-
2
-
-
33646778780
-
Bringing DNA computers to life
-
E. Shapiro and Y. Benenson, Bringing DNA computers to life, Sci. Am. 45-51 (2006).
-
(2006)
Sci. Am
, pp. 45-51
-
-
Shapiro, E.1
Benenson, Y.2
-
3
-
-
80053550490
-
50th anniversary of the discovery of the genetic code
-
2011
-
V. A. Erdmann and J. Barciszewski, 2011: 50th anniversary of the discovery of the genetic code, Angew. Chem. Int. Ed. 50, 9546-9552 (2011).
-
(2011)
Angew. Chem. Int. Ed.
, vol.50
, pp. 9546-9552
-
-
Erdmann, V.A.1
Barciszewski, J.2
-
4
-
-
18844413446
-
Structural insight into translational fidelity
-
J. M. Ogle and V. Ramakrishnan, Structural insight into translational fidelity, Annu. Rev. Biochem. 74, 129-177 (2005).
-
(2005)
Annu. Rev. Biochem
, vol.74
, pp. 129-177
-
-
Ogle, J.M.1
Ramakrishnan, V.2
-
5
-
-
60149099539
-
Fidelity at the molecular level: Lessons from protein synthesis
-
H. S. Zaher and R. Green, Fidelity at the molecular level: Lessons from protein synthesis, Cell 136, 746-762 (2009).
-
(2009)
Cell
, vol.136
, pp. 746-762
-
-
Zaher, H.S.1
Green, R.2
-
6
-
-
70549111391
-
RNA polymerase fidelity and transcriptional proofreading
-
J. F. Sydow and P. Cramer, RNA polymerase fidelity and transcriptional proofreading, Curr. Opinion Struct. Biol. 19, 732-739 (2009).
-
(2009)
Curr. Opinion Struct. Biol
, vol.19
, pp. 732-739
-
-
Sydow, J.F.1
Cramer, P.2
-
8
-
-
0010146684
-
The thermodynamics of computation-A review
-
C. H. Bennett, The thermodynamics of computation-a review, Int. J. Theor. Phys. 21, 905-940 (1982).
-
(1982)
Int. J. Theor. Phys
, vol.21
, pp. 905-940
-
-
Bennett, C.H.1
-
9
-
-
0018633663
-
Dissipation-error tradeoff in proofreading
-
C. H. Bennett, Dissipation-error tradeoff in proofreading, Biosystems 11, 85-91 (1979).
-
(1979)
Biosystems
, vol.11
, pp. 85-91
-
-
Bennett, C.H.1
-
10
-
-
51849150828
-
Thermodynamics of error correction: Speed-error-dissipation tradeoff in copying
-
C. H. Bennett and M. Donkor, Thermodynamics of Error Correction: Speed-Error-Dissipation Tradeoff in Copying, Information Theory Workshop (IEEE, 2008).
-
(2008)
Information Theory Workshop IEEE
-
-
Bennett, C.H.1
Donkor, M.2
-
11
-
-
84858190920
-
Viral polymerases, in Viral Molecular Machines
-
eds. M. G. Rossmann and V. B. Rao
-
K. H. Choi, Viral polymerases, in Viral Molecular Machines, eds. M. G. Rossmann and V. B. Rao, Adv. Expt. Med. Biol. 726, 267-304 (2012).
-
(2012)
Adv. Expt. Med. Biol
, vol.726
, pp. 267-304
-
-
Choi, K.H.1
-
12
-
-
37649032089
-
Random walks of cytoskeletal motors in open and closed compartments
-
R. Lipowsky, S. Klumpp and T. M. Nieuwenhuizen, Random walks of cytoskeletal motors in open and closed compartments, Phys. Rev. Lett. 87, 108101 (2001).
-
(2001)
Phys. Rev. Lett
, vol.87
, pp. 108101
-
-
Lipowsky, R.1
Klumpp, S.2
Nieuwenhuizen, T.M.3
-
13
-
-
0037471125
-
Phase coexistence in driven onedimensional transport
-
A. Parmeggiani, T. Franosch and E. Frey, Phase coexistence in driven onedimensional transport, Phys. Rev. Lett. 90, 086601 (2003).
-
(2003)
Phys. Rev. Lett
, vol.90
, pp. 086601
-
-
Parmeggiani, A.1
Franosch, T.2
Frey, E.3
-
14
-
-
42749106314
-
Shock formation in an exclusion process with creation and annihilation
-
M. R. Evans, R. Juhasz and L. Santen, Shock formation in an exclusion process with creation and annihilation, Phys. Rev. E 68, 026117 (2003).
-
(2003)
Phys. Rev. e
, vol.68
, pp. 026117
-
-
Evans, M.R.1
Juhasz, R.2
Santen, L.3
-
15
-
-
42749106700
-
Localization of shocks in driven diffusive systems without particle number conservation
-
V. Popkov, A. Rakos, R. D. Williams, A. B. Kolomeisky and G. M. Sch?utz, Localization of shocks in driven diffusive systems without particle number conservation, Phys. Rev. E 67, 066117 (2003).
-
(2003)
Phys. Rev. e
, vol.67
, pp. 066117
-
-
Popkov, V.1
Rakos, A.2
Williams, R.D.3
Kolomeisky, A.B.4
Schutz, G.M.5
-
16
-
-
17844365841
-
'Life is motion' Multiscale motility of molecular motors
-
R. Lipowsky and S. Klumpp, 'Life is motion': Multiscale motility of molecular motors, Physica A 352, 53-112 (2005).
-
(2005)
Physica A
, vol.352
, pp. 53-112
-
-
Lipowsky, R.1
Klumpp, S.2
-
17
-
-
33748934552
-
Molecular motor traffic: From biological nanomachines to macroscopic transport
-
R. Lipowsky, Y. Chai, S. Klumpp, S. Liepelt and M. J. I. M?uller, Molecular motor traffic: From biological nanomachines to macroscopic transport, Physica A 372, 34-51 (2006).
-
(2006)
Physica A
, vol.372
, pp. 34-51
-
-
Lipowsky, R.1
Chai, Y.2
Klumpp, S.3
Liepelt, S.4
Muller, M.J.I.5
-
18
-
-
0032478549
-
RNA polymerase as a molecular motor
-
J. Gelles and R. Landick, RNA polymerase as a molecular motor, Cell 93, 13-16 (1998).
-
(1998)
Cell
, vol.93
, pp. 13-16
-
-
Gelles, J.1
Landick, R.2
-
19
-
-
33846958387
-
Mechano-chemical kinetics of transcription elongation
-
L. Bai, R. M. Fulbright and M. D. Wang, Mechano-chemical kinetics of transcription elongation, Phys. Rev. Lett. 98, 068103 (2007).
-
(2007)
Phys. Rev. Lett
, vol.98
, pp. 068103
-
-
Bai, L.1
Fulbright, R.M.2
Wang, M.D.3
-
20
-
-
12944320326
-
Machinations of a Maxwellian Demon
-
R. Sousa, Machinations of a Maxwellian Demon, Cell 120, 155-158 (2005).
-
(2005)
Cell
, vol.120
, pp. 155-158
-
-
Sousa, R.1
-
21
-
-
33645097171
-
Translocation by T7 RNA polymerase: A sensitively poised Brownian ratchet
-
Q. Guo and R. Sousa, Translocation by T7 RNA polymerase: A sensitively poised Brownian ratchet, J. Mol. Biol. 358, 241-254 (2006).
-
(2006)
J. Mol. Biol
, vol.358
, pp. 241-254
-
-
Guo, Q.1
Sousa, R.2
-
22
-
-
28544432440
-
Direct observation of base-pair stepping by RNA polymerase
-
E. A. Abbondanzieri, W. J. Greenleaf, J. W. Shaevitz, R. Landick and S. M. Block, Direct observation of base-pair stepping by RNA polymerase, Nature 438, 460-465 (2005).
-
(2005)
Nature
, vol.438
, pp. 460-465
-
-
Abbondanzieri, E.A.1
Greenleaf, W.J.2
Shaevitz, J.W.3
Landick, R.4
Block, S.M.5
-
23
-
-
48249103199
-
Structure of eukaryotic RNA polymerases
-
P. Cramer, K. J. Armache, S. Baumli, S. Benkert, F. Brueckner, C. Buchen, G. E. Damshma, S. Dengl, S. R. Geiger, A. J. Jasiak, A. Jawhari, S. Jennebach, T. Kamenski, H. Kettenberger, C. D. Kuhn, E. Lehmann, K. Leike, J. F. Sydow and A. Vannini, Structure of eukaryotic RNA polymerases, Annu. Rev. Biophys. 37, 337-352 (2008).
