stem of escherichia coli tRNAala: Role of the g3.u70 base pair in synthetase recognition
-
Ramos, A. and Varani, G. (1997) Structure of the acceptor stem of Escherichia coli tRNAAla: role of the G3.U70 base pair in synthetase recognition. Nucleic Acids Res., 25, 2083-2090.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2083-2090
-
-
Ramos, A.1
Varani, G.2
-
102
-
-
29844453234
-
Topology of three-way junctions in folded RNAs
-
Lescoute, A. and Westhof, E. (2006) Topology of three-way junctions in folded RNAs. RNA, 12, 83-93.
-
(2006)
RNA
, vol.12
, pp. 83-93
-
-
Lescoute, A.1
Westhof, E.2
-
103
-
-
77950366458
-
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and cryo-EM
-
Relova, K., Razga, F., Li, W., Gao, H., Frank, J. and Sponer, J. (2010) Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res., 38, 1325-1340.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1325-1340
-
-
Relova, K.1
Razga, F.2
Li, W.3
Gao, H.4
Frank, J.5
Sponer, J.6
-
104
-
-
79952747147
-
Clustering to identify RNA conformations constrained by secondary structure
-
Sim, A.Y. and Levitt, M. (2011) Clustering to identify RNA conformations constrained by secondary structure. Proc. Natl Acad. Sci. USA, 108, 3590-3595.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 3590-3595
-
-
Sim, A.Y.1
Levitt, M.2
-
105
-
-
37549017736
-
Visualizing spatially correlated dynamics that directs RNA conformational transitions
-
Zhang, Q., Stelzer, A.C., Fisher, C.K. and Al-Hashimi, H.M. (2007) Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature, 450, 1263-1267.
-
(2007)
Nature
, vol.450
, pp. 1263-1267
-
-
Zhang, Q.1
Stelzer, A.C.2
Fisher, C.K.3
Al-Hashimi, H.M.4
-
106
-
-
34250728646
-
Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings
-
Bailor, M.H., Musselman, C., Hansen, A.L., Gulati, K., Patel, D.J. and Al-Hashimi, H.M. (2007) Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nat. Protoc., 2, 1536-1546.
-
(2007)
Nat. Protoc
, vol.2
, pp. 1536-1546
-
-
Bailor, M.H.1
Musselman, C.2
Hansen, A.L.3
Gulati, K.4
Patel, D.J.5
Al-Hashimi, H.M.6
-
107
-
-
67649891135
-
Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: New insights into RNA dynamics and adaptive ligand recognition
-
Frank, A.T., Stelzer, A.C., Al-Hashimi, H.M. and Andricioaei, I. (2009) Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Res., 37, 3670-3679.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 3670-3679
-
-
Frank, A.T.1
Stelzer, A.C.2
Al-Hashimi, H.M.3
Andricioaei, I.4
-
108
-
-
74249115345
-
Topology links RNA secondary structure with global conformation, dynamics, and adaptation
-
Bailor, M.H., Sun, X. and Al-Hashimi, H.M. (2010) Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science, 327, 202-206.
-
(2010)
Science
, vol.327
, pp. 202-206
-
-
Bailor, M.H.1
Sun, X.2
Al-Hashimi, H.M.3
-
109
-
-
0037273378
-
The crystal structure of a 26-nucleotide RNA containing a hook-turn
-
Szep, S., Wang, J. and Moore, P.B. (2003) The crystal structure of a 26-nucleotide RNA containing a hook-turn. RNA, 9, 44-51.
-
(2003)
RNA
, vol.9
, pp. 44-51
-
-
Szep, S.1
Wang, J.2
Moore, P.B.3
-
110
-
-
0035942248
-
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
-
Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B. and Steitz, T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA, 98, 4899-4903.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4899-4903
-
-
Nissen, P.1
Ippolito, J.A.2
Ban, N.3
Moore, P.B.4
Steitz, T.A.5
-
111
-
-
36448954303
-
FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
-
Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol., 56, 215-252.
-
(2008)
J. Math. Biol
, vol.56
, pp. 215-252
-
-
Sarver, M.1
Zirbel, C.L.2
Stombaugh, J.3
Mokdad, A.4
Leontis, N.B.5
-
112
-
-
33745951899
-
The UAA/GAN internal loop motif: A new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions
-
Lee, J.C., Gutell, R.R. and Russell, R. (2006) The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. J. Mol. Biol., 360, 978-988.
-
(2006)
J. Mol. Biol
, vol.360
, pp. 978-988
-
-
Lee, J.C.1
Gutell, R.R.2
Russell, R.3
-
113
-
-
69849114530
-
Classification and energetics of the base-phosphate interactions in RNA
-
Zirbel, C.L., Sponer, J.E., Sponer, J., Stombaugh, J. and Leontis, N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 4898-4918
-
-
Zirbel, C.L.1
Sponer, J.E.2
Sponer, J.3
Stombaugh, J.4
Leontis, N.B.5
|