-
1
-
-
34347233462
-
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
-
Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S (2007) Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci USA 104: 8293-8298
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8293-8298
-
-
Bessho, Y.1
Shibata, R.2
Sekine, S.3
Murayama, K.4
Higashijima, K.5
Hori-Takemoto, C.6
Shirouzu, M.7
Kuramitsu, S.8
Yokoyama, S.9
-
2
-
-
42149193165
-
One SmpB molecule accompanies tmRNA during its passage through the ribosomes
-
Bugaeva EY, Shpanchenko OV, Felden B, Isaksson LA, Dontsova OA (2008) One SmpB molecule accompanies tmRNA during its passage through the ribosomes. FEBS Lett 582: 1532-1536
-
(2008)
FEBS Lett
, vol.582
, pp. 1532-1536
-
-
Bugaeva, E.Y.1
Shpanchenko, O.V.2
Felden, B.3
Isaksson, L.A.4
Dontsova, O.A.5
-
3
-
-
0001832403
-
Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function
-
Chapman MS (1995) Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr A 51 : 69-80
-
(1995)
Acta Crystallogr A
, vol.51
, pp. 69-80
-
-
Chapman, M.S.1
-
4
-
-
76749086986
-
TmRNA ■ SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes
-
Cheng K, Ivanova N, Scheres SHW, Pavlov MY, Carazo JM, Hebert H, Ehrenberg M, Lindahl M (2010) tmRNA ■ SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes. J Struct Biol 169: 342-348
-
(2010)
J Struct Biol
, vol.169
, pp. 342-348
-
-
Cheng, K.1
Ivanova, N.2
Shw, S.3
Pavlov, M.Y.4
Carazo, J.M.5
Hebert, H.6
Ehrenberg, M.7
Lindahl, M.8
-
5
-
-
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 SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J (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
Chapman, M.S.11
Frank, J.12
-
6
-
-
39149091041
-
Preparation of macromo-lecular complexes for cryo-electron microscopy
-
Grassucci RA, Taylor DJ, Frank J (2007) Preparation of macromo-lecular complexes for cryo-electron microscopy. Nat Protoc 2: 3239-3246
-
(2007)
Nat Protoc
, vol.2
, pp. 3239-3246
-
-
Grassucci, R.A.1
Taylor, D.J.2
Frank, J.3
-
7
-
-
0041737720
-
Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB
-
Gutmann S, Haebel PW, Metzinger L, Sutter M, Felden B, Ban N (2003) Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature 424: 699-703
-
(2003)
Nature
, vol.424
, pp. 699-703
-
-
Gutmann, S.1
Haebel, P.W.2
Metzinger, L.3
Sutter, M.4
Felden, B.5
Ban, N.6
-
8
-
-
34247338538
-
Structure probing of tmRNA in distinct stages of trans-translation
-
Ivanova N, Lindell M, Pavlov M, Holmberg Schiavone L, Wagner EG, Ehrenberg M (2007) Structure probing of tmRNA in distinct stages of trans-translation. RNA 13: 713-722
-
(2007)
RNA
, vol.13
, pp. 713-722
-
-
Ivanova, N.1
Lindell, M.2
Pavlov, M.3
Holmberg Schiavone, L.4
Wagner, E.G.5
Ehrenberg, M.6
-
9
-
-
21744443970
-
TmRNA-induced release of messenger RNA from stalled ribosomes
-
Ivanova N, Pavlov MY, Ehrenberg M (2005) tmRNA-induced release of messenger RNA from stalled ribosomes. J Mol Biol 350: 897-905
-
(2005)
J Mol Biol
, vol.350
, pp. 897-905
-
-
Ivanova, N.1
Pavlov, M.Y.2
Ehrenberg, M.3
-
10
-
-
0037029139
-
How does tmRNA move through the ribosome?
