-
1
-
-
0023212383
-
A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction
-
Yonath A, Leonard KR, Wittmann HG (1987) A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction. Science 236: 813-816.
-
(1987)
Science
, vol.236
, pp. 813-816
-
-
Yonath, A.1
Leonard, K.R.2
Wittmann, H.G.3
-
2
-
-
0034637161
-
The structural basis of ribosome activity in peptide bond synthesis
-
Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289: 920-930.
-
(2000)
Science
, vol.289
, pp. 920-930
-
-
Nissen, P.1
Hansen, J.2
Ban, N.3
Moore, P.B.4
Steitz, T.A.5
-
3
-
-
18444411651
-
The social life of ribosomal proteins
-
Brodersen DE, Nissen P (2005) The social life of ribosomal proteins. Febs J 272: 2098-2108.
-
(2005)
Febs J
, vol.272
, pp. 2098-2108
-
-
Brodersen, D.E.1
Nissen, P.2
-
4
-
-
30944437007
-
Nascent peptide in the "birth canal" of the ribosome
-
Mankin AS (2006) Nascent peptide in the "birth canal" of the ribosome. Trends Biochem Sci 31: 11-13.
-
(2006)
Trends Biochem Sci
, vol.31
, pp. 11-13
-
-
Mankin, A.S.1
-
6
-
-
42449085840
-
Modulating the activity of the peptidyl transferase center of the ribosome
-
Beringer M (2008) Modulating the activity of the peptidyl transferase center of the ribosome. RNA 14: 795-801.
-
(2008)
RNA
, vol.14
, pp. 795-801
-
-
Beringer, M.1
-
7
-
-
34547569922
-
Mapping the electrostatic potential within the ribosomal exit tunnel
-
Lu J, Kobertz WR, Deutsch C (2007) Mapping the electrostatic potential within the ribosomal exit tunnel. J Mol Biol 371: 1378-1391.
-
(2007)
J Mol Biol
, vol.371
, pp. 1378-1391
-
-
Lu, J.1
Kobertz, W.R.2
Deutsch, C.3
-
8
-
-
54249096045
-
Electrostatics in the ribosomal tunnel modulate chain elongation rates
-
Lu J, Deutsch C (2008) Electrostatics in the ribosomal tunnel modulate chain elongation rates. J Mol Biol 384: 73-86.
-
(2008)
J Mol Biol
, vol.384
, pp. 73-86
-
-
Lu, J.1
Deutsch, C.2
-
9
-
-
30044447928
-
Ribosome exit tunnel can entropically stabilize alpha-helices
-
Ziv G, Haran G, Thirumalai D (2005) Ribosome exit tunnel can entropically stabilize alpha-helices. P Natl Acad Sci USA 102: 18956-18961.
-
(2005)
P Natl Acad Sci USA
, vol.102
, pp. 18956-18961
-
-
Ziv, G.1
Haran, G.2
Thirumalai, D.3
-
10
-
-
1542358892
-
Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins
-
Woolhead CA, McCormick PJ, Johnson AE (2004) Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 116: 725-736.
-
(2004)
Cell
, vol.116
, pp. 725-736
-
-
Woolhead, C.A.1
McCormick, P.J.2
Johnson, A.E.3
-
11
-
-
28544449949
-
Folding zones inside the ribosomal exit tunnel
-
Lu J, Deutsch C (2005) Folding zones inside the ribosomal exit tunnel. Nat Struct Mol Biol 12: 1123-1129.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 1123-1129
-
-
Lu, J.1
Deutsch, C.2
-
12
-
-
33744551950
-
Translation arrest requires two-way communication between a nascent polypeptide and the ribosome
-
Woolhead CA, Johnson AE, Bernstein HD (2006) Translation arrest requires two-way communication between a nascent polypeptide and the ribosome. Mol Cell 22: 587-598.
-
(2006)
Mol Cell
, vol.22
, pp. 587-598
-
-
Woolhead, C.A.1
Johnson, A.E.2
Bernstein, H.D.3
-
13
-
-
77949270274
-
alpha- Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel
-
Bhushan S, Gartmann M, Halic M, Armache JP, Jarasch A, et al. (2010) alpha- Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel. Nat Struct Mol Biol 17: 313-317.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 313-317
-
-
Bhushan, S.1
Gartmann, M.2
Halic, M.3
Armache, J.P.4
Jarasch, A.5
-
14
-
-
71549124362
-
Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling
-
Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache J-P, et al. (2009) Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling. Science 326: 1412-1415.
