-
1
-
-
0032982866
-
EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
-
Agrawal R.K., Heagle A.B., Penczek P., Grassucci R.A., Frank J. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nat. Struct. Biol. 6:1999;643-647
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 643-647
-
-
Agrawal, R.K.1
Heagle, A.B.2
Penczek, P.3
Grassucci, R.A.4
Frank, J.5
-
2
-
-
0034618071
-
Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle
-
Agrawal R.K., Spahn C.M., Penczek P., Grassucci R.A., Nierhaus K.H., Frank J. Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle. J. Cell Biol. 150:2000;447-460
-
(2000)
J. Cell Biol.
, vol.150
, pp. 447-460
-
-
Agrawal, R.K.1
Spahn, C.M.2
Penczek, P.3
Grassucci, R.A.4
Nierhaus, K.H.5
Frank, J.6
-
3
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan A.R., Durell S.R., Jernigan R.L., Demirel M.C., Keskin O., Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:2001;505-515
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
4
-
-
0033596908
-
Cooperative fluctuations and subunit communication in tryptophan synthase
-
Bahar I., Jernigan R.L. Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry. 38:1999;3478-3490
-
(1999)
Biochemistry
, vol.38
, pp. 3478-3490
-
-
Bahar, I.1
Jernigan, R.L.2
-
5
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:1997;173-181
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
6
-
-
0030729453
-
Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations
-
Bahar I., Erman B., Haliloglu T., Jernigan R.L. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry. 36:1997;13512-13523
-
(1997)
Biochemistry
, vol.36
, pp. 13512-13523
-
-
Bahar, I.1
Erman, B.2
Haliloglu, T.3
Jernigan, R.L.4
-
7
-
-
0000496772
-
Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability
-
Bahar I., Atilgan A.R., Demirel M.C., Erman B. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys. Rev. Lett. 80:1998;2733-2736
-
(1998)
Phys. Rev. Lett.
, vol.80
, pp. 2733-2736
-
-
Bahar, I.1
Atilgan, A.R.2
Demirel, M.C.3
Erman, B.4
-
8
-
-
3342877839
-
Collective motions in HIV-1 reverse transcriptase: Examination of flexibility and enzyme function
-
Bahar I., Erman B., Jernigan R.L., Atilgan A.R., Covell D.G. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J. Mol. Biol. 285:1999;1023-1037
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1023-1037
-
-
Bahar, I.1
Erman, B.2
Jernigan, R.L.3
Atilgan, A.R.4
Covell, D.G.5
-
9
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
-
Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4. Å resolution Science. 289:2000;905-920
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
10
-
-
0034699519
-
Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
-
Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 407:2000;340-348
-
(2000)
Nature
, vol.407
, pp. 340-348
-
-
Carter, A.P.1
Clemons, W.M.2
Brodersen, D.E.3
Morgan-Warren, R.J.4
Wimberly, B.T.5
Ramakrishnan, V.6
-
11
-
-
0037079578
-
Dynamics of large proteins through hierarchical levels of coarse-grained structures
-
Doruker P., Jernigan R.L., Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:2002;119-127
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 119-127
-
-
Doruker, P.1
Jernigan, R.L.2
Bahar, I.3
-
12
-
-
0034691576
-
A ratchet-like inter-subunit reorganization of the ribosome during translocation
-
Frank J., Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 406:2000;318-322
-
(2000)
Nature
, vol.406
, pp. 318-322
-
-
Frank, J.1
Agrawal, R.K.2
-
13
-
-
0033397413
-
Animation of the dynamical events of the elongation cycle based on cryoelectron microscopy of functional complexes of the ribosome
-
Frank J., Heagle A.B., Agrawal R.K. Animation of the dynamical events of the elongation cycle based on cryoelectron microscopy of functional complexes of the ribosome. J. Struct. Biol. 128:1999;15-18
-
(1999)
