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For: Adamczyk AJ, Warshel A. Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Proc Natl Acad Sci U S A 2011;108:9827-32. [PMID: 21617092 DOI: 10.1073/pnas.1105714108] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024;19:1259-1279. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
2
Shi D, Zhu X, Zhang H, Yan J, Bai C. Catalytic mechanism study of ATP-citrate lyase during citryl-CoA synthesis process. iScience 2024;27:110605. [PMID: 39220258 PMCID: PMC11365397 DOI: 10.1016/j.isci.2024.110605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]  Open
3
Shi D, An K, Zhang H, Xu P, Bai C. Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines. ENTROPY 2022;24:e24050620. [PMID: 35626506 PMCID: PMC9140642 DOI: 10.3390/e24050620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 12/14/2022]
4
Hassan A, Byju S, Whitford PC. The energetics of subunit rotation in the ribosome. Biophys Rev 2021;13:1029-1037. [PMID: 35059025 PMCID: PMC8724491 DOI: 10.1007/s12551-021-00877-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022]  Open
5
Paleskava A, Kaiumov MY, Kirillov SV, Konevega AL. Peculiarities in Activation of Hydrolytic Activity of Elongation Factors. BIOCHEMISTRY (MOSCOW) 2021;85:1422-1433. [PMID: 33280582 DOI: 10.1134/s0006297920110103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
6
A steric gate controls P/E hybrid-state formation of tRNA on the ribosome. Nat Commun 2020;11:5706. [PMID: 33177497 PMCID: PMC7658246 DOI: 10.1038/s41467-020-19450-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]  Open
7
Fenwick MK, Ealick SE. Structural basis of elongation factor 2 switching. Curr Res Struct Biol 2020;2:25-34. [PMID: 34235467 PMCID: PMC8244253 DOI: 10.1016/j.crstbi.2020.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022]  Open
8
Warias M, Grubmüller H, Bock LV. tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition. Biophys J 2020;118:151-161. [PMID: 31711607 PMCID: PMC6950810 DOI: 10.1016/j.bpj.2019.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/25/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022]  Open
9
Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S, Ehrenberg M, Frank J. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Nucleic Acids Res 2019;46:5861-5874. [PMID: 29733411 PMCID: PMC6009598 DOI: 10.1093/nar/gky346] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/30/2018] [Indexed: 11/25/2022]  Open
10
Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019;141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
11
Studying ribosome dynamics with simplified models. Methods 2019;162-163:128-140. [DOI: 10.1016/j.ymeth.2019.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/24/2022]  Open
12
Sanbonmatsu KY. Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR. Curr Opin Struct Biol 2019;55:104-113. [PMID: 31125796 DOI: 10.1016/j.sbi.2019.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022]
13
How Ricin Damages the Ribosome. Toxins (Basel) 2019;11:toxins11050241. [PMID: 31035546 PMCID: PMC6562825 DOI: 10.3390/toxins11050241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022]  Open
14
Kürkçüoğlu Ö. Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis. Turk J Biol 2018;42:392-404. [PMID: 30930623 PMCID: PMC6438126 DOI: 10.3906/biy-1802-77] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
15
Rodnina MV. Translation in Prokaryotes. Cold Spring Harb Perspect Biol 2018;10:cshperspect.a032664. [PMID: 29661790 DOI: 10.1101/cshperspect.a032664] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
16
EF-Tu and EF-G are activated by allosteric effects. Proc Natl Acad Sci U S A 2018. [PMID: 29531062 DOI: 10.1073/pnas.1800054115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
17
Barrozo A, Liao Q, Esguerra M, Marloie G, Florián J, Williams NH, Kamerlin SCL. Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase. Org Biomol Chem 2018;16:2060-2073. [DOI: 10.1039/c8ob00312b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
18
Rodnina MV, Fischer N, Maracci C, Stark H. Ribosome dynamics during decoding. Philos Trans R Soc Lond B Biol Sci 2017;372:rstb.2016.0182. [PMID: 28138068 PMCID: PMC5311926 DOI: 10.1098/rstb.2016.0182] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 11/24/2022]  Open
19
Lai J, Ghaemi Z, Luthey-Schulten Z. The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains. Biochemistry 2017;56:5972-5979. [PMID: 29045140 DOI: 10.1021/acs.biochem.7b00591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
20
Barrozo A, Blaha-Nelson D, Williams NH, Kamerlin SCL. The effect of magnesium ions on triphosphate hydrolysis. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-1125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
21
Carter CW. High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction. Annu Rev Biophys 2017;46:433-453. [PMID: 28375734 DOI: 10.1146/annurev-biophys-070816-033811] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
22
Lu X, Ovchinnikov V, Demapan D, Roston D, Cui Q. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin. Biochemistry 2017;56:1482-1497. [PMID: 28225609 DOI: 10.1021/acs.biochem.7b00016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
23
Maracci C, Rodnina MV. Review: Translational GTPases. Biopolymers 2017;105:463-75. [PMID: 26971860 PMCID: PMC5084732 DOI: 10.1002/bip.22832] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 01/26/2023]
24
Tripathi R, Glaves R, Marx D. The GTPase hGBP1 converts GTP to GMP in two steps via proton shuttle mechanisms. Chem Sci 2017;8:371-380. [PMID: 28451182 PMCID: PMC5365056 DOI: 10.1039/c6sc02045c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/21/2016] [Indexed: 11/21/2022]  Open
25
Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 2016;540:80-85. [PMID: 27842381 DOI: 10.1038/nature20560] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/24/2016] [Indexed: 01/29/2023]