-
Ivanov PV, Zvereva MI, Shpanchenko OV, Dontsova OA, Bogdanov AA, Aglyamova GV, Lim VI, Teraoka Y, Nierhaus KH (2002) How does tmRNA move through the ribosome? FEBS Lett 514: 55-59
-
(2002)
FEBS Lett
, vol.514
, pp. 55-59
-
-
Ivanov, P.V.1
Zvereva, M.I.2
Shpanchenko, O.V.3
Dontsova, O.A.4
Bogdanov, A.A.5
Aglyamova, G.V.6
Lim, V.I.7
Teraoka, Y.8
Nierhaus, K.H.9
-
11
-
-
77955405123
-
Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
-
Jossinet F, Ludwig TE, Westhof E (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26: 2057-2059
-
(2010)
Bioinformatics
, vol.26
, pp. 2057-2059
-
-
Jossinet, F.1
Ludwig, T.E.2
Westhof, E.3
-
12
-
-
25144458057
-
Sequence to structure (S2S): Display, manipulate and interconnect RNA data from sequence to structure
-
Jossinet F, Westhof E (2005) Sequence to structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 21 : 3320-3321
-
(2005)
Bioinformatics
, vol.21
, pp. 3320-3321
-
-
Jossinet, F.1
Westhof, E.2
-
13
-
-
33750838456
-
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome
-
Kaur S, Gillet R, Li W, Gursky R, Frank J (2006) Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Proc Natl Acad Sci USA 103: 16484-16489
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 16484-16489
-
-
Kaur, S.1
Gillet, R.2
Li, W.3
Gursky, R.4
Frank, J.5
-
14
-
-
0030024281
-
Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA
-
Keiler KC, Waller PR, Sauer RT (1996a) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271: 990-993
-
(1996)
Science
, vol.271
, pp. 990-993
-
-
Keiler, K.C.1
Waller, P.R.2
Sauer, R.T.3
-
15
-
-
0030024281
-
Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA
-
Keiler KC, Waller PRH, Sauer RT (1996b) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271: 990-993
-
(1996)
Science
, vol.271
, pp. 990-993
-
-
Keiler, K.C.1
Waller, P.R.H.2
Sauer, R.T.3
-
16
-
-
34748881977
-
A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation
-
Konno T, Kurita D, Takada K, Muto A, Himeno H (2007) A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA 13: 1723-1731
-
(2007)
RNA
, vol.13
, pp. 1723-1731
-
-
Konno, T.1
Kurita, D.2
Takada, K.3
Muto, A.4
Himeno, H.5
-
17
-
-
51549117861
-
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome
-
LeBarron J, Grassucci RA, Shaikh TR, Baxter WT, Sengupta J, Frank J (2008) Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. J Struct Biol 164: 24-32
-
(2008)
J Struct Biol
, vol.164
, pp. 24-32
-
-
Lebarron, J.1
Grassucci, R.A.2
Shaikh, T.R.3
Baxter, W.T.4
Sengupta, J.5
Frank, J.6
-
18
-
-
0034951396
-
Determinants on tmRNA for initiating efficient and precise trans-translation: Some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro
-
Lee S, Ishii M, Tadaki T, Muto A, Himeno H (2001) Determinants on tmRNA for initiating efficient and precise trans-translation: some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro. RNA 7: 999-1012
-
(2001)
RNA
, vol.7
, pp. 999-1012
-
-
Lee, S.1
Ishii, M.2
Tadaki, T.3
Muto, A.4
Himeno, H.5
-
19
-
-
15444370401
-
Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope
-
Lei J, Frank J (2005) Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J Struct Biol 150: 69-80
-
(2005)
J Struct Biol
, vol.150
, pp. 69-80
-
-
Lei, J.1
Frank, J.2
-
20
-
-
12544252576
-
Analysis of recognition of transfer-messenger RNA by the ribosomal decoding center
-
Lim VI, Garber MB (2005) Analysis of recognition of transfer-messenger RNA by the ribosomal decoding center. J Mol Biol 346: 395-398
-
(2005)
J Mol Biol
, vol.346
, pp. 395-398
-
-
Lim, V.I.1
Garber, M.B.2
-
21
-
-
13444266488
-
A simple and fast secondary structure prediction method using hidden neural networks
-
Lin K, Simossis VA, Taylor WR, Heringa J (2005) A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 21 : 152-159
-
(2005)
Bioinformatics
, vol.21
, pp. 152-159
-
-
Lin, K.1
Simossis, V.A.2
Taylor, W.R.3
Heringa, J.4
-
22
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
more..