J. Struct. Biol.
, vol.128
, pp. 15-18
-
-
Frank, J.1
Heagle, A.B.2
Agrawal, R.K.3
-
14
-
-
0038275890
-
Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement
-
Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J. Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell. 113:2003;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
-
16
-
-
0032006209
-
Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
-
Hayward S., Berendsen H.J. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 30:1998;144-154
-
(1998)
Proteins
, vol.30
, pp. 144-154
-
-
Hayward, S.1
Berendsen, H.J.2
-
17
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
-
Hayward S., Kitao A., Berendsen H.J. Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins. 27:1997;425-437
-
(1997)
Proteins
, vol.27
, pp. 425-437
-
-
Hayward, S.1
Kitao, A.2
Berendsen, H.J.3
-
18
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:1998;417-429
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
19
-
-
0033557178
-
Analysis of domain motions in large proteins
-
Hinsen K., Thomas A., Field M.J. Analysis of domain motions in large proteins. Proteins. 34:1999;369-382
-
(1999)
Proteins
, vol.34
, pp. 369-382
-
-
Hinsen, K.1
Thomas, A.2
Field, M.J.3
-
20
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., Schulten, K., 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-8, 27-8
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
21
-
-
0036154101
-
Functional motions of influenza virus hemagglutinin: A structure-based analytical approach
-
Isin B., Doruker P., Bahar I. Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. Biophys. J. 82:2002;569-581
-
(2002)
Biophys. J.
, vol.82
, pp. 569-581
-
-
Isin, B.1
Doruker, P.2
Bahar, I.3
-
23
-
-
0037080323
-
Molecular mechanisms of chaperonin GroEL-GroES function
-
Keskin O., Bahar I., Flatow D., Covell D.G., Jernigan R.L. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41:2002;491-501
-
(2002)
Biochemistry
, vol.41
, pp. 491-501
-
-
Keskin, O.1
Bahar, I.2
Flatow, D.3
Covell, D.G.4
Jernigan, R.L.5
-
24
-
-
0035996975
-
Relating molecular flexibility to function: A case study of tubulin
-
Keskin O., Durell S.R., Bahar I., Jernigan R.L., Covell D.G. Relating molecular flexibility to function: a case study of tubulin. Biophys. J. 83:2002;663-680
-
(2002)
Biophys. J.
, vol.83
, pp. 663-680
-
-
Keskin, O.1
Durell, S.R.2
Bahar, I.3
Jernigan, R.L.4
Covell, D.G.5
-
25
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs W.G., Alexandrov V., Wilson C.A., Echols N., Yu H., Gerstein M. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48:2002;682-695
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
Alexandrov, V.2
Wilson, C.A.3
Echols, N.4
Yu, H.5
Gerstein, M.6
-
26
-
-
0035996990
-
Dynamics of proteins in crystals: Comparison of experiment with simple models
-
Kundu S., Melton J.S., Sorensen D.C., Phillips G.N. Jr. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys. J. 83:2002;723-732
-
(2002)
Biophys. J.
, vol.83
, pp. 723-732
-
-
Kundu, S.1
Melton, J.S.2
Sorensen, D.C.3
Phillips Jr., G.N.4
-
27
-
-
0037229886
-
Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex
-
Lynch S.R., Gonzalez R.L., Puglisi J.D. Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure. 11:2003;43-53
-
(2003)
Structure
, vol.11
, pp. 43-53
-
-
Lynch, S.R.1
Gonzalez, R.L.2
Puglisi, J.D.3
-
28
-
-
0030700726
-
Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis
-
Ma J.P., Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274:1997;114-131
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 114-131
-
-
Ma, J.P.1
Karplus, M.2
-
29
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
Marques O., Sanejouand Y.H. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins. 23:1995;557-560
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.H.2
-
30
-
-
0037029028
-
Translocation of tRNA during protein synthesis
-
Noller H.F., Yusupov M.M., Yusupova G.Z., Baucom A., Cate J.H. Translocation of tRNA during protein synthesis. FEBS Lett. 514:2002;11-16
-
(2002)
FEBS Lett.