-
(2009)
Science
, vol.326
, pp. 1412-1415
-
-
Seidelt, B.1
Innis, C.A.2
Wilson, D.N.3
Gartmann, M.4
Armache, J.-P.5
-
15
-
-
23044445236
-
Features of Ribosome-Peptidyl-tRNA Interactions Essential for Tryptophan Induction of tna Operon Expression
-
Cruz-Vera LR, Rajagopal S, Squires C, Yanofsky C (2005) Features of Ribosome-Peptidyl-tRNA Interactions Essential for Tryptophan Induction of tna Operon Expression. Mol Cell 19: 333-343.
-
(2005)
Mol Cell
, vol.19
, pp. 333-343
-
-
Cruz-Vera, L.R.1
Rajagopal, S.2
Squires, C.3
Yanofsky, C.4
-
16
-
-
0037040411
-
The Ribosomal Exit Tunnel Functions as a Discriminating Gate
-
Nakatogawa H, Ito K (2002) The Ribosomal Exit Tunnel Functions as a Discriminating Gate. Cell 108: 629-636.
-
(2002)
Cell
, vol.108
, pp. 629-636
-
-
Nakatogawa, H.1
Ito, K.2
-
17
-
-
22244433549
-
Antibiotics targeting ribosomes: Resistance, selectivity, synergism and cellular regulation
-
Yonath A (2005) Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation. Annu Rev Biochem 74: 649-679.
-
(2005)
Annu Rev Biochem
, vol.74
, pp. 649-679
-
-
Yonath, A.1
-
18
-
-
0035950132
-
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria
-
Schlunzen F, Zarivach R, Harms J, Bashan A, Tocilj A, et al. (2001) Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413: 814-821.
-
(2001)
Nature
, vol.413
, pp. 814-821
-
-
Schlunzen, F.1
Zarivach, R.2
Harms, J.3
Bashan, A.4
Tocilj, A.5
-
20
-
-
35748981771
-
Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli
-
Zaman S, Fitzpatrick M, Lindahl L, Zengel J (2007) Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli. Mol Microbiol 66: 1039-1050.
-
(2007)
Mol Microbiol
, vol.66
, pp. 1039-1050
-
-
Zaman, S.1
Fitzpatrick, M.2
Lindahl, L.3
Zengel, J.4
-
21
-
-
43049089746
-
Molecular Mechanism of Drug- Dependent Ribosome Stalling
-
Vazquez-Laslop N, Thum C, Mankin AS (2008) Molecular Mechanism of Drug- Dependent Ribosome Stalling. Mol Cell 30: 190-202.
-
(2008)
Mol Cell
, vol.30
, pp. 190-202
-
-
Vazquez-Laslop, N.1
Thum, C.2
Mankin, A.S.3
-
22
-
-
42449111684
-
How hydrophobic buckminsterfullerene affects surrounding water structure
-
Weiss DR, Raschke TM, Levitt M (2008) How hydrophobic buckminsterfullerene affects surrounding water structure. J Phys Chem B 112: 2981-2990.
-
(2008)
J Phys Chem B
, vol.112
, pp. 2981-2990
-
-
Weiss, D.R.1
Raschke, T.M.2
Levitt, M.3
-
23
-
-
4344644050
-
Structure, dynamics and reactions of protein hydration water
-
Smith JC, Merzel F, Bondar AN, Tournier A, Fischer S (2004) Structure, dynamics and reactions of protein hydration water. Philos Trans R Soc Lond B 359: 1181-1190.
-
(2004)
Philos Trans R Soc Lond B
, vol.359
, pp. 1181-1190
-
-
Smith, J.C.1
Merzel, F.2
Bondar, A.N.3
Tournier, A.4
Fischer, S.5
-
24
-
-
43049122273
-
Water in nonpolar confinement: From nanotubes to proteins and beyond
-
Rasaiah JC, Garde S, Hummer G (2008) Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu Rev Phys Chem 59: 713-740.
-
(2008)
Annu Rev Phys Chem
, vol.59
, pp. 713-740
-
-
Rasaiah, J.C.1
Garde, S.2
Hummer, G.3
-
25
-
-
0037195604
-
Chemistry. Water in confinement
-
Levinger NE (2002) Chemistry. Water in confinement. Science 298: 1722-1723.
-
(2002)
Science
, vol.298
, pp. 1722-1723
-
-
Levinger, N.E.1
-
26
-
-
0032533454
-
Crystallographic water sites from a theoretical perspective
-
Feig M, Pettitt BM (1998) Crystallographic water sites from a theoretical perspective. Structure 6: 1351-1354.
-
(1998)
Structure
, vol.6
, pp. 1351-1354
-
-
Feig, M.1
Pettitt, B.M.2
-
27
-
-
0028921999
-
Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
-
Ernst JA, Clubb RT, Zhou HX, Gronenborn AM, Clore GM (1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267: 1813-1817.
