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Items: 1 to 20 of 21

1.
Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification
Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J. R. Heck
Nat Commun. 2017; 8: 15473. Published online 2017 May 19. doi: 10.1038/ncomms15473
PMCID:
PMC5454533
AbstractArticlePDF–1.5M
2.
The binary protein-protein interaction landscape of Escherichia coli
Seesandra V. Rajagopala, Patricia Sikorski, Ashwani Kumar, Roberto Mosca, James Vlasblom, Roland Arnold, Jonathan Franca-Koh, Suman B. Pakala, Sadhna Phanse, Arnaud Ceol, Roman Häuser, Gabriella Siszler, Stefan Wuchty, Andrew Emili, Mohan Babu, Patrick Aloy, Rembert Pieper, Peter Uetz
Nat Biotechnol. Author manuscript; available in PMC 2014 Sep 1.
Published in final edited form as: Nat Biotechnol. 2014 Mar; 32(3): 285–290. Published online 2014 Feb 23. doi: 10.1038/nbt.2831
PMCID:
PMC4123855
AbstractArticlePDF–1.1M
3.
Structures of the ribosome in intermediate states of ratcheting
Wen Zhang, Jack Dunkle, Jamie H. D. Cate
Science. Author manuscript; available in PMC 2010 Aug 10.
Published in final edited form as: Science. 2009 Aug 21; 325(5943): 1014–1017. doi: 10.1126/science.1175275
PMCID:
PMC2919209
AbstractArticlePDF–2.2M
4.
Regulation of the protein-conducting channel by a bound ribosome
James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, Klaus Schulten
Structure. Author manuscript; available in PMC 2010 Nov 11.
Published in final edited form as: Structure. 2009 Nov 11; 17(11): 1453–1464. doi: 10.1016/j.str.2009.09.010
PMCID:
PMC2778611
AbstractArticlePDF–3.1M
5.
Concurrent Nucleation of 16S Folding and Induced Fit in 30 S Ribosome Assembly
Tadepalli Adilakshmi, Deepti L. Bellur, Sarah A. Woodson
Nature. Author manuscript; available in PMC 2009 Oct 30.
Published in final edited form as: Nature. 2008 Oct 30; 455(7217): 1268–1272. Published online 2008 Sep 10. doi: 10.1038/nature07298
PMCID:
PMC2720798
AbstractArticlePDF–1.0M
6.
Protein abundance profiling of the Escherichia coli cytosol
Yasushi Ishihama, Thorsten Schmidt, Juri Rappsilber, Matthias Mann, F Ulrich Hartl, Michael J Kerner, Dmitrij Frishman
BMC Genomics. 2008; 9: 102. Published online 2008 Feb 27. doi: 10.1186/1471-2164-9-102
PMCID:
PMC2292177
AbstractArticlePDF–1.0M
7.
Essentiality of Ribosomal and Transcription Antitermination Proteins Analyzed by Systematic Gene Replacement in Escherichia coli
Mikhail Bubunenko, Teresa Baker, Donald L. Court
J Bacteriol. 2007 Apr; 189(7): 2844–2853. Published online 2007 Feb 2. doi: 10.1128/JB.01713-06
PMCID:
PMC1855809
AbstractArticlePDF–198K
8.
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
Tomoya Baba, Takeshi Ara, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, Kirill A Datsenko, Masaru Tomita, Barry L Wanner, Hirotada Mori
Mol Syst Biol. 2006; 2: 2006.0008. Published online 2006 Feb 21. doi: 10.1038/msb4100050
PMCID:
PMC1681482
AbstractArticlePDF–400K
9.
Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110
Koji Hayashi, Naoki Morooka, Yoshihiro Yamamoto, Katsutoshi Fujita, Katsumi Isono, Sunju Choi, Eiichi Ohtsubo, Tomoya Baba, Barry L Wanner, Hirotada Mori, Takashi Horiuchi
Mol Syst Biol. 2006; 2: 2006.0007. Published online 2006 Feb 21. doi: 10.1038/msb4100049
PMCID:
PMC1681481
AbstractArticlePDF–141K
10.