-
(2008)
Annu. Rev. Biophys
, vol.37
, pp. 337-352
-
-
Cramer, P.1
Armache, K.J.2
Baumli, S.3
Benkert, S.4
Brueckner, F.5
Buchen, C.6
Damshma, G.E.7
Dengl, S.8
Geiger, S.R.9
Jasiak, A.J.10
Jawhari, A.11
Jennebach, S.12
Kamenski, T.13
Kettenberger, H.14
Kuhn, C.D.15
Lehmann, E.16
Leike, K.17
Sydow, J.F.18
Vannini, A.19
-
24
-
-
12944324227
-
A ratchet mechanism of transcription elongation and control
-
G. Bar-Nahum, V. Epshtein, A. E. Ruckenstein, R. Rafikov, A. Mustaev and E. Nudler, A ratchet mechanism of transcription elongation and control, Cell 120, 183-193 (2005).
-
(2005)
Cell
, vol.120
, pp. 183-193
-
-
Bar-Nahum, G.1
Epshtein, V.2
Ruckenstein, A.E.3
Rafikov, R.4
Mustaev, A.5
Nudler, E.6
-
25
-
-
84863082064
-
A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription
-
J. Yu and G. Oster, A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription, Biophys. J. 102, 532-541 (2012).
-
(2012)
Biophys. J
, vol.102
, pp. 532-541
-
-
Yu, J.1
Oster, G.2
-
26
-
-
38749103885
-
Interacting RNA polymerase motors on a DNA track: Effects of traffic congestion and intrinsic noise on RNA synthesis
-
T. Tripathi and D. Chowdhury, Interacting RNA polymerase motors on a DNA track: Effects of traffic congestion and intrinsic noise on RNA synthesis, Phys. Rev. E 77, 011921 (2008).
-
(2008)
Phys. Rev. e
, vol.77
, pp. 011921
-
-
Tripathi, T.1
Chowdhury, D.2
-
27
-
-
67649388550
-
A look-ahead model for the elongation dynamics of transcription
-
Y. R. Yamada and C. S. Peskin, A look-ahead model for the elongation dynamics of transcription, Biophys. J. 96, 30153031 (2009).
-
(2009)
Biophys. J
, vol.96
, pp. 30153031
-
-
Yamada, Y.R.1
Peskin, C.S.2
-
28
-
-
78349309327
-
The influence of look-ahead on the error rate of transcription
-
Y. R. Yamada and C. S. Peskin, The influence of look-ahead on the error rate of transcription, Math. Model. Nat. Phenom. 27, 206-227 (2010).
-
(2010)
Math. Model. Nat. Phenom
, vol.27
, pp. 206-227
-
-
Yamada, Y.R.1
Peskin, C.S.2
-
29
-
-
70449421542
-
RNA polymerase motors: Dwell time distribution, velocity and dynamical phases
-
T. Tripathi, G. M. Schutz and D. Chowdhury, RNA polymerase motors: Dwell time distribution, velocity and dynamical phases, J. Stat. Mech. Theor. Exp. P08018 (2009).
-
(2009)
J. Stat. Mech. Theor. Exp
, vol.P08018
-
-
Tripathi, T.1
Schutz, G.M.2
Chowdhury, D.3
-
30
-
-
33845456360
-
A long time in the making-The nobel prize for RNA polymerase
-
R. Landick, A long time in the making-the nobel prize for RNA polymerase, Cell 127, 1087-1090 (2006).
-
(2006)
Cell
, vol.127
, pp. 1087-1090
-
-
Landick, R.1
-
31
-
-
0346258014
-
Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
-
J. W. Shaevitz, E. A. Abbondanzieri, R. Landick and S. M. Block, Backtracking by single RNA polymerase molecules observed at near-base-pair resolution, Nature 426, 684-687 (2003).
-
(2003)
Nature
, vol.426
, pp. 684-687
-
-
Shaevitz, J.W.1
Abbondanzieri, E.A.2
Landick, R.3
Block, S.M.4
-
32
-
-
34147206187
-
Backtracking determines the force sensitivity of RNAPII in a factor-dependent manner
-
E. A. Galburt, S. W. Grill, A. Wiedmann, L. Lubkowska, J. Choy, E. Nogales, M. Kashlev and C. Bustamante, Backtracking determines the force sensitivity of RNAPII in a factor-dependent manner, Nature 446, 820-823 (2007).
-
(2007)
Nature
, vol.446
, pp. 820-823
-
-
Galburt, E.A.1
Grill, S.W.2
Wiedmann, A.3
Lubkowska, L.4
Choy, J.5
Nogales, E.6
Kashlev, M.7
Bustamante, C.8
-
33
-
-
7444253928
-
Sequence-dependent kinetic model for transcription elongation by RNA polymerase
-
L. Bai, A. Shundrovsky and M. D. Wang, Sequence-dependent kinetic model for transcription elongation by RNA polymerase, J. Mol. Biol. 344, 335-349 (2004).
-
(2004)
J. Mol. Biol
, vol.344
, pp. 335-349
-
-
Bai, L.1
Shundrovsky, A.2
Wang, M.D.3
-
34
-
-
67049154068
-
Transcriptional pausing without backtracking
-
R. Landick, Transcriptional pausing without backtracking, Proc. Natl. Acad. Sci. 106, 8797-8798 (2009).
-
(2009)
Proc. Natl. Acad. Sci
, vol.106
, pp. 8797-8798
-
-
Landick, R.1
-
35
-
-
33745965527
-
Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing
-
R. V. Dalal, M. H. Larson, K. C. Neuman, J. Gelles, R. Landick and S. M. Block, Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing, Molecular Cell 23, 231-239 (2006).
-
(2006)
Molecular Cell
, vol.23
, pp. 231-239
-
-
Dalal, R.V.1
Larson, M.H.2
Neuman, K.C.3
Gelles, J.4
Landick, R.5
Block, S.M.6
-
36
-
-
38349008878
-
Fluctuations, pauses, and backtracking in DNA transcription
-
M. Voliotis, N. Cohen, C. Molina-Paris and T. B. Liverpool, Fluctuations, pauses, and backtracking in DNA transcription, Biophys. J. 94, 334-348 (2008).
-
(2008)
Biophys. J
, vol.94
, pp. 334-348
-
-
Voliotis, M.1
Cohen, N.2
Molina-Paris, C.3
Liverpool, T.B.4
-
37
-
-
66149143165
-
The Origin of Short Transcriptional Pauses
-
M. Depken, E. A. Galburt and S. W. Grill, The Origin of Short Transcriptional Pauses, Biophys. J. 93, 2189-2193 (2009).
-
(2009)
Biophys. J
, vol.93
, pp. 2189-2193
-
-
Depken, M.1
Galburt, E.A.2
Grill, S.W.3
-
38
-
-
48049117117
-
A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase
-
P. Xie, A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase, BioSystem 93, 199-210 (2008).
-
(2008)
BioSystem
, vol.93
, pp. 199-210
-
-
Xie, P.1
-
40
-
-
84863782507
-
A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases
-
P. Xie, A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases, Proteins: Structure, Function and Bioinformatics 80, 2020-2034 (2012).
-
(2012)
Proteins: Structure, Function and Bioinformatics
, vol.80
, pp. 2020-2034
-
-
Xie, P.1
-
41
-
-
67649312058
-
Backtracking and proofreading in DNA transcription
-
M. Voliotis, N. Cohen, C. Molina-Pars and T. B. Liverpool, Backtracking and proofreading in DNA transcription, Phys. Rev. Lett. 102, 258101 (2009).
-
(2009)
Phys. Rev. Lett
, vol.102
, pp. 258101
-
-
Voliotis, M.1
Cohen, N.2
Molina-Pars, C.3
Liverpool, T.B.4
-
42
-
-
83755167911
-
Transcriptional proofreading in dense RNA polymerase traffic
-
M. Sahoo and S. Klumpp, Transcriptional proofreading in dense RNA polymerase traffic, EPL 96, 60004 (2011).
-
(2011)
EPL
, vol.96
, pp. 60004
-
-
Sahoo, M.1
Klumpp, S.2
-
43
-
-
0038756088
-
Cooperation between RNA polymerase molecules in transcription elongation
-
V. Epshtein and E. Nudler, Cooperation between RNA polymerase molecules in transcription elongation, Science 300, 801-805 (2003).
-
(2003)
Science
, vol.300
, pp. 801-805
-
-
Epshtein, V.1
Nudler, E.2
-
44
-
-
0141625269
-
Transcription through roadblocks: The role of RNA polymerase cooperation
-
V. Epshtein, F. Toulme, A. R. Borukhov and E. Nudler, Transcription through roadblocks: The role of RNA polymerase cooperation, EMBO J. 22, 4719-4727 (2003).
-
(2003)
EMBO J
, vol.22
, pp. 4719-4727
-
-
Epshtein, V.1
Toulme, F.2
Borukhov, A.R.3
Nudler, E.4
-
46
-
-
67651095903
-
Stability, fexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes
-
H. Saeki and J. Q. Svejstrup, Stability, fexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes, Mol. Cell 35, 191-205 (2009).
-
(2009)
Mol. Cell
, vol.35
, pp. 191-205
-
-
Saeki, H.1
Svejstrup, J.Q.2
-
47
-
-
12544251077
-
A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli
-
K. Sneppen, I. B. Dodd, K. E. Shearwin, A. C. Palmer, R. A. Schubert, B. P. Callen and J. B. Egan, A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli, J. Mol. Biol. 346, 399-409 (2005).
