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Photoactivation of the Photoactive Yellow Protein chemistry department Imperial Colege London London SW7 2AZ United Kingdom Gerrit Groenhof, Berk Hess,

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Presