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Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin.

Aranda R, Levin EJ, Schotte F, Anfinrud PA, Phillips GN
Acta Crystallogr D Biol Crystallogr 62 776-83 (2006)
Related entries: 2g0s, 2g0v, 2g0x, 2g0z, 2g10, 2g11, 2g12, 2g14

Cited: 31 times
EuropePMC logo PMID: 16790933

Abstract

Picosecond time-resolved crystallography was used to follow the dissociation of carbon monoxide from the heme pocket of a mutant sperm whale myoglobin and the resultant conformational changes. Electron-density maps have previously been created at various time points and used to describe amino-acid side-chain and carbon monoxide movements. In this work, difference refinement was employed to generate atomic coordinates at each time point in order to create a more explicit quantitative representation of the photo-dissociation process. After photolysis the carbon monoxide moves to a docking site, causing rearrangements in the heme-pocket residues, the coordinate changes of which can be plotted as a function of time. These include rotations of the heme-pocket phenylalanine concomitant with movement of the distal histidine toward the solvent, potentially allowing carbon monoxide movement in and out of the protein and proximal displacement of the heme iron. The degree of relaxation toward the intermediate and deoxy states was probed by analysis of the coordinate movements in the time-resolved models, revealing a non-linear progression toward the unbound state with coordinate movements that begin in the heme-pocket area and then propagate throughout the rest of the protein.

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  4. Water stabilizes an alternate turn conformation in horse heart myoglobin. Bronstein A, Marx A. Sci Rep 13 6094 (2023)


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  2. E pluribus unum, no more: from one crystal, many conformations. Woldeyes RA, Sivak DA, Fraser JS. Curr Opin Struct Biol 28 56-62 (2014)
  3. A new paradigm for atomically detailed simulations of kinetics in biophysical systems. Elber R. Q Rev Biophys 50 e8 (2017)
  4. Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins. Samuni U, Dantsker D, Roche CJ, Friedman JM. Gene 398 234-248 (2007)
  5. Protein ensembles link genotype to phenotype. Nussinov R, Tsai CJ, Jang H. PLoS Comput Biol 15 e1006648 (2019)
  6. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. Miller MD, Phillips GN. J Biol Chem 296 100749 (2021)
  7. Kinetic mechanisms for O2 binding to myoglobins and hemoglobins. Olson JS. Mol Aspects Med 84 101024 (2022)

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  1. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Barends TR, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, Burghardt I, Hummer G, Boutet S, Schlichting I. Science 350 445-450 (2015)
  2. Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case. Papaleo E, Mereghetti P, Fantucci P, Grandori R, De Gioia L. J Mol Graph Model 27 889-899 (2009)
  3. Primary protein response after ligand photodissociation in carbonmonoxy myoglobin. Sato A, Gao Y, Kitagawa T, Mizutani Y. Proc Natl Acad Sci U S A 104 9627-9632 (2007)
  4. Structural analysis of fish versus mammalian hemoglobins: effect of the heme pocket environment on autooxidation and hemin loss. Aranda R, Cai H, Worley CE, Levin EJ, Li R, Olson JS, Phillips GN, Richards MP. Proteins 75 217-230 (2009)
  5. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Kondrashov DA, Zhang W, Aranda R, Stec B, Phillips GN. Proteins 70 353-362 (2008)
  6. Determination of ligand pathways in globins: apolar tunnels versus polar gates. Salter MD, Blouin GC, Soman J, Singleton EW, Dewilde S, Moens L, Pesce A, Nardini M, Bolognesi M, Olson JS. J Biol Chem 287 33163-33178 (2012)
  7. Blocking the gate to ligand entry in human hemoglobin. Birukou I, Soman J, Olson JS. J Biol Chem 286 10515-10529 (2011)
  8. The apolar channel in Cerebratulus lacteus hemoglobin is the route for O2 entry and exit. Salter MD, Nienhaus K, Nienhaus GU, Dewilde S, Moens L, Pesce A, Nardini M, Bolognesi M, Olson JS. J Biol Chem 283 35689-35702 (2008)
  9. Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy. Lima FA, Penfold TJ, van der Veen RM, Reinhard M, Abela R, Tavernelli I, Rothlisberger U, Benfatto M, Milne CJ, Chergui M. Phys Chem Chem Phys 16 1617-1631 (2014)
  10. A computational study of water and CO migration sites and channels inside myoglobin. Lapelosa M, Abrams CF. J Chem Theory Comput 9 1265-1271 (2013)
  11. Direct observation of myoglobin structural dynamics from 100 picoseconds to 1 microsecond with picosecond X-ray solution scattering. Kim KH, Oang KY, Kim J, Lee JH, Kim Y, Ihee H. Chem Commun (Camb) 47 289-291 (2011)
  12. Straight-chain alkyl isocyanides open the distal histidine gate in crystal structures of myoglobin . Smith RD, Blouin GC, Johnson KA, Phillips GN, Olson JS. Biochemistry 49 4977-4986 (2010)
  13. Structural identification of spectroscopic substates in neuroglobin. Nienhaus K, Lutz S, Meuwly M, Nienhaus GU. Chemphyschem 11 119-129 (2010)
  14. Time-resolved Laue diffraction of excited species at atomic resolution: 100 ps single-pulse diffraction of the excited state of the organometallic complex Rh2(μ-PNP)2(PNP)2·BPh4. Benedict JB, Makal A, Sokolow JD, Trzop E, Scheins S, Henning R, Graber T, Coppens P. Chem Commun (Camb) 47 1704-1706 (2011)
  15. Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics. Choi M, Kim JG, Muniyappan S, Kim H, Kim TW, Lee Y, Lee SJ, Kim SO, Ihee H. Chem Sci 12 8207-8217 (2021)
  16. The stretching frequencies of bound alkyl isocyanides indicate two distinct ligand orientations within the distal pocket of myoglobin. Blouin GC, Olson JS. Biochemistry 49 4968-4976 (2010)
  17. A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space. Lynch ML, Dudek MF, Bowman SEJ. Patterns (N Y) 1 100024 (2020)
  18. Construction of a subnanosecond time-resolved, high-resolution ultraviolet resonance Raman measurement system and its application to reveal the dynamic structures of proteins. Kubo M, Uchida T, Nakashima S, Kitagawa T. Appl Spectrosc 62 30-37 (2008)
  19. The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations. Anselmi M, Di Nola A, Amadei A. Proteins 79 867-879 (2011)
  20. Ultrafast Structural Changes Decomposed from Serial Crystallographic Data. Ren Z. J Phys Chem Lett 10 7148-7163 (2019)


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