-
(2005)
J. Mol. Biol
, vol.346
, pp. 399-409
-
-
Sneppen, K.1
Dodd, I.B.2
Shearwin, K.E.3
Palmer, A.C.4
Schubert, R.A.5
Callen, B.P.6
Egan, J.B.7
-
48
-
-
58149527756
-
Growth-rate-dependent partitioning of RNA polymerases in bacteria
-
S. Klumpp and T. Hwa, Growth-rate-dependent partitioning of RNA polymerases in bacteria, Proc. Natl. Acad. Sci. USA, 105, 20245-20250 (2008).
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 20245-20250
-
-
Klumpp, S.1
Hwa, T.2
-
49
-
-
80055005365
-
Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cells
-
Y. Ohta, T. Kodama and S. Ihara, Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cells, Phys. Rev. E 84, 041922 (2011).
-
(2011)
Phys. Rev. e
, vol.84
, pp. 041922
-
-
Ohta, Y.1
Kodama, T.2
Ihara, S.3
-
50
-
-
0034594940
-
Single-molecule studies of the effect of template tension on T7 DNA polymerase activity
-
G. J. L.Wuite, S. B. Smith, M. Young, D. Keller and C. Bustamante, Single-molecule studies of the effect of template tension on T7 DNA polymerase activity, Nature 404, 103-106 (2000).
-
(2000)
Nature
, vol.404
, pp. 103-106
-
-
Wuite, G.J.L.1
Smith, S.B.2
Young, M.3
Keller, D.4
Bustamante, C.5
-
51
-
-
0034710990
-
Replication by a single DNA polymerase of a stretched single-stranded DNA
-
B. Maier, D. Bensimon and V. Croquette, Replication by a single DNA polymerase of a stretched single-stranded DNA, Proc. Natl. Acad. Sci. USA 97, 12002-12007 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 12002-12007
-
-
Maier, B.1
Bensimon, D.2
Croquette, V.3
-
52
-
-
0035902580
-
Tuning DNA strings" Modulating the rate of DNA replication with mechanical tension
-
A. Goel, M. D. Frank-Kamenetskii, T. Ellenberger and D. Herschbach, Tuning DNA "strings": Modulating the rate of DNA replication with mechanical tension, Proc. Natl. Acad. Sci. USA 98, 8485-8489 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 8485-8489
-
-
Goel, A.1
Frank-Kamenetskii, M.D.2
Ellenberger, T.3
Herschbach, D.4
-
53
-
-
0042693074
-
Tuning and switching a DNA polymerase motor with mechanical tension
-
A. Goel, R. D. Astumian and D. Herschbach, Tuning and switching a DNA polymerase motor with mechanical tension, Proc. Natl. Acad. Sci. USA 100, 9699-9704 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9699-9704
-
-
Goel, A.1
Astumian, R.D.2
Herschbach, D.3
-
54
-
-
4444318769
-
Dependence of DNA polymerase replication rate on external forces: A model based on molecular dynamics simulations
-
I. Andricioaei, A. Goel, D. Herschbach and M. Karplus, Dependence of DNA polymerase replication rate on external forces: A model based on molecular dynamics simulations, Biophys. J. 87, 1478-1497 (2004).
-
(2004)
Biophys. J
, vol.87
, pp. 1478-1497
-
-
Andricioaei, I.1
Goel, A.2
Herschbach, D.3
Karplus, M.4
-
55
-
-
77949568225
-
DNA polymerase proofreading: Multiple roles maintain genome stability
-
L. J. Reha-Krantz, DNA polymerase proofreading: Multiple roles maintain genome stability, Biochim. Biophys. Acta. 1804, 1049-1063 (2010).
-
(2010)
Biochim. Biophys. Acta 1804
, pp. 1049-1063
-
-
Reha-Krantz, L.J.1
-
56
-
-
70349213246
-
Proofreading dynamics of a processive DNA polymerase
-
B. Ibarra, Y. R. Chemla, S. Plyasunov, S. B. Smith, J. M. Lzaro, M. Salas and C Bustamante, Proofreading dynamics of a processive DNA polymerase, EMBO J. 28, 2794-2802 (2009).
-
(2009)
EMBO J
, vol.28
, pp. 2794-2802
-
-
Ibarra, B.1
Chemla, Y.R.2
Plyasunov, S.3
Smith, S.B.4
Lzaro, J.M.5
Salas, M.6
Bustamante, C.7
-
57
-
-
0020328629
-
Kinetic basis of spontaneous mutation: Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli
-
A. R. Fersht, J. W. Knill-Jones and W. C. Tsui, Kinetic basis of spontaneous mutation: Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli, J. Mol. Biol. 156, 37-51 (1982).
-
(1982)
J. Mol. Biol
, vol.156
, pp. 37-51
-
-
Fersht, A.R.1
Knill-Jones, J.W.2
Tsui, W.C.3
-
58
-
-
84863960184
-
Error correction during DNA replication
-
A. K. Sharma and D. Chowdhury, Error correction during DNA replication, Phys. Rev. E 86, 011913 (2012).
-
(2012)
Phys. Rev. e
, vol.86
, pp. 011913
-
-
Sharma, A.K.1
Chowdhury, D.2
-
59
-
-
77949570420
-
The kinetic and chemical mechanism of high-fidelity DNA polymerases
-
K. A. Johnson, The kinetic and chemical mechanism of high-fidelity DNA polymerases, Biochimica et Biophysica Acta 1804, 1041-1048 (2010).
-
(2010)
Biochimica et Biophysica Acta 1804
, pp. 1041-1048
-
-
Johnson, K.A.1
-
60
-
-
0034816941
-
A sliding clamp monkey wrench
-
L. B. Bloom and M. F. Goodman, A sliding clamp monkey wrench, Nat. Struct. Biol. 8, 829-831 (2001).
-
(2001)
Nat. Struct. Biol
, vol.8
, pp. 829-831
-
-
Bloom, L.B.1
Goodman, M.F.2
-
61
-
-
33745071496
-
Dynamics of loading the Escherichia coli DNA polymerase processivity clamp
-
L. B. Bloom, Dynamics of loading the Escherichia coli DNA polymerase processivity clamp, Crit. Rev. Biochem. and Mol. Biol. 41, 179-208 (2006).
-
(2006)
Crit. Rev. Biochem. and Mol. Biol
, vol.41
, pp. 179-208
-
-
Bloom, L.B.1
-
63
-
-
33749033347
-
The replication clamp-loading machine at work in the three domains of life
-
C. Indiani and M. O'Donnell, The replication clamp-loading machine at work in the three domains of life, Nat. Rev. Mol. Cell Biol. 7, 751-761 (2006).
-
(2006)
Nat. Rev. Mol. Cell Biol
, vol.7
, pp. 751-761
-
-
Indiani, C.1
O'Donnell, M.2
-
64
-
-
0035929237
-
Opening of the clamp
-
V. Ellison and B. Stillman, Opening of the clamp, Cell 106, 655-660 (2001).
-
(2001)
Cell
, vol.106
, pp. 655-660
-
-
Ellison, V.1
Stillman, B.2
-
65
-
-
29044442277
-
DNA sliding clamps: Just the right twist to load onto DNA
-
D. Barsky and C. Venclovas, DNA sliding clamps: Just the right twist to load onto DNA. Curr. Biol. 15, R989-R992 (2005).
-
(2005)
Curr. Biol
, vol.15
-
-
Barsky, D.1
Venclovas, C.2
-
67
-
-
0032489041
-
Polymerases and the replisome: Machines within machines
-
T. A. Baker and S. P. Bell, Polymerases and the replisome: Machines within machines, Cell 92, 295-305 (1998).
-
(1998)
Cell
, vol.92
, pp. 295-305
-
-
Baker, T.A.1
Bell, S.P.2
-
69
-
-
22244478079
-
Cellular DNA replicases: Components and dynamics at the replication fork
-
A. Johnson and M. O'Donnel, Cellular DNA replicases: Components and dynamics at the replication fork, Annu. Rev. Biochem. 74, 283-315 (2005).