Large-scale identification of protein–protein interaction of Escherichia coli K-12
Mohammad Arifuzzaman, Maki Maeda, Aya Itoh, Kensaku Nishikata, Chiharu Takita, Rintaro Saito, Takeshi Ara, Kenji Nakahigashi, Hsuan-Cheng Huang, Aki Hirai, Kohei Tsuzuki, Seira Nakamura, Mohammad Altaf-Ul-Amin, Taku Oshima, Tomoya Baba, Natsuko Yamamoto, Tomoyo Kawamura, Tomoko Ioka-Nakamichi, Masanari Kitagawa, Masaru Tomita, Shigehiko Kanaya, Chieko Wada, Hirotada Mori
Genome Res. 2006 May; 16(5): 686–691. doi: 10.1101/gr.4527806
PMCID:
PMC1457052
AbstractArticlePDF–536K
11.
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005
Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, Barry L. Wanner
Nucleic Acids Res. 2006; 34(1): 1–9. Published online 2006 Jan 5. doi: 10.1093/nar/gkj405
PMCID:
PMC1325200
AbstractArticlePDF–204K
12.
A novel GTPase activated by the small subunit of ribosome
Hyouta Himeno, Kyoko Hanawa-Suetsugu, Takatsugu Kimura, Kuniaki Takagi, Wakana Sugiyama, Shinobu Shirata, Tomoyuki Mikami, Fujiko Odagiri, Yukiko Osanai, Daisuke Watanabe, Simon Goto, Liliya Kalachnyuk, Chisato Ushida, Akira Muto
Nucleic Acids Res. 2004; 32(17): 5303–5309. Published online 2004 Oct 5. doi: 10.1093/nar/gkh861
PMCID:
PMC521671
AbstractArticlePDF–261K
13.
Creating ribosomes with an all-RNA 30S subunit P site
Lee Hoang, Kurt Fredrick, Harry F. Noller
Proc Natl Acad Sci U S A. 2004 Aug 24; 101(34): 12439–12443. Published online 2004 Aug 12. doi: 10.1073/pnas.0405227101
PMCID:
PMC515080
AbstractArticlePDF–496K
14.
Requirement of Proteins S5 and S9 from 30S Subunits for the Ribosome-Dependent GTPase Activity of Elongation Factor G
Robert C. Marsh, Andrea Parmeggiani
Proc Natl Acad Sci U S A. 1973 Jan; 70(1): 151–155. doi: 10.1073/pnas.70.1.151
PMCID:
PMC433204
SummaryPage BrowsePDF–917K
15.
Temperature Sensitivity Caused by Mutant Release Factor 1 Is Suppressed by Mutations That Affect 16S rRNA Maturation
Magdalena Kaczanowska, Monica Rydén-Aulin
J Bacteriol. 2004 May; 186(10): 3046–3055. doi: 10.1128/JB.186.10.3046-3055.2004
PMCID:
PMC400638
AbstractArticlePDF–1.0M
16.
Studies of the Interaction of Escherichia coli YjeQ with the Ribosome In Vitro
Denis M. Daigle, Eric D. Brown
J Bacteriol. 2004 Mar; 186(5): 1381–1387. doi: 10.1128/JB.186.5.1381-1387.2004
PMCID:
PMC344419
AbstractArticlePDF–656K
17.
Protein binding sites on Escherichia coli 16S RNA; RNA regions that are protected by proteins S7, S14 and S19 in the presence or absence of protein S9.
L Wiener, R Brimacombe
Nucleic Acids Res. 1987 May 11; 15(9): 3653–3670. doi: 10.1093/nar/15.9.3653
PMCID:
PMC340774
SummaryPage BrowsePDF–2.0M
18.
Multiple crosslinks of proteins S7, S9, S13 to domains 3 and 4 of 16S RNA in the 30S particle.
E Hajnsdorf, A Favre, A Expert-Bezançon
Nucleic Acids Res. 1986 May 27; 14(10): 4009–4023. doi: 10.1093/nar/14.10.4009
PMCID:
PMC339842
SummaryPage BrowsePDF–1.5M
19.
Protein binding sites on Escherichia coli 16S ribosomal RNA; RNA regions that are protected by proteins S7, S9 and S19, and by proteins S8, S15 and S17.
L Wiener, D Schüler, R Brimacombe
Nucleic Acids Res. 1988 Feb 25; 16(4): 1233–1250. doi: 10.1093/nar/16.4.1233
PMCID:
PMC336311
SummaryPage BrowsePDF–1.8M
20.
The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site.
M Osswald, T Döring, R Brimacombe
Nucleic Acids Res. 1995 Nov 25; 23(22): 4635–4641. doi: 10.1093/nar/23.22.4635
PMCID:
PMC307437
SummaryPage BrowsePDF–1.6M

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