, vol.514
, pp. 11-16
-
-
Noller, H.F.1
Yusupov, M.M.2
Yusupova, G.Z.3
Baucom, A.4
Cate, J.H.5
-
32
-
-
0034268836
-
Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution
-
Schluenzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell. 102:2000;615-623
-
(2000)
Cell
, vol.102
, pp. 615-623
-
-
Schluenzen, F.1
Tocilj, A.2
Zarivach, R.3
Harms, J.4
Gluehmann, M.5
Janell, D.6
Bashan, A.7
Bartels, H.8
Agmon, I.9
Franceschi, F.10
Yonath, A.11
-
33
-
-
0036307741
-
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
-
Tama F., Brooks C.L. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J. Mol. Biol. 318:2002;733-747
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 733-747
-
-
Tama, F.1
Brooks, C.L.2
-
34
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama F., Gadea F.X., Marques O., Sanejouand Y.H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:2000;1-7
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.H.4
-
35
-
-
0036382958
-
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
-
Tama F., Wriggers W., Brooks C.L. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:2002;297-305
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 297-305
-
-
Tama, F.1
Wriggers, W.2
Brooks, C.L.3
-
36
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama F., Valle M., Frank J., Brooks C.L. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:2003;9319-9323
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks, C.L.4
-
37
-
-
0036782103
-
Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase
-
Temiz N.A., Bahar I. Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase. Proteins. 49:2002;61-70
-
(2002)
Proteins
, vol.49
, pp. 61-70
-
-
Temiz, N.A.1
Bahar, I.2
-
38
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1996;1905-1908
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
39
-
-
0036646535
-
Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process
-
Valle M., Sengupta J., Swami N.K., Grassucci R.A., Burkhardt N., Nierhaus K.H., Agrawal R.K., Frank J. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21:2002;3557-3567
-
(2002)
EMBO J.
, vol.21
, pp. 3557-3567
-
-
Valle, M.1
Sengupta, J.2
Swami, N.K.3
Grassucci, R.A.4
Burkhardt, N.5
Nierhaus, K.H.6
Agrawal, R.K.7
Frank, J.8
-
40
-
-
0034624039
-
Movement of the decoding region of the 16S ribosomal RNA accompanies tRNA translocation
-
VanLoock M.S., Agrawal R.K., Gabashvili I.S., Qi L., Frank J., Harvey S.C. Movement of the decoding region of the 16S ribosomal RNA accompanies tRNA translocation. J. Mol. Biol. 304:2000;507-515
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 507-515
-
-
Vanloock, M.S.1
Agrawal, R.K.2
Gabashvili, I.S.3
Qi, L.4
Frank, J.5
Harvey, S.C.6
-
41
-
-
0034699518
-
Structure of the 30S ribosomal subunit
-
Wimberly B.T., Brodersen D.E., Clemons W.M. Jr., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 407:2000;327-339
-
(2000)
Nature
, vol.407
, pp. 327-339
-
-
Wimberly, B.T.1
Brodersen, D.E.2
Clemons Jr., W.M.3
Morgan-Warren, R.J.4
Carter, A.P.5
Vonrhein, C.6
Hartsch, T.7
Ramakrishnan, V.8
-
42
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word J.M., Lovell S.C., Richardson J.S., Richardson D.C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285:1999;1735-1747
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
43
-
-
0030883755
-
Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
-
Wriggers W., Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins. 29:1997;1-14
-
(1997)
Proteins
, vol.29
, pp. 1-14
-
-
Wriggers, W.1
Schulten, K.2
-
44
-
-
0033863336
-
Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures
-
Wriggers W., Agrawal R.K., Drew D.L., McCammon A., Frank J. Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures. Biophys. J. 79:2000;1670-1678
-
(2000)
Biophys. J.
, vol.79
, pp. 1670-1678
-
-
Wriggers, W.1
Agrawal, R.K.2
Drew, D.L.3
McCammon, A.4
Frank, J.5
-
45
-
-
0035805213
-
Crystal structure of the ribosome at 5.5 Å resolution
-
Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., Noller H.F. Crystal structure of the ribosome at 5.5. Å resolution Science. 292:2001;883-896
-
(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.6
Noller, H.F.7
|