-
(2005)
Annu. Rev. Biochem
, vol.74
, pp. 283-315
-
-
Johnson, A.1
O'Donnel, M.2
-
71
-
-
0043066735
-
DNA replication: A complex matter
-
I. Frouin, A. Montecucco, S. Spadari and G. Maga, DNA replication: A complex matter, EMBO Rep. 4, 666-670 (2003).
-
(2003)
EMBO Rep
, vol.4
, pp. 666-670
-
-
Frouin, I.1
Montecucco, A.2
Spadari, S.3
Maga, G.4
-
72
-
-
0030034288
-
DNA polymerase III: Running rings around the fork
-
D. R. Herendeen and T. J. Kelley, DNA polymerase III: Running rings around the fork, Cell 84, 5-8 (1996).
-
(1996)
Cell
, vol.84
, pp. 5-8
-
-
Herendeen, D.R.1
Kelley, T.J.2
-
73
-
-
0025646208
-
Eukaryotic DNA replication
-
P. Thommes and U. Hubscher, Eukaryotic DNA replication, Eur. J. Biochem. 194, 699-712 (1990).
-
(1990)
Eur. J. Biochem
, vol.194
, pp. 699-712
-
-
Thommes, P.1
Hubscher, U.2
-
74
-
-
0035997368
-
DNA replication in eukaryotic cells
-
S. P. Bell and A. Dutta, DNA replication in eukaryotic cells, Annu. Rev. Biochem. 71, 333-374 (2002).
-
(2002)
Annu. Rev. Biochem
, vol.71
, pp. 333-374
-
-
Bell, S.P.1
Dutta, A.2
-
75
-
-
18044384092
-
DNA polymerases that propagate the eukaryotic DNA replication fork
-
P. Garg and P. M. J. Burgers, DNA polymerases that propagate the eukaryotic DNA replication fork, Crit. Rev. Biochem. and Mol. Biol. 40, 115-128 (2005).
-
(2005)
Crit. Rev. Biochem. and Mol. Biol
, vol.40
, pp. 115-128
-
-
Garg, P.1
Burgers, P.M.J.2
-
77
-
-
45849087612
-
Extra-chromosomal elements and the evolution of cellular DNA replication machineries
-
A. T. McGeoch and S. D. Bell, Extra-chromosomal elements and the evolution of cellular DNA replication machineries, Nat. Rev. Mol. Cell Biol. 9, 569-574 (2008).
-
(2008)
Nat. Rev. Mol. Cell Biol
, vol.9
, pp. 569-574
-
-
McGeoch, A.T.1
Bell, S.D.2
-
78
-
-
77952934028
-
Single-molecule studies of the replisome
-
A. M. van Oijen and J. J. Loparo, Single-molecule studies of the replisome, Annu. Rev. Biophys. 39, 429-448 (2010).
-
(2010)
Annu. Rev. Biophys
, vol.39
, pp. 429-448
-
-
Van Oijen, A.M.1
Loparo, J.J.2
-
79
-
-
77949567580
-
Single-molecule studies of DNA replisome function
-
S. K. Perumal, H. Yue, M. M. Spiering and S. J. Benkovic, Single-molecule studies of DNA replisome function, Biochim. Biophys. Acta-proteins & proteomics 1804, 1094-1112 (2010).
-
(2010)
Biochim Biophys. Acta-proteins & Proteomics 1804
, pp. 1094-1112
-
-
Perumal, S.K.1
Yue, H.2
Spiering, M.M.3
Benkovic, S.J.4
-
80
-
-
80053575452
-
Dynamic coupling between the motors of DNA replication: Hexameric helicase, DNA polymerase, and primase
-
S. S. Patel, M. Pandey and D. Nandakumar, Dynamic coupling between the motors of DNA replication: Hexameric helicase, DNA polymerase, and primase, Curr. Opin. Chem. Biol. 15, 595-605 (2011).
-
(2011)
Curr. Opin. Chem. Biol
, vol.15
, pp. 595-605
-
-
Patel, S.S.1
Pandey, M.2
Nandakumar, D.3
-
81
-
-
31844453991
-
DNA primase acts as a molecular brake in DNA replication
-
J. B. Lee, R. K. Hite, S. M. Hamdan, X. S. Xie, C. C. Richardson and A. M. van Oijen, DNA primase acts as a molecular brake in DNA replication, Nature 439, 621-624 (2006).
-
(2006)
Nature
, vol.439
, pp. 621-624
-
-
Lee, J.B.1
Hite, R.K.2
Hamdan, S.M.3
Xie, X.S.4
Richardson, C.C.5
Van Oijen, A.M.6
-
82
-
-
77952693715
-
Mechanism of sequencespecific template binding by the DNA primase of bacteriophage T7
-
S. J. Lee, B. Zhu, S. M. Hamdan and C. C. Richardson, Mechanism of sequencespecific template binding by the DNA primase of bacteriophage T7, Nucl. Acids Res. 38, 4372-4383 (2010).
-
(2010)
Nucl. Acids Res
, vol.38
, pp. 4372-4383
-
-
Lee, S.J.1
Zhu, B.2
Hamdan, S.M.3
Richardson, C.C.4
-
83
-
-
0018370008
-
RNA replication: Function and structure of Qβ-replicase
-
T. Blumenthal and G. G. Carmichael, RNA replication: Function and structure of Qβ-replicase, Annu. Rev. Biochem. 48, 525-548 (1979).
-
(1979)
Annu. Rev. Biochem
, vol.48
, pp. 525-548
-
-
Blumenthal, T.1
Carmichael, G.G.2
-
84
-
-
33750285215
-
Structure and function of RNA replication
-
J. Ortin and F. Parra, Structure and function of RNA replication, Annu. Rev. Microbiol. 60, 305-326 (2006).
-
(2006)
Annu. Rev. Microbiol
, vol.60
, pp. 305-326
-
-
Ortin, J.1
Parra, F.2
-
85
-
-
40649100793
-
Structure-function relationships among RNA-dependent RNA polymerases
-
K. K. S. Ng, J. J. Arnold and C. E. Cameron, Structure-function relationships among RNA-dependent RNA polymerases, Curr. Top. Microbiol. Immunol. 320, 137-156 (2008).
-
(2008)
Curr. Top. Microbiol. Immunol
, vol.320
, pp. 137-156
-
-
Ng, K.K.S.1
Arnold, J.J.2
Cameron, C.E.3
-
86
-
-
50549097204
-
Bluetongue virus: Dissection of the polymerase complex
-
P. Roy, Bluetongue virus: Dissection of the polymerase complex, J. Gen. Virology 89, 1789-1804 (2008).
-
(2008)
J. Gen. Virology
, vol.89
, pp. 1789-1804
-
-
Roy, P.1
-
87
-
-
32344432085
-
A comparison of viral RNA-dependent RNA polymerases
-
C. Ferrer-Orta, A. Arias, C. Escarmis and N. Verdaguer, A comparison of viral RNA-dependent RNA polymerases, Curr. Opin. Struct. Biol. 16, 27-34 (2006).
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 27-34
-
-
Ferrer-Orta, C.1
Arias, A.2
Escarmis, C.3
Verdaguer, N.4
-
90
-
-
84855178837
-
Retroviruses
-
eds C. E. Cameron et al Springer
-
R. Galetto and M. Negroni, Retroviruses, in Viral Genome Replication, eds. C. E. Cameron et al. 109-128 (Springer, 2009).
-
(2009)
Viral Genome Replication
, pp. 109-128
-
-
Galetto, R.1
Negroni, M.2
-
91
-
-
84858231693
-
Human immunodeficiency virus reverse transcriptase
-
eds C. E. Cameron et al Springer
-
M. Wendeler, J. T. Miller and S. F. J. Le Grice, Human immunodeficiency virus reverse transcriptase, in Viral Genome Replication, eds. C. E. Cameron et al. (Springer, 2009).
-
(2009)
Viral Genome Replication
-
-
Wendeler, M.1
Miller, J.T.2
Le Grice, S.F.J.3
-
92
-
-
43049087696
-
Retroviral reverse transcriptase (other than those of HIV-1 and murine leukemia virus): A comparison of their molecular and biochemical properties
-
A. Hizi and A. Herschhorn, Retroviral reverse transcriptase (other than those of HIV-1 and murine leukemia virus): A comparison of their molecular and biochemical properties, Virus Res. 134, 203-220 (2008).
-
(2008)
Virus Res
, vol.134
, pp. 203-220
-
-
Hizi, A.1
Herschhorn, A.2
-
93
-
-
77955702253
-
Retroviral reverse transcriptase
-
A. Herschhorn and A. Hizi, Retroviral reverse transcriptase, Cell. Mol. Life Sci. 67, 2717-2747 (2010).
-
(2010)
Cell. Mol. Life Sci
, vol.67
, pp. 2717-2747
-
-
Herschhorn, A.1
Hizi, A.2
-
94
-
-
79952083478
-
HIV-1 ribonuclease H: Structure, catalytic mechanism and inhibitors
-
G. L. Beilhartz and M. G?otte, HIV-1 ribonuclease H: Structure, catalytic mechanism and inhibitors, Viruses 2, 900-926 (2010).
-
(2010)
Viruses
, vol.2
, pp. 900-926
-
-
Beilhartz, G.L.1
Gotte, M.2
-
95
-
-
43449118968
-
Dynamic binding orientations direct activity of HIV reverse transcriptase
-
E. A. Abbondanzieri et al., Dynamic binding orientations direct activity of HIV reverse transcriptase, Nature 453, 184-189 (2008).
