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Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.

Colletier JP, Bourgeois D, Sanson B, Fournier D, Sussman JL, Silman I, Weik M
Proc Natl Acad Sci U S A 105 11742-7 (2008)
Related entries: 2vja, 2vjb, 2vjc, 2vjd, 2vt6

Cited: 28 times
EuropePMC logo PMID: 18701720

Abstract

Although x-ray crystallography is the most widely used method for macromolecular structure determination, it does not provide dynamical information, and either experimental tricks or complementary experiments must be used to overcome the inherently static nature of crystallographic structures. Here we used specific x-ray damage during temperature-controlled crystallographic experiments at a third-generation synchrotron source to trigger and monitor (Shoot-and-Trap) structural changes putatively involved in an enzymatic reaction. In particular, a nonhydrolyzable substrate analogue of acetylcholinesterase, the "off-switch" at cholinergic synapses, was radiocleaved within the buried enzymatic active site. Subsequent product clearance, observed at 150 K but not at 100 K, indicated exit from the active site possibly via a "backdoor." The simple strategy described here is, in principle, applicable to any enzyme whose structure in complex with a substrate analogue is available and, therefore, could serve as a standard procedure in kinetic crystallography studies.

Articles - 2vt7 mentioned but not cited (2)

  1. Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography. Colletier JP, Bourgeois D, Sanson B, Fournier D, Sussman JL, Silman I, Weik M. Proc Natl Acad Sci U S A 105 11742-11747 (2008)
  2. Chiral Separation, X-ray Structure, and Biological Evaluation of a Potent and Reversible Dual Binding Site AChE Inhibitor. Catto M, Pisani L, de la Mora E, Belviso BD, Mangiatordi GF, Pinto A, Palma A, Denora N, Caliandro R, Colletier JP, Silman I, Nicolotti O, Altomare CD. ACS Med Chem Lett 11 869-876 (2020)


Reviews citing this publication (3)

  1. Resurrection and Reactivation of Acetylcholinesterase and Butyrylcholinesterase. Franjesevic AJ, Sillart SB, Beck JM, Vyas S, Callam CS, Hadad CM. Chemistry 25 5337-5371 (2019)
  2. A Comprehensive Review of Cholinesterase Modeling and Simulation. De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. Biomolecules 11 580 (2021)
  3. Radiation chemists look at damage in redox proteins induced by X-rays. Wherland S, Pecht I. Proteins 86 817-826 (2018)

Articles citing this publication (23)

  1. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. Nature 539 43-47 (2016)
  2. Backdoor opening mechanism in acetylcholinesterase based on X-ray crystallography and molecular dynamics simulations. Sanson B, Colletier JP, Xu Y, Lang PT, Jiang H, Silman I, Sussman JL, Weik M. Protein Sci 20 1114-1118 (2011)
  3. Protein dynamics investigated by inherent structure analysis. Rao F, Karplus M. Proc Natl Acad Sci U S A 107 9152-9157 (2010)
  4. Energy landscape in protein folding and unfolding. Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Baglioni P, Buldyrev SV, Chen SH, Stanley HE. Proc Natl Acad Sci U S A 113 3159-3163 (2016)
  5. Long route or shortcut? A molecular dynamics study of traffic of thiocholine within the active-site gorge of acetylcholinesterase. Xu Y, Colletier JP, Weik M, Qin G, Jiang H, Silman I, Sussman JL. Biophys J 99 4003-4011 (2010)
  6. Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade. Tetreau G, Banneville AS, Andreeva EA, Brewster AS, Hunter MS, Sierra RG, Teulon JM, Young ID, Burke N, Grünewald TA, Beaudouin J, Snigireva I, Fernandez-Luna MT, Burt A, Park HW, Signor L, Bafna JA, Sadir R, Fenel D, Boeri-Erba E, Bacia M, Zala N, Laporte F, Després L, Weik M, Boutet S, Rosenthal M, Coquelle N, Burghammer M, Cascio D, Sawaya MR, Winterhalter M, Gratton E, Gutsche I, Federici B, Pellequer JL, Sauter NK, Colletier JP. Nat Commun 11 1153 (2020)
  7. Raman-assisted crystallography suggests a mechanism of X-ray-induced disulfide radical formation and reparation. Carpentier P, Royant A, Weik M, Bourgeois D. Structure 18 1410-1419 (2010)
  8. Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy. Kekilli D, Dworkowski FS, Pompidor G, Fuchs MR, Andrew CR, Antonyuk S, Strange RW, Eady RR, Hasnain SS, Hough MA. Acta Crystallogr D Biol Crystallogr 70 1289-1296 (2014)
  9. Finding new cures for neurological disorders: a possible fringe benefit of biodefense research? Jett DA. Sci Transl Med 2 23ps12 (2010)
  10. Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography. Correy GJ, Carr PD, Meirelles T, Mabbitt PD, Fraser NJ, Weik M, Jackson CJ. Structure 24 977-987 (2016)
  11. Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: a combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B). Liu B, Zhang Y, Sage JT, Soltis SM, Doukov T, Chen Y, Stout CD, Fee JA. Biochim Biophys Acta 1817 658-665 (2012)
  12. Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis. Maeki M, Ito S, Takeda R, Ueno G, Ishida A, Tani H, Yamamoto M, Tokeshi M. Chem Sci 11 9072-9087 (2020)
  13. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. van den Bedem H, Wilson MA. J Synchrotron Radiat 26 958-966 (2019)
  14. Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies. De Zitter E, Coquelle N, Oeser P, Barends TRM, Colletier JP. Commun Biol 5 640 (2022)
  15. Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study. Ilizaliturri-Flores I, Correa-Basurto J, Bello M, Rosas-Trigueros JL, Zamora-López B, Benítez-Cardoza CG, Zamorano-Carrillo A. J Mol Model 22 98 (2016)
  16. Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction. Sousa CM, Carpentier P, Matias PM, Testa F, Pinho F, Sarti P, Giuffrè A, Bandeiras TM, Romão CV. Acta Crystallogr D Biol Crystallogr 71 2236-2247 (2015)
  17. On the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation. Wang J, Liu Z, Crabtree RH, Frank J, Moore PB. Protein Sci 27 2051-2061 (2018)
  18. Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure. Gerlits O, Blakeley MP, Keen DA, Radić Z, Kovalevsky A. Curr Res Struct Biol 3 206-215 (2021)
  19. Slow cooling and temperature-controlled protein crystallography. Warkentin M, Thorne RE. J Struct Funct Genomics 11 85-89 (2010)
  20. Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II. Sippel KH, Genis C, Govindasamy L, Agbandje-McKenna M, Kiddle JJ, Tripp BC, McKenna R. J Phys Chem Lett 1 2898-2902 (2010)
  21. On quantum mechanical--molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase. Nemukhin AV, Grigorenko BL, Morozov DI, Kochetov MS, Lushchekina SV, Varfolomeev SD. Chem Biol Interact 203 51-56 (2013)
  22. Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin. Juers DH, Weik M. J Synchrotron Radiat 18 329-337 (2011)
  23. Structural basis of femtomolar inhibitors for acetylcholinesterase subtype selectivity: insights from computational simulations. Zhu XL, Yu NX, Hao GF, Yang WC, Yang GF. J Mol Graph Model 41 55-60 (2013)


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