26
Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernández IS. Structural characterization of ribosome recruitment and translocation by type IV IRES. eLife 2016;5. [PMID: 27159451 PMCID: PMC4861600 DOI: 10.7554/elife.13567] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/04/2016] [Indexed: 12/20/2022]  Open
27
Katava M, Kalimeri M, Stirnemann G, Sterpone F. Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue. J Phys Chem B 2016;120:2721-30. [DOI: 10.1021/acs.jpcb.6b00306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
28
Åqvist J, Kamerlin SCL. Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
29
Nguyen K, Whitford PC. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nat Commun 2016;7:10586. [PMID: 26838673 PMCID: PMC4742886 DOI: 10.1038/ncomms10586] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/31/2015] [Indexed: 12/01/2022]  Open
30
Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Theoretical Insights on the Mechanism of the GTP Hydrolysis Catalyzed by the Elongation Factor Tu (EF-Tu). J Phys Chem B 2015;120:89-101. [PMID: 26653849 DOI: 10.1021/acs.jpcb.5b10145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Åqvist J, Kamerlin SCL. Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome. Sci Rep 2015;5:15817. [PMID: 26497916 PMCID: PMC4620562 DOI: 10.1038/srep15817] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/06/2015] [Indexed: 11/09/2022]  Open
32
Barrozo A, Duarte F, Bauer P, Carvalho ATP, Kamerlin SCL. Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2015;137:9061-76. [PMID: 26091851 PMCID: PMC4513756 DOI: 10.1021/jacs.5b03945] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
33
Kirmizialtin S, Loerke J, Behrmann E, Spahn CMT, Sanbonmatsu KY. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods Enzymol 2015;558:497-514. [PMID: 26068751 DOI: 10.1016/bs.mie.2015.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
34
Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis. Proc Natl Acad Sci U S A 2015;112:E2561-8. [PMID: 25941362 DOI: 10.1073/pnas.1505231112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015;16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022]  Open
36
Carvalho ATP, Szeler K, Vavitsas K, Åqvist J, Kamerlin SCL. Modeling the mechanisms of biological GTP hydrolysis. Arch Biochem Biophys 2015;582:80-90. [PMID: 25731854 DOI: 10.1016/j.abb.2015.02.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/19/2015] [Accepted: 02/21/2015] [Indexed: 01/11/2023]
37
Dubiez E, Aleksandrov A, Lazennec-Schurdevin C, Mechulam Y, Schmitt E. Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2. Nucleic Acids Res 2015;43:2946-57. [PMID: 25690901 PMCID: PMC4357699 DOI: 10.1093/nar/gkv053] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
38
Åqvist J, Kamerlin SCL. The conformation of a catalytic loop is central to GTPase activity on the ribosome. Biochemistry 2014;54:546-56. [PMID: 25515218 DOI: 10.1021/bi501373g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
39
Duarte F, Åqvist J, Williams NH, Kamerlin SCL. Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis. J Am Chem Soc 2014;137:1081-93. [PMID: 25423607 PMCID: PMC4311964 DOI: 10.1021/ja5082712] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
40
Maracci C, Peske F, Dannies E, Pohl C, Rodnina MV. Ribosome-induced tuning of GTP hydrolysis by a translational GTPase. Proc Natl Acad Sci U S A 2014;111:14418-23. [PMID: 25246550 PMCID: PMC4210003 DOI: 10.1073/pnas.1412676111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
41
Kuhle B, Ficner R. A monovalent cation acts as structural and catalytic cofactor in translational GTPases. EMBO J 2014;33:2547-63. [PMID: 25225612 DOI: 10.15252/embj.201488517] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
42
Sanbonmatsu KY. Flipping through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics. J Mol Biol 2014;426:3197-3200. [DOI: 10.1016/j.jmb.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
43
Quantitative exploration of the molecular origin of the activation of GTPase. Proc Natl Acad Sci U S A 2013;110:20509-14. [PMID: 24282301 DOI: 10.1073/pnas.1319854110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
44
Translocation at work. Nat Struct Mol Biol 2013;20:1019-22. [PMID: 24008560 DOI: 10.1038/nsmb.2661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
45
Kalimeri M, Rahaman O, Melchionna S, Sterpone F. How conformational flexibility stabilizes the hyperthermophilic elongation factor G-domain. J Phys Chem B 2013;117:13775-85. [PMID: 24087838 DOI: 10.1021/jp407078z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
46
Energetics of activation of GTP hydrolysis on the ribosome. Nat Commun 2013;4:1733. [PMID: 23591900 DOI: 10.1038/ncomms2741] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 03/13/2013] [Indexed: 11/09/2022]  Open
47
Aleksandrov A, Field M. Mechanism of activation of elongation factor Tu by ribosome: catalytic histidine activates GTP by protonation. RNA (NEW YORK, N.Y.) 2013;19:1218-1225. [PMID: 23864225 PMCID: PMC3753929 DOI: 10.1261/rna.040097.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 06/02/2023]
48
Tourigny DS, Fernández IS, Kelley AC, Ramakrishnan V. Elongation factor G bound to the ribosome in an intermediate state of translocation. Science 2013;340:1235490. [PMID: 23812720 PMCID: PMC3836249 DOI: 10.1126/science.1235490] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
49
Voorhees RM, Ramakrishnan V. Structural Basis of the Translational Elongation Cycle. Annu Rev Biochem 2013;82:203-36. [DOI: 10.1146/annurev-biochem-113009-092313] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
50
Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A. Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces. J Phys Chem B 2013;117:12807-19. [PMID: 23601038 DOI: 10.1021/jp4020146] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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