-
(2008)
Nature
, vol.453
, pp. 184-189
-
-
Abbondanzieri, E.A.1
-
96
-
-
0030929648
-
It's prime time for reverse transcriptase
-
H. L. Levin, It's prime time for reverse transcriptase, Cell 88, 5-8 (1997).
-
(1997)
Cell
, vol.88
, pp. 5-8
-
-
Levin, H.L.1
-
97
-
-
0031806738
-
Retrovirus mutation rates and their role in genetic variation
-
L. M. Mansky, Retrovirus mutation rates and their role in genetic variation, J. Gen. Virology, 79, 1337-1345 (1998).
-
(1998)
J. Gen. Virology
, vol.79
, pp. 1337-1345
-
-
Mansky, L.M.1
-
98
-
-
84873446515
-
-
A. K. Sharma and D. Chowdhury to be published
-
A. K. Sharma and D. Chowdhury (to be published).
-
-
-
-
99
-
-
1842377482
-
Bacteriophage phi29 DNA replication arrest caused by codirectional collisions with the transcription machinery
-
M. Elas-Arnanz and M. Salas, Bacteriophage phi29 DNA replication arrest caused by codirectional collisions with the transcription machinery, The EMBO Journal 16, 5775-5783 (1997).
-
(1997)
The EMBO Journal
, vol.16
, pp. 5775-5783
-
-
Elas-Arnanz, M.1
Salas, M.2
-
100
-
-
0033570150
-
Resolution of head-on collisions between the transcription machinery and bacteriophage Φ 29 DNA polymerase is dependent on RNA polymerase translocation
-
M. Elas-Arnanz and M. Salas, Resolution of head-on collisions between the transcription machinery and bacteriophage Φ 29 DNA polymerase is dependent on RNA polymerase translocation, The EMBO J. 18, 5675-5682 (1999).
-
(1999)
The EMBO J
, vol.18
, pp. 5675-5682
-
-
Elas-Arnanz, M.1
Salas, M.2
-
101
-
-
79958724964
-
The replication-transcription conflict
-
P. Soultanas, The replication-transcription conflict, Transcription 2, 140-144 (2011).
-
(2011)
Transcription
, vol.2
, pp. 140-144
-
-
Soultanas, P.1
-
102
-
-
0003567483
-
-
Kluwer Academic/Plenum
-
A. S. Spirin, Ribosomes (Kluwer Academic/Plenum, 1999).
-
(1999)
Ribosomes
-
-
Spirin, A.S.1
-
103
-
-
0037029091
-
Ribosome as a molecular machine
-
A. S. Spirin, Ribosome as a molecular machine, FEBS Lett. 514, 2-10 (2002).
-
(2002)
FEBS Lett
, vol.514
, pp. 2-10
-
-
Spirin, A.S.1
-
104
-
-
34250821011
-
The ribosome as an RNA-based molecular machine
-
A. S. Spirin, The ribosome as an RNA-based molecular machine, RNA Biology 1, 3-9 (2004).
-
(2004)
RNA Biology
, vol.1
, pp. 3-9
-
-
Spirin, A.S.1
-
105
-
-
67651178174
-
The ribosome as a conveying thermal ratchet machine
-
A. S. Spirin, The ribosome as a conveying thermal ratchet machine, J. Biol. Chem. 284, 21103-21119 (2009).
-
(2009)
J. Biol. Chem
, vol.284
, pp. 21103-21119
-
-
Spirin, A.S.1
-
106
-
-
84861765128
-
Computational studies of molecular machines: The ribosome
-
K. Y. Sanbonmatsu, Computational studies of molecular machines: The ribosome, Curr. Opin. Struct. Biol. 22, 168-174 (2012).
-
(2012)
Curr. Opin. Struct. Biol
, vol.22
, pp. 168-174
-
-
Sanbonmatsu, K.Y.1
-
107
-
-
0030584663
-
A complex profile of protein elongation: Translating chemical energy into molecular movement
-
K. Abel and F. Jurnak, A complex profile of protein elongation: Translating chemical energy into molecular movement, Structure 4, 229-238 (1996).
-
(1996)
Structure
, vol.4
, pp. 229-238
-
-
Abel, K.1
Jurnak, F.2
-
108
-
-
70349545940
-
Aminoacyl-tRNA synthesis and translational quality control
-
J. Ling, N. Reynolds and M. Ibba, Aminoacyl-tRNA synthesis and translational quality control, Annu. Rev. Microbiol. 63, 61-78 (2009).
-
(2009)
Annu. Rev. Microbiol
, vol.63
, pp. 61-78
-
-
Ling, J.1
Reynolds, N.2
Ibba, M.3
-
109
-
-
55849145559
-
DNA polymerases and aminoacyl-tRNA synthetases: Shared mechanisms for ensuring fidelity of gene expression
-
C. S. Francklyn, DNA polymerases and aminoacyl-tRNA synthetases: Shared mechanisms for ensuring fidelity of gene expression, Biochem. 47, 11695-11703 (2008).
-
(2008)
Biochem
, vol.47
, pp. 11695-11703
-
-
Francklyn, C.S.1
-
110
-
-
0034595256
-
Atomic glimpses on a billion-year-old molecular machine
-
E. Westhof and N. Leontis, Atomic glimpses on a billion-year-old molecular machine, Angew. Chem. Int. Ed. 39, 1587-1591 (2000).
-
(2000)
Angew. Chem. Int. Ed
, vol.39
, pp. 1587-1591
-
-
Westhof, E.1
Leontis, N.2
-
111
-
-
0043268903
-
The structural basis of large ribosomal subunit function
-
P. B. Moore and T. A. Steitz, The structural basis of large ribosomal subunit function, Annu. Rev. Biochem. 72, 813-850 (2003).
-
(2003)
Annu. Rev. Biochem
, vol.72
, pp. 813-850
-
-
Moore, P.B.1
Steitz, T.A.2
-
112
-
-
39749138785
-
A structural understanding of the dynamic ribosome machine
-
T. A. Steitz, A structural understanding of the dynamic ribosome machine, Nat. Rev. Mol. Cell Biol. 9, 242-253 (2008).
-
(2008)
Nat. Rev. Mol. Cell Biol
, vol.9
, pp. 242-253
-
-
Steitz, T.A.1
-
113
-
-
77953663699
-
From the structure and function of the ribosome to new antibiotics (Nobel Lecture)
-
T. A. Steitz, From the structure and function of the ribosome to new antibiotics (Nobel Lecture), Angew. Chem. Int. Ed. 49, 4381-4398 (2010).
-
(2010)
Angew. Chem. Int. Ed
, vol.49
, pp. 4381-4398
-
-
Steitz, T.A.1
-
114
-
-
0036082654
-
The search and its outcome: High-resolution structures of ribosomal particles from mesophilic, thermophilic and halophilic bacteria at various functional states
-
A. Yonath, The search and its outcome: High-resolution structures of ribosomal particles from mesophilic, thermophilic and halophilic bacteria at various functional states, Annu. Rev. Biophys. & Biomol. Struct. 31, 257-273 (2002).
-
(2002)
Annu. Rev. Biophys. & Biomol. Struct
, vol.31
, pp. 257-273
-
-
Yonath, A.1
-
115
-
-
77953682688
-
Hibernating bears, antibiotics and evolving ribosome (Nobel lecture)
-
A. Yonath, Hibernating bears, antibiotics and evolving ribosome (Nobel lecture), Angew. Chem. Int. Ed. 49, 4340-4354 (2010).
-
(2010)
Angew. Chem. Int. Ed
, vol.49
, pp. 4340-4354
-
-
Yonath, A.1
-
116
-
-
0037154986
-
Ribosome structure and the mechanism of translation
-
V. Ramakrishnan, Ribosome structure and the mechanism of translation, Cell 108, 557-572 (2002).
-
(2002)
Cell
, vol.108
, pp. 557-572
-
-
Ramakrishnan, V.1
-
117
-
-
70350654363
-
What recent ribosome structure have revealed about the mechanism of translation
-
T. M. Schmering and V. Ramakrishnan, What recent ribosome structure have revealed about the mechanism of translation, Nature 461, 1234-1242 (2009).
-
(2009)
Nature
, vol.461
, pp. 1234-1242
-
-
Schmering, T.M.1
Ramakrishnan, V.2
-
118
-
-
77953681445
-
Unraveling the structure of the ribosome (Nobel Lecture)
-
V. Ramakrishnan, Unraveling the structure of the ribosome (Nobel Lecture), Angew. Chem. Int. Ed. 49, 4355-4380 (2010).
-
(2010)
Angew. Chem. Int. Ed
, vol.49
, pp. 4355-4380
-
-
Ramakrishnan, V.1
-
119
-
-
0034044736
-
The ribosome-A macromolecular machine par excellence
-
J. Frank, The ribosome-a macromolecular machine par excellence, Chem. & Biol. 7, R133-R141 (2000).
-
(2000)
Chem. & Biol
, vol.7
-
-
Frank, J.1
-
120
-
-
77449133028
-
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu
-
X. Agirrezabala and J. Frank, Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu, Quart. Rev. Biophys. 42, 159-200 (2009).
-
(2009)
Quart. Rev. Biophys
, vol.42
, pp. 159-200
-
-
Agirrezabala, X.1
Frank, J.2
-
121
-
-
77953625418
-
Structure and dynamics of a processive Brownian motor: The translating ribosome
-
J. Frank and R. L. Gonzales, Structure and dynamics of a processive Brownian motor: The translating ribosome, Annu. Rev. Biochem. 79, 381-412 (2010).