-
24
-
-
50649123783
-
The highest affinity binding site of small protein B on transfer messenger RNA is outside the tRNA domain
-
Metzinger L, Hallier M, Felden B (2008) The highest affinity binding site of small protein B on transfer messenger RNA is outside the tRNA domain. RNA 14: 1761-1772
-
(2008)
RNA
, vol.14
, pp. 1761-1772
-
-
Metzinger, L.1
Hallier, M.2
Felden, B.3
-
25
-
-
48249108321
-
The role of upstream sequences in selecting the reading frame on tmRNA
-
Miller MR, Healey DW, Robison SG, Dewey JD, Buskirk AR (2008) The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol 6: 29
-
(2008)
BMC Biol
, vol.6
, pp. 29
-
-
Miller, M.R.1
Healey, D.W.2
Robison, S.G.3
Dewey, J.D.4
Buskirk, A.R.5
-
26
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
27
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
28
-
-
0036568279
-
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
-
Pollastri G, Przybylski D, Rost B, Baldi P (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47: 228-235
-
(2002)
Proteins
, vol.47
, pp. 228-235
-
-
Pollastri, G.1
Przybylski, D.2
Rost, B.3
Baldi, P.4
-
29
-
-
0347985836
-
Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: A case study
-
Rath BK, Frank J (2004) Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study. J Struct Biol 145: 84-90
-
(2004)
J Struct Biol
, vol.145
, pp. 84-90
-
-
Rath, B.K.1
Frank, J.2
-
30
-
-
0032840381
-
Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu
-
Rudinger-Thirion J, Giege R, Felden B (1999) Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. RNA 5: 989-992
-
(1999)
RNA
, vol.5
, pp. 989-992
-
-
Rudinger-Thirion, J.1
Giege, R.2
Felden, B.3
-
31
-
-
33845939047
-
Disentangling conformational states of macro-molecules in 3D-EM through likelihood optimization
-
Scheres SH, Gao H, Valle M, Herman GT, Eggermont PP, Frank J, Carazo JM (2007) Disentangling conformational states of macro-molecules in 3D-EM through likelihood optimization. Nat Methods 4: 27-29
-
(2007)
Nat Methods
, vol.4
, pp. 27-29
-
-
Scheres, S.H.1
Gao, H.2
Valle, M.3
Herman, G.T.4
Eggermont, P.P.5
Frank, J.6
Carazo, J.M.7
-
32
-
-
27644491082
-
Structures of the bacterial ribosome at 3.5 A resolution
-
Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (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.7
-
33
-
-
58049204808
-
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs
-
Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 3: 1941-1974
-
(2008)
Nat Protoc
, vol.3
, pp. 1941-1974
-
-
Shaikh, T.R.1
Gao, H.2
Baxter, W.T.3
Asturias, F.J.4
Boisset, N.5
Leith, A.6
Frank, J.7
-
34
-
-
42949089487
-
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
-
Trabuco LG, Villa E, Mitra K, Frank J, 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
-
35
-
-
1942533456
-
TRNA slippage at the tmRNA resume codon
-
Trimble MJ, Minnicus A, Williams KP (2004) tRNA slippage at the tmRNA resume codon. RNA 10: 805-812
-
(2004)
RNA
, vol.10
, pp. 805-812
-
-
Trimble, M.J.1
Minnicus, A.2
Williams, K.P.3
-
36
