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Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase.

Berry MB, Bae E, Bilderback TR, Glaser M, Phillips GN
Proteins 62 555-6 (2006)
Cited: 32 times
EuropePMC logo PMID: 16302237

Reviews - 2eck mentioned but not cited (1)

  1. Strategies for the Production of Molecular Animations. Werner E. Front Bioinform 2 793914 (2022)

Articles - 2eck mentioned but not cited (15)

  1. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. Beckstein O, Denning EJ, Perilla JR, Woolf TB. J Mol Biol 394 160-176 (2009)
  2. WEBnm@ v2.0: Web server and services for comparing protein flexibility. Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N. BMC Bioinformatics 15 427 (2014)
  3. On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase. Brokaw JB, Chu JW. Biophys J 99 3420-3429 (2010)
  4. Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes. Kantarci-Carsibasi N, Haliloglu T, Doruker P. Biophys J 95 5862-5873 (2008)
  5. The energy profiles of atomic conformational transition intermediates of adenylate kinase. Feng Y, Yang L, Kloczkowski A, Jernigan RL. Proteins 77 551-558 (2009)
  6. Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase. Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS. Proteins 80 2536-2551 (2012)
  7. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation. Moritsugu K, Koike R, Yamada K, Kato H, Kidera A. PLoS One 10 e0131583 (2015)
  8. Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method. Molloy K, Shehu A. BMC Struct Biol 13 Suppl 1 S8 (2013)
  9. LIBRA-WA: a web application for ligand binding site detection and protein function recognition. Toti D, Viet Hung L, Tortosa V, Brandi V, Polticelli F. Bioinformatics 34 878-880 (2018)
  10. Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics. Stiller JB, Kerns SJ, Hoemberger M, Cho YJ, Otten R, Hagan MF, Kern D. Nat Catal 2 726-734 (2019)
  11. Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. Li Z, Hirst JD. Chem Sci 8 4318-4333 (2017)
  12. SCEDS: protein fragments for molecular replacement in Phaser. McCoy AJ, Nicholls RA, Schneider TR. Acta Crystallogr D Biol Crystallogr 69 2216-2225 (2013)
  13. Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method. Sherman DB, Zhang S, Pitner JB, Tropsha A. Proteins 56 828-838 (2004)
  14. Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics. Kanada R, Terayama K, Tokuhisa A, Matsumoto S, Okuno Y. J Chem Theory Comput 18 2062-2074 (2022)
  15. Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. Li J, Wang L, Zhu Z, Song C. J Chem Inf Model 64 301-315 (2024)


Reviews citing this publication (1)

  1. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. Miller MD, Phillips GN. J Biol Chem 296 100749 (2021)

Articles citing this publication (15)

  1. Illuminating the mechanistic roles of enzyme conformational dynamics. Hanson JA, Duderstadt K, Watkins LP, Bhattacharyya S, Brokaw J, Chu JW, Yang H. Proc Natl Acad Sci U S A 104 18055-18060 (2007)
  2. Elucidating the site of protein-ATP binding by top-down mass spectrometry. Yin S, Loo JA. J Am Soc Mass Spectrom 21 899-907 (2010)
  3. Which electrospray-based ionization method best reflects protein-ligand interactions found in solution? a comparison of ESI, nanoESI, and ESSI for the determination of dissociation constants with mass spectrometry. Jecklin MC, Touboul D, Bovet C, Wortmann A, Zenobi R. J Am Soc Mass Spectrom 19 332-343 (2008)
  4. Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case. Li D, Liu MS, Ji B. Biophys J 109 647-660 (2015)
  5. The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer. Bellinzoni M, Haouz A, Graña M, Munier-Lehmann H, Shepard W, Alzari PM. Protein Sci 15 1489-1493 (2006)
  6. Second-harmonic generation for studying structural motion of biological molecules in real time and space. Salafsky JS. Phys Chem Chem Phys 9 5704-5711 (2007)
  7. Hierarchical description and extensive classification of protein structural changes by Motion Tree. Koike R, Ota M, Kidera A. J Mol Biol 426 752-762 (2014)
  8. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Gong Z, Gu XH, Guo DC, Wang J, Tang C. Angew Chem Int Ed Engl 56 1002-1006 (2017)
  9. Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism. Ping J, Hao P, Li YX, Wang JF. Biomed Res Int 2013 628536 (2013)
  10. ATP and AMP mutually influence their interaction with the ATP-binding cassette (ABC) adenylate kinase cystic fibrosis transmembrane conductance regulator (CFTR) at separate binding sites. Randak CO, Dong Q, Ver Heul AR, Elcock AH, Welsh MJ. J Biol Chem 288 27692-27701 (2013)
  11. Automated Illustration of Molecular Flexibility. Bryden A, Phillips GN, Gleicher M. IEEE Trans Vis Comput Graph 18 132-145 (2012)
  12. Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase. Ye C, Ding C, Ma R, Wang J, Zhang Z. Proteins 87 337-347 (2019)
  13. Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration. Sim J, Sim J, Park E, Lee J. Proteins 83 1054-1067 (2015)
  14. Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase. Scheerer D, Adkar BV, Bhattacharyya S, Levy D, Iljina M, Riven I, Dym O, Haran G, Shakhnovich EI. Proc Natl Acad Sci U S A 120 e2219855120 (2023)
  15. Addressing the unmet need for visualizing conditional random fields in biological data. Ray WC, Wolock SL, Callahan NW, Dong M, Li QQ, Liang C, Magliery TJ, Bartlett CW. BMC Bioinformatics 15 202 (2014)


Related citations provided by authors (1)

  1. The Closed Conformation of a Highly Flexible Protein: The Structure of E. Coli Adenylate Kinase with Bound AMP and Amppnp. Berry MB, Meador B, Bilderback T, Liang P, Glaser M, Phillips Jr GN Proteins 19 183- (1994)

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