-
(2010)
Annu. Rev. Biochem
, vol.79
, pp. 381-412
-
-
Frank, J.1
Gonzales, R.L.2
-
122
-
-
0035805213
-
Crystal structure of the ribosome at 5.5A0 resolution
-
M. M. Yusupov, G. Z. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. D. Cate and H. F. Noller, Crystal structure of the ribosome at 5.5A0 resolution, Science 292, 883-896 (2001).
-
(2001)
Science
, vol.292
, pp. 883-896
-
-
Yusupov, M.M.1
Yusupova, G.Z.2
Baucom, A.3
Lieberman, K.4
Earnest, T.N.5
Cate, J.H.D.6
Noller, H.F.7
-
123
-
-
26944462598
-
Structure of the ribosome
-
eds. K. H. Nierhaus and D. N. Wilson Wiley-VCH
-
G. Blaha and P. Ivanov, Structure of the ribosome, in Protein Synthesis and Ribosome Structure, eds. K. H. Nierhaus and D. N. Wilson (Wiley-VCH, 2004).
-
(2004)
Protein Synthesis and Ribosome Structure
-
-
Blaha, G.1
Ivanov, P.2
-
124
-
-
47249110711
-
Translation at the single-molecule level
-
R. A. Marshall, C. E. Aitken, M. Dorywalska and J. D. Puglisi, Translation at the single-molecule level, Annu. Rev. Biochem. 77, 177-203 (2008).
-
(2008)
Annu. Rev. Biochem
, vol.77
, pp. 177-203
-
-
Marshall, R.A.1
Aitken, C.E.2
Dorywalska, M.3
Puglisi, J.D.4
-
125
-
-
4744365694
-
TRNA selection and kinetic proofreading in translation
-
S. Blanchard, R. L. Gonzalez Jr., H. D. Kim, S. Chu and J. D. Puglisi, tRNA selection and kinetic proofreading in translation, Nat. Str. & Mol. Biol. 11, 1008-1014 (2004).
-
(2004)
Nat. Str. & Mol. Biol
, vol.11
, pp. 1008-1014
-
-
Blanchard, S.1
Gonzalez Jr., R.L.2
Kim, H.D.3
Chu, S.4
Puglisi, J.D.5
-
126
-
-
33947501707
-
Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome
-
S. Uemura, M. Dorywalska, T. H. Lee, H. D. Kim, J. D. Puglisi and S. Chu, Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome, Nature 446, 454-457 (2007).
-
(2007)
Nature
, vol.446
, pp. 454-457
-
-
Uemura, S.1
Dorywalska, M.2
Lee, T.H.3
Kim, H.D.4
Puglisi, J.D.5
Chu, S.6
-
127
-
-
42249103513
-
A new view of protein synthesis Mapping the free energy landscape of the ribosome using singlemolecule FRET
-
J. B. Munro, A. Vaiana, K. Y. Sanbonmatsu and S. C. Blanchard, A new view of protein synthesis: Mapping the free energy landscape of the ribosome using singlemolecule FRET, Biopolymers 89, 565-577 (2008).
-
(2008)
Biopolymers
, vol.89
, pp. 565-577
-
-
Munro, J.B.1
Vaiana, A.2
Sanbonmatsu, K.Y.3
Blanchard, S.C.4
-
128
-
-
68349096239
-
Navigating the ribosome's metastable energy landscape
-
J. B. Munro, K. Y. Sanbonmatsu, C. M. T. Spahn and S. C. Blanchard, Navigating the ribosome's metastable energy landscape, Trends in Biochem. Sci. 34, 390-400 (2009).
-
(2009)
Trends in Biochem Sci
, vol.34
, pp. 390-400
-
-
Munro, J.B.1
Sanbonmatsu, K.Y.2
Spahn, C.M.T.3
Blanchard, S.C.4
-
129
-
-
60349097663
-
Single-molecule observations of ribosome function
-
S. C. Blanchard, Single-molecule observations of ribosome function, Curr. Opin. Struct. Biol. 19, 103-109 (2009).
-
(2009)
Curr. Opin. Struct. Biol
, vol.19
, pp. 103-109
-
-
Blanchard, S.C.1
-
130
-
-
77951107295
-
Real-time tRNA transit on single translating ribosome at codon resolution
-
S. Uemura, C. E. Aitken, J. Korlach, B. A. Flusberg, S. W. Turner and J. D. Puglisi, Real-time tRNA transit on single translating ribosome at codon resolution, Nature 464, 1012-1017 (2010).
-
(2010)
Nature
, vol.464
, pp. 1012-1017
-
-
Uemura, S.1
Aitken, C.E.2
Korlach, J.3
Flusberg, B.A.4
Turner, S.W.5
Puglisi, J.D.6
-
131
-
-
77954383845
-
Following the intersubunit conformation of the ribosome during translation in real time
-
C. E. Aitken and J. D. Puglisi, Following the intersubunit conformation of the ribosome during translation in real time, Nat. Struct. Mol. Biol. 17, 793-800 (2010).
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 793-800
-
-
Aitken, C.E.1
Puglisi, J.D.2
-
132
-
-
0141521419
-
Protein synthesis by single ribosomes
-
F. Vanzi, S. Vladimirov, C. R. Knudsen, Y. E. Goldman and B. S. Cooperman, Protein synthesis by single ribosomes, RNA, 9, 1174-1179 (2003).
-
(2003)
RNA
, vol.9
, pp. 1174-1179
-
-
Vanzi, F.1
Vladimirov, S.2
Knudsen, C.R.3
Goldman, Y.E.4
Cooperman, B.S.5
-
133
-
-
34648813439
-
Single-molecule structural dynamics of EF-Gribosome interaction during translocation
-
Y. Wang, H. Qin, R. D. Kudaravalli, S. V. Kirillov, G. T. Dempsey, D. Pan, B. S. Cooperman and Y. E. Goldman, Single-molecule structural dynamics of EF-Gribosome interaction during translocation, Biochemistry 46, 10767-10775 (2007).
-
(2007)
Biochemistry
, vol.46
, pp. 10767-10775
-
-
Wang, Y.1
Qin, H.2
Kudaravalli, R.D.3
Kirillov, S.V.4
Dempsey, G.T.5
Pan, D.6
Cooperman, B.S.7
Goldman, Y.E.8
-
134
-
-
41149155366
-
Following translation by single ribosome one codon at a time
-
J. D. Wen, L. Lancaster, C. Hodges, A. C. Zeri, S. H. Yoshimura, H. F. Noller, C. Bustamante and I. Tinoco Jr., Following translation by single ribosome one codon at a time, Nature 452, 598-603 (2008).
-
(2008)
Nature
, vol.452
, pp. 598-603
-
-
Wen, J.D.1
Lancaster, L.2
Hodges, C.3
Zeri, A.C.4
Yoshimura, S.H.5
Noller, H.F.6
Bustamante, C.7
Tinoco Jr., I.8
-
135
-
-
68349152494
-
Simulation and analysis of single-ribosome translation, Phys
-
I. Tinoco Jr. and J. D. Wen, Simulation and analysis of single-ribosome translation, Phys. Biol. 6, 025006 (2009).
-
(2009)
Biol
, vol.6
, pp. 025006
-
-
Tinoco Jr., I.1
Wen, D.J.2
-
136
-
-
34548446795
-
Halting a cellular production line: Responses to ribosomal pausing during translation
-
J. R. Buchan and I. Stansfield, Halting a cellular production line: Responses to ribosomal pausing during translation, Biol. Cell 99, 475-487 (2007).
-
(2007)
Biol. Cell
, vol.99
, pp. 475-487
-
-
Buchan, J.R.1
Stansfield, I.2
-
137
-
-
68949085318
-
Stochastic kinetics of ribosomes: Single motor properties and collective behavior
-
A. Garai, D. Chowdhury and T. V. Ramakrishnan, Stochastic kinetics of ribosomes: Single motor properties and collective behavior, Phys. Rev. E 80, 011908 (2009).
-
(2009)
Phys. Rev. e
, vol.80
, pp. 011908
-
-
Garai, A.1
Chowdhury, D.2
Ramakrishnan, T.V.3
-
138
-
-
79954510329
-
Distribution of dwell times of a ribosome: Effects of infidelity, kinetic proofreading and ribosome crowding
-
A. K. Sharma and D. Chowdhury, Distribution of dwell times of a ribosome: Effects of infidelity, kinetic proofreading and ribosome crowding, Physical Biology, 8, 026005 (2011).
-
(2011)
Physical Biology
, vol.8
, pp. 026005
-
-
Sharma, A.K.1
Chowdhury, D.2
-
139
-
-
0001405969
-
Statistical physics of vehicular traffic and some related systems
-
D. Chowdhury, L. Santen and A. Schadschneider, Statistical physics of vehicular traffic and some related systems, Phys. Rep. 329, 199-329 (2000).