-
-
0028906813
-
C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide
-
Tu GF, Reid GE, Zhang JG, Moritz RL, Simpson RJ (1995) C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide. J Biol Chem 270: 9322-9326
-
(1995)
J Biol Chem
, vol.270
, pp. 9322-9326
-
-
Tu, G.F.1
Reid, G.E.2
Zhang, J.G.3
Moritz, R.L.4
Simpson, R.J.5
-
37
-
-
0242515749
-
Visualizing tmRNA entry into a stalled ribosome
-
Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J (2003) Visualizing tmRNA entry into a stalled ribosome. Science 300: 127-130
-
(2003)
Science
, vol.300
, pp. 127-130
-
-
Valle, M.1
Gillet, R.2
Kaur, S.3
Henne, A.4
Ramakrishnan, V.5
Frank, J.6
-
38
-
-
0042307441
-
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli
-
Vila-Sanjurjo A, Ridgeway WK, Seymaner V, Zhang W, Santoso S, Yu K, Cate JH (2003) X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci USA 100: 8682-8687
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 8682-8687
-
-
Vila-Sanjurjo, A.1
Ridgeway, W.K.2
Seymaner, V.3
Zhang, W.4
Santoso, S.5
Yu, K.6
Cate, J.H.7
-
39
-
-
67650656654
-
SmpB contributes to reading frame selection in the translation of transfer-messenger RNA
-
Watts T, Cazier D, Healey D, Buskirk A (2009) SmpB contributes to reading frame selection in the translation of transfer-messenger RNA. J Mol Biol 391: 275-281
-
(2009)
J Mol Biol
, vol.391
, pp. 275-281
-
-
Watts, T.1
Cazier, D.2
Healey, D.3
Buskirk, A.4
-
40
-
-
78449312624
-
The role of tmRNA nucleotides and the SmpB protein in setting the translational frame on tmRNA
-
Watts T, Healey D, Jones D, Buskirk A (2008) The role of tmRNA nucleotides and the SmpB protein in setting the translational frame on tmRNA. FASEB J 22: 224
-
(2008)
FASEB J
, vol.22
, pp. 224
-
-
Watts, T.1
Healey, D.2
Jones, D.3
Buskirk, A.4
-
41
-
-
75149143993
-
Accommodation of tmRNA-SmpB into stalled ribosomes: A cryo-EM study
-
Weis F, Bron P, Rolland JP, Thomas D, Felden B, Gillet R (2010) Accommodation of tmRNA-SmpB into stalled ribosomes: a cryo-EM study. RNA 16: 299-306
-
(2010)
RNA
, vol.16
, pp. 299-306
-
-
Weis, F.1
Bron, P.2
Rolland, J.P.3
Thomas, D.4
Felden, B.5
Gillet, R.6
-
42
-
-
0033215307
-
Resuming translation on tmRNA: A unique mode of determining a reading frame
-
Williams KP, Martindale KA, Bartel DP (1999) Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J 18: 5423-5433
-
(1999)
EMBO J
, vol.18
, pp. 5423-5433
-
-
Williams, K.P.1
Martindale, K.A.2
Bartel, D.P.3
-
43
-
-
11144236530
-
Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation
-
Wower IK, Zwieb C, Wower J (2004) Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation. J Biol Chem 279: 54202-54209
-
(2004)
J Biol Chem
, vol.279
, pp. 54202-54209
-
-
Wower, I.K.1
Zwieb, C.2
Wower, J.3
-
44
-
-
17844398246
-
Transfer-messenger RNA unfolds as it transits the ribosome
-
Wower IK, Zwieb C, Wower J (2005) Transfer-messenger RNA unfolds as it transits the ribosome. RNA 11: 668-673
-
(2005)
RNA
, vol.11
, pp. 668-673
-
-
Wower, I.K.1
Zwieb, C.2
Wower, J.3
|