-
(1995)
Science
, vol.267
, pp. 1813-1817
-
-
Ernst, J.A.1
Clubb, R.T.2
Zhou, H.X.3
Gronenborn, A.M.4
Clore, G.M.5
-
28
-
-
0033850087
-
High apparent dielectric constants in the interior of a protein reflect water penetration
-
Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, et al. (2000) High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys J 79: 1610-1620.
-
(2000)
Biophys J
, vol.79
, pp. 1610-1620
-
-
Dwyer, J.J.1
Gittis, A.G.2
Karp, D.A.3
Lattman, E.E.4
Spencer, D.S.5
-
29
-
-
26944481188
-
Interfaces and the driving force of hydrophobic assembly
-
Chandler D (2005) Interfaces and the driving force of hydrophobic assembly. Nature 437: 640-647.
-
(2005)
Nature
, vol.437
, pp. 640-647
-
-
Chandler, D.1
-
30
-
-
33646597782
-
Nanotube confinement denatures protein helices
-
Sorin EJ, Pande VS (2006) Nanotube confinement denatures protein helices. J Am Chem Soc 128: 6316-6317.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 6316-6317
-
-
Sorin, E.J.1
Pande, V.S.2
-
31
-
-
34547496252
-
Protein folding under confinement: A role for solvent
-
Lucent D, Vishal V, Pande VS (2007) Protein folding under confinement: a role for solvent. P Natl Acad Sci USA 104: 10430-10434.
-
(2007)
P Natl Acad Sci USA
, vol.104
, pp. 10430-10434
-
-
Lucent, D.1
Vishal, V.2
Pande, V.S.3
-
32
-
-
4944246231
-
Competition of hydrophobic and Coulombic interactions between nanosized solutes
-
Dzubiella J, Hansen JP (2004) Competition of hydrophobic and Coulombic interactions between nanosized solutes. J Chem Phys 121: 5514-5530.
-
(2004)
J Chem Phys
, vol.121
, pp. 5514-5530
-
-
Dzubiella, J.1
Hansen, J.P.2
-
33
-
-
0347319435
-
Reduction of the hydrophobic attraction between charged solutes in water
-
Dzubiella J, Hansen JP (2003) Reduction of the hydrophobic attraction between charged solutes in water. J Chem Phys 119: 12049-12052.
-
(2003)
J Chem Phys
, vol.119
, pp. 12049-12052
-
-
Dzubiella, J.1
Hansen, J.P.2
-
36
-
-
55949101455
-
Potential for modulation of the hydrophobic effect inside chaperonins
-
England JL, Pande VS (2008) Potential for modulation of the hydrophobic effect inside chaperonins. Biophys J 95: 3391-3399.
-
(2008)
Biophys J
, vol.95
, pp. 3391-3399
-
-
England, J.L.1
Pande, V.S.2
-
37
-
-
51749084427
-
A role for confined water in chaperonin function
-
England JL, Lucent D, Pande VS (2008) A role for confined water in chaperonin function. J Am Chem Soc 130: 11838-11839.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 11838-11839
-
-
England, J.L.1
Lucent, D.2
Pande, V.S.3
-
38
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
Trylska J, Tozzini V, McCammon JA (2005) Exploring global motions and correlations in the ribosome. Biophys J 89: 1455-1463.
-
(2005)
Biophys J
, vol.89
, pp. 1455-1463
-
-
Trylska, J.1
Tozzini, V.2
McCammon, J.A.3
-
39
-
-
4344715419
-
Ribosome motions modulate electrostatic properties
-
Trylska J, Konecny R, Tama F, Brooks CL, 3rd, McCammon JA (2004) Ribosome motions modulate electrostatic properties. Biopolymers 74: 423-431.
-
(2004)
Biopolymers
, vol.74
, pp. 423-431
-
-
Trylska, J.1
Konecny, R.2
Tama, F.3
Brooks III, C.L.4
McCammon, J.A.5
-
40
-
-
27644502679
-
Simulating movement of tRNA into the ribosome during decoding
-
Sanbonmatsu KY, Joseph S, Tung CS (2005) Simulating movement of tRNA into the ribosome during decoding. P Natl Acad Sci USA 102: 15854-15859.
-
(2005)
P Natl Acad Sci USA
, vol.102
, pp. 15854-15859
-
-
Sanbonmatsu, K.Y.1
Joseph, S.2
Tung, C.S.3
-
41
-
-
38549131880
-
Lattice simulations of cotranslational folding of single domain proteins
-
Peiyu Wang DKK (2008) Lattice simulations of cotranslational folding of single domain proteins. Proteins 70: 925-937.