-
(2000)
Phys. Rep
, vol.329
, pp. 199-329
-
-
Chowdhury, D.1
Santen, L.2
Schadschneider, A.3
-
141
-
-
28844464300
-
Physics of transport and traffic phenomena in biology: From molecular motors and cells to organisms
-
D. Chowdhury, A. Schadschneider and K. Nishinari, Physics of transport and traffic phenomena in biology: From molecular motors and cells to organisms, Phys. of Life Rev. 2, 318-352 (2005).
-
(2005)
Phys. of Life Rev
, vol.2
, pp. 318-352
-
-
Chowdhury, D.1
Schadschneider, A.2
Nishinari, K.3
-
142
-
-
0000763816
-
Electron microscope studies of ribosomal clusters synthesizing hemoglobin
-
J. R. Warner, A. Rich and C. E. Hall, Electron microscope studies of ribosomal clusters synthesizing hemoglobin, Science 138, 1399-1403 (1962).
-
(1962)
Science
, vol.138
, pp. 1399-1403
-
-
Warner, J.R.1
Rich, A.2
Hall, C.E.3
-
144
-
-
3943067805
-
The excitement of discovery
-
A. Rich, The excitement of discovery, Annu. Rev. Biochem. 73, 1-37 (2004).
-
(2004)
Annu. Rev. Biochem
, vol.73
, pp. 1-37
-
-
Rich, A.1
-
145
-
-
58149163468
-
The discovery of polyribosomes
-
H. Noll, The discovery of polyribosomes, Bioessays 30, 1220-1234 (2008).
-
(2008)
Bioessays
, vol.30
, pp. 1220-1234
-
-
Noll, H.1
-
146
-
-
49349113285
-
Ribosome collisions and translation efficiency: Optimization by codon usage and mRNA destabilization
-
N. Mitarai, K. Sneppen and S. Pedersen, Ribosome collisions and translation efficiency: Optimization by codon usage and mRNA destabilization, J. Mol. Biol. 382, 236-245 (2008).
-
(2008)
J. Mol. Biol
, vol.382
, pp. 236-245
-
-
Mitarai, N.1
Sneppen, K.2
Pedersen, S.3
-
147
-
-
0037388094
-
Genonewide analysis of mRNA translation profiles in Saccharomyces cerevisiae
-
Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown and D. Herschlag, Genonewide analysis of mRNA translation profiles in Saccharomyces cerevisiae, Proc. Natl. Acad. Sci. USA 100, 3889-3894 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3889-3894
-
-
Arava, Y.1
Wang, Y.2
Storey, J.D.3
Liu, C.L.4
Brown, P.O.5
Herschlag, D.6
-
148
-
-
20544439035
-
Native polysomes of Saccharomyces cerevisiae in liquid solution observed by atomic force microscopy
-
E. Mikamo, C. Tanaka, T. Kanno, H. Akiyama, G. Jung, H. Tanaka and T. Kawai, Native polysomes of Saccharomyces cerevisiae in liquid solution observed by atomic force microscopy, J. Struct. Biol. 151, 106-110 (2005).
-
(2005)
J. Struct. Biol
, vol.151
, pp. 106-110
-
-
Mikamo, E.1
Tanaka, C.2
Kanno, T.3
Akiyama, H.4
Jung, G.5
Tanaka, H.6
Kawai, T.7
-
149
-
-
17844395239
-
Dissecting eukaryotic translation and its control by ribosome density mapping
-
Y. Arava, F. E. Boas, P. O. Brown and D. Herschlag, Dissecting eukaryotic translation and its control by ribosome density mapping, Nucl. Acids Res. 33, 2421-2432 (2005).
-
(2005)
Nucl. Acids Res
, vol.33
, pp. 2421-2432
-
-
Arava, Y.1
Boas, F.E.2
Brown, P.O.3
Herschlag, D.4
-
150
-
-
62549134121
-
Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
N. T. Ingolia, S. Ghaemmaghami, J. R. S. Newman and J. S. Weissman, Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science 324, 218-223 (2009).
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.S.3
Weissman, J.S.4
-
151
-
-
77955644289
-
Mammalian microRNAs predominantly act to decrease target mRNA levels
-
H. Guo, N. T. Ingolia, J. S. Weissman and D. P. Bartel, Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature 466, 835-840 (2010).
-
(2010)
Nature
, vol.466
, pp. 835-840
-
-
Guo, H.1
Ingolia, N.T.2
Weissman, J.S.3
Bartel, D.P.4
-
152
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteosomes
-
N. T. Ingolia, L. F. Lareau and J. S. Weissman, Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteosomes, Cell 147, 789-802 (2011).
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
153
-
-
80055088002
-
Nonequilibrium statistical mechanics: From a paradigmatic model to biological transport
-
T. Chou, K. Mallick and R. K. P. Zia, Nonequilibrium statistical mechanics: From a paradigmatic model to biological transport, Rep. Prog. Phys. 74, 116601 (2011).
-
(2011)
Rep. Prog. Phys
, vol.74
, pp. 116601
-
-
Chou, T.1
Mallick, K.2
Zia, R.K.P.3
-
154
-
-
84873429816
-
Mathematical and computational modelling of ribosomal movement and protein synthesis: An overview
-
T. von der Haar, Mathematical and computational modelling of ribosomal movement and protein synthesis: An overview, Comp. and Struct. Biotechnol. J. 1, e201204002 (2012).
-
(2012)
Comp. and Struct. Biotechnol. J
, vol.1
-
-
Haar Der T.Von1
-
155
-
-
33846838995
-
Traffic of interacting ribosomes: Effects of single-machine mechanochemistry on protein synthesis
-
A. Basu and D. Chowdhury, Traffic of interacting ribosomes: effects of single-machine mechanochemistry on protein synthesis, Phys. Rev. E 75, 021902 (2007).
-
(2007)
Phys. Rev e
, vol.75
, pp. 021902
-
-
Basu, A.1
Chowdhury, D.2
-
156
-
-
80052524231
-
Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript
-
A. K. Sharma and D. Chowdhury, Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript, J. Theor. Biol. 289, 36-46 (2011).
-
(2011)
J. Theor. Biol
, vol.289
, pp. 36-46
-
-
Sharma, A.K.1
Chowdhury, D.2
-
157
-
-
34250701119
-
Mining and engineering natural product biosynthetic pathways
-
B.Wilkinson and J. Micklefield, Mining and engineering natural product biosynthetic pathways, Nat. Chem. Biol. 3, 379-386 (2007).
-
(2007)
Nat. Chem. Biol
, vol.3
, pp. 379-386
-
-
Wilkinson, B.1
Micklefield, J.2
-
158
-
-
78449290452
-
New insights into the formation of fungal aromatic polyketides
-
J. M. Crawford and C. A. Townsend, New insights into the formation of fungal aromatic polyketides, Nat. Rev. Microbiol. 8, 879-889 (2010).
-
(2010)
Nat. Rev. Microbiol
, vol.8
, pp. 879-889
-
-
Crawford, J.M.1
Townsend, C.A.2
-
159
-
-
73349085562
-
Working outside the protein synthesis rules: Insights into nonribosomal peptide synthesis
-
M. A. Marahiel, Working outside the protein synthesis rules: Insights into nonribosomal peptide synthesis, J. Peptide Sci. 15, 799-807 (2009).
-
(2009)
J. Peptide Sci
, vol.15
, pp. 799-807
-
-
Marahiel, M.A.1
-
160
-
-
0034887171
-
Polyketide biosynthesis: A millenium review
-
J. Staunton and K. J. Weissman, Polyketide biosynthesis: A millenium review, Nat. Prod. Rep. 18, 380-416 (2001).
-
(2001)
Nat. Prod. Rep
, vol.18
, pp. 380-416
-
-
Staunton, J.1
Weissman, K.J.2
-
161
-
-
33748631825
-
Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms
-
M. A. Fischbach and C. T. Walsh, Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms, Chem. Rev. 106, 3468-3496 (2006).
-
(2006)
Chem Rev
, vol.106
, pp. 3468-3496
-
-
Fischbach, M.A.1
Walsh, C.T.2
-
162
-
-
68949159560
-
The chemical biology of modular biosynthetic enzymes
-
J. L. Meier and M. D. Burkart, The chemical biology of modular biosynthetic enzymes, Chem Soc. Rev. 38, 2012-2045 (2009).
-
(2009)
Chem Soc. Rev
, vol.38
, pp. 2012-2045
-
-
Meier, J.L.1
Burkart, M.D.2
-
163
-
-
8644253596
-
Biologically inspired molecular assembly lines
-
B. Chow and J.M. Jacobson, Biologically inspired molecular assembly lines, BT Technool. J. 22, 270-277 (2004).
-
(2004)
BT Technool. J
, vol.22
, pp. 270-277
-
-
Chow, B.1
Jacobson, J.M.2
-
164
-
-
65349098181
-
Revisiting the modularity of modular polyketide synthases
-
C. Khosla, S. Kapur and D. E. Cane, Revisiting the modularity of modular polyketide synthases, Curr. Opin. Chem. Biol. 13, 135-143 (2009).
-
(2009)
Curr. Opin. Chem. Biol
, vol.13
, pp. 135-143
-
-
Khosla, C.1
Kapur, S.2
Cane, D.E.3
-
165
-
-
22244466130
-
The structural biology of type II fatty acid biosynthesis
-
S. W. White, J. Zheng, Y. M. Zhang and C. O. Rock, The structural biology of type II fatty acid biosynthesis, Annu. Rev. Biochem. 74, 791-831 (2005).
-
(2005)
Annu. Rev. Biochem
, vol.74
, pp. 791-831
-
-
White, S.W.1
Zheng, J.2
Zhang, Y.M.3
Rock, C.O.4
-
166
-
-
33947286240
-
Fatty acid synthesis and elongation in yeast, Biochim
-
O. Tehlivets, K. Scheuringer and S. D. Kohlwein, Fatty acid synthesis and elongation in yeast, Biochim. Biophys. Acta 1771, 255-270 (2007).
-
(2007)
Biophys. Acta
, vol.1771
, pp. 255-270
-
-
Tehlivets, O.1
Scheuringer, K.2
Kohlwein, S.D.3
-
167
-
-
33646018341
-
Fatty acid elongases in mammals: Their regulation and roles in metabolism
-
A. Jakobsson, R. Westerberg and A. Jacobsson, Fatty acid elongases in mammals: Their regulation and roles in metabolism, Prof. Lipis Res. 45, 237-249 (2006).
-
(2006)
Prof Lipis Res
, vol.45
, pp. 237-249
-
-
Jakobsson, A.1
Westerberg, R.2
Jacobsson, A.3
-
168
-
-
0242636435
-
Elongation of long-chain fatty acids
-
A. E. Leonard, S. L. Pereira, H. Sprecher and Y. S. Huang, Elongation of long-chain fatty acids, Prog. Lipid Res. 43, 36-54 (2004).
-
(2004)
Prog Lipid Res
, vol.43
, pp. 36-54
-
-
Leonard, A.E.1
Pereira, S.L.2
Sprecher, H.3
Huang, Y.S.4
-
169
-
-
0037411269
-
Strctural and functional organization of the animal fatty acid synthase
-
S. Smith, A. Witkowski and A. K. Joshi, Strctural and functional organization of the animal fatty acid synthase, Prog. Lipid Res. 42, 289-317 (2003).
-
(2003)
Prog. Lipid Res
, vol.42
, pp. 289-317
-
-
Smith, S.1
Witkowski, A.2
Joshi, A.K.3
-
170
-
-
68149132445
-
Structural insights into nonribosomal peptide enzymatic assembly lines
-
A. Koglin and C. T. Walsh, Structural insights into nonribosomal peptide enzymatic assembly lines, Nat. Prod. Rep. 26, 987-1000 (2009).
-
(2009)
Nat. Prod. Rep
, vol.26
, pp. 987-1000
-
-
Koglin, A.1
Walsh, C.T.2
-
171
-
-
9944250036
-
Structural aspects of nonribosomal peptide biosynthesis
-
G. L. Challis and J. H. Naismith, Structural aspects of nonribosomal peptide biosynthesis, Current Opin. Struct. Biol. 14, 748-756 (2004).
-
(2004)
Current Opin. Struct. Biol
, vol.14
, pp. 748-756
-
-
Challis, G.L.1
Naismith, J.H.2
-
172
-
-
0030267847
-
A functional chimeric modular polyketide synthase generated via domain replacement
-
D. Bedford, J. R. Jacobsen, G. Luo, D. E. Cane and C. Khosla, A functional chimeric modular polyketide synthase generated via domain replacement, Chem. & Biol. 3, 827-831 (1996).
-
(1996)
Chem. & Biol
, vol.3
, pp. 827-831
-
-
Bedford, D.1
Jacobsen, J.R.2
Luo, G.3
Cane, D.E.4
Khosla, C.5
-
173
-
-
12344283741
-
Structure and function of animal fatty acid synthase
-
S. S. Chirala and S. J. Wakil, Structure and Function of Animal Fatty Acid Synthase, Lipids 39, 1045-1053 (2004).
-
(2004)
Lipids
, vol.39
, pp. 1045-1053
-
-
Chirala, S.S.1
Wakil, S.J.2
-
174
-
-
3142672123
-
Substrate recognition by nonribosomal peptide synthetase multi-enzymes
-
S. Lautru and G. L. Challis, Substrate recognition by nonribosomal peptide synthetase multi-enzymes, Microbiol. 150, 1629-1636 (2004).
-
(2004)
Microbiol
, vol.150
, pp. 1629-1636
-
-
Lautru, S.1
Challis, G.L.2
-
175
-
-
0032860405
-
Tolerance and specificity of polyketide synthases
-
C. Khosla, R. S. Gokhale, J. R. Jacobsen and D. E. Cane, Tolerance and specificity of polyketide synthases, Annu. Rev. Biochem. 68, 219-253 (1999).
-
(1999)
Annu. Rev. Biochem
, vol.68
, pp. 219-253
-
-
Khosla, C.1
Gokhale, R.S.2
Jacobsen, J.R.3
Cane, D.E.4
-
176
-
-
33645116726
-
Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides
-
J. Gr?unewald and M. A. Marahiel, Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides, Microbiol. Mol. Biol. Rev. 70, 121-146 (2006).
-
(2006)
Microbiol. Mol. Biol. Rev
, vol.70
, pp. 121-146
-
-
Grunewald, J.1
Marahiel, M.A.2
-
178
-
-
9244234513
-
Biosynthesis of nonribosomal peptides
-
R. Finking and M. A. Marahiel, Biosynthesis of nonribosomal peptides, Annu. Rev. Microbiol. 58, 453-488 (2004).
-
(2004)
Annu. Rev. Microbiol
, vol.58
, pp. 453-488
-
-
Finking, R.1
Marahiel, M.A.2
-
180
-
-
37049046706
-
Entropy in template-directed polymerization
-
B. K. Davis, Entropy in template-directed polymerization, Nature 206, 183-184 (1965).
-
(1965)
Nature
, vol.206
, pp. 183-184
-
-
Davis, B.K.1
-
181
-
-
84864992970
-
Entropy involved in fidelity of DNA replication
-
J. R. Arias-Gonzalez, Entropy involved in fidelity of DNA replication, PLoS ONE 7(8), e42272 (2012).
-
(2012)
PLoS ONE
, vol.7
, Issue.8
-
-
Arias-Gonzalez, J.R.1
-
182
-
-
47749114982
-
Nonequilibrium generation of information in copolymerization processes
-
D. Andrieux and P. Gaspard, Nonequilibrium generation of information in copolymerization processes, Proc. Natl. Acad. Sci USA 105, 9516-9521 (2008).
-
(2008)
Proc. Natl. Acad. Sci USA
, vol.105
, pp. 9516-9521
-
-
Andrieux, D.1
Gaspard, P.2
-
183
-
-
58149515858
-
Molecular information processing in nonequilibrium copolymerizations
-
D. Andrieux and P. Gaspard, Molecular information processing in nonequilibrium copolymerizations, J. Chem. Phys. 130, 014901 (2009).
-
(2009)
J. Chem. Phys
, vol.130
, pp. 014901
-
-
Andrieux, D.1
Gaspard, P.2
-
184
-
-
84960561455
-
On computable numbers, with an application to the entscheidungsproblem
-
A. Turing, On computable numbers, with an application to the entscheidungsproblem, Proc. Lond. Math. Soc. 43, 230-265 (1936).
-
(1936)
Proc. Lond. Math. Soc
, vol.43
, pp. 230-265
-
-
Turing, A.1
-
185
-
-
0031801743
-
Information processing by RNA polymerase: Recognition of regulatory signals during RNA chain elongation
-
R. A. Mooney, I. Artsimovitch and R. Landick, Information processing by RNA polymerase: Recognition of regulatory signals during RNA chain elongation, J. Bacteriol. 180, 3265-3275 (1998).
-
(1998)
J. Bacteriol
, vol.180
, pp. 3265-3275
-
-
Mooney, R.A.1
Artsimovitch, I.2
Landick, R.3
-
186
-
-
85008815032
-
Thermodynamic description of a copolymerisation process: The link between Maxwell's demon and the drive to compile genetic information
-
H. H. Klump, Thermodynamic description of a copolymerisation process: The link between Maxwell's demon and the drive to compile genetic information, Trans. Roy. Soc. South Afr. 64, 73-75 (2009).
-
(2009)
Trans. Roy. Soc. South Afr
, vol.64
, pp. 73-75
-
-
Klump, H.H.1
-
187
-
-
79955820940
-
Stochastic thermodynamics of single enzymes and molecular motors
-
U. Seifert, Stochastic thermodynamics of single enzymes and molecular motors, Eur. Phys. J. E 34, 26 (2011).
-
(2011)
Eur. Phys. J e
, vol.34
, pp. 26
-
-
Seifert, U.1
|