-
(2008)
Proteins
, vol.70
, pp. 925-937
-
-
Peiyu Wang, D.K.K.1
-
42
-
-
66149167201
-
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
-
Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL (2009) Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 75: 837-845.
-
(2009)
Proteins
, vol.75
, pp. 837-845
-
-
Kurkcuoglu, O.1
Kurkcuoglu, Z.2
Doruker, P.3
Jernigan, R.L.4
-
43
-
-
33746592161
-
Molecular simulations of cotranslational protein folding: Fragment stabilities, folding cooperativity, and trapping in the ribosome
-
Elcock AH (2006) Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS Comput Biol 2: e98.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Elcock, A.H.1
-
44
-
-
0342394897
-
The Dielectric Polarization of Polar Liquids
-
Kirkwood JG (1939) The Dielectric Polarization of Polar Liquids. J Chem Phys 7: 911-919.
-
(1939)
J Chem Phys
, vol.7
, pp. 911-919
-
-
Kirkwood, J.G.1
-
45
-
-
0034885664
-
The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22
-
Gabashvili IS, Gregory ST, Valle M, Grassucci R, Worbs M, et al. (2001) The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22. Mol Cell 8: 181-188.
-
(2001)
Mol Cell
, vol.8
, pp. 181-188
-
-
Gabashvili, I.S.1
Gregory, S.T.2
Valle, M.3
Grassucci, R.4
Worbs, M.5
-
47
-
-
77649273304
-
A folding zone in the ribosomal exit tunnel for Kv1.3 helix formation
-
Tu LW, Deutsch C (2010) A folding zone in the ribosomal exit tunnel for Kv1.3 helix formation. J Mol Biol 396: 1346-1360.
-
(2010)
J Mol Biol
, vol.396
, pp. 1346-1360
-
-
Tu, L.W.1
Deutsch, C.2
-
48
-
-
64049105717
-
Tertiary interactions within the ribosomal exit tunnel
-
Kosolapov A, Deutsch C (2009) Tertiary interactions within the ribosomal exit tunnel. Nat Struct Mol Biol 16: 405-411.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 405-411
-
-
Kosolapov, A.1
Deutsch, C.2
-
49
-
-
33645981305
-
Electrostatics calculations: Latest methodological advances
-
Koehl P (2006) Electrostatics calculations: latest methodological advances. Curr Opin Struct Biol 16: 142-151.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 142-151
-
-
Koehl, P.1
-
50
-
-
61549101824
-
Beyond the Poisson-Boltzmann model: Modeling biomolecule-water and water-water interactions
-
Koehl P, Orland H, Delarue M (2009) Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Phys Rev Lett 102: 087801.
-
(2009)
Phys Rev Lett
, vol.102
, pp. 087801
-
-
Koehl, P.1
Orland, H.2
Delarue, M.3
-
51
-
-
17444416451
-
Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory
-
Imai T, Kovalenko A, Hirata F (2005) Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory. J Phys Chem B 109: 6658-6665.
-
(2005)
J Phys Chem B
, vol.109
, pp. 6658-6665
-
-
Imai, T.1
Kovalenko, A.2
Hirata, F.3
-
52
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgenson WL, Chandrasekhar J, Madura JD (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgenson, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
-
53
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl E, Hesss B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hesss, B.2
van der Spoel, D.3
-
54
-
-
0034623787
-
Screen savers of the world, Unite!
-
Shirts MR, Pande VS (2000) Screen savers of the world, Unite! Science 290: 1903-1904.
-
(2000)
Science
, vol.290
, pp. 1903-1904
-
-
Shirts, M.R.1
Pande, V.S.2
-
55
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
Sorin EJ, Pande VS (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J 88: 2472-2493.
-
(2005)
Biophys J
, vol.88
, pp. 2472-2493
-
-
Sorin, E.J.1
Pande, V.S.2
-
56
-
-
33750587438
-
Molecular Dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular Dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
57
-
-
0002296048
-
The influence of boundary conditions used in machine simulations on the structure of polar systems
-
Neumann M, Steinhauser O (1980) The influence of boundary conditions used in machine simulations on the structure of polar systems. Mol Phys 39: 437-454.
-
(1980)
Mol Phys
, vol.39
, pp. 437-454
-
-
Neumann, M.1
Steinhauser, O.2
-
58
-
-
0036708447
-
Bridging implicit and explicit solvent approaches for membrane electrostatics
-
Lin JH, Baker NA, McCammon JA (2002) Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys J 83: 1374-1379.
-
(2002)
Biophys J
, vol.83
, pp. 1374-1379
-
-
Lin, J.H.1
Baker, N.A.2
McCammon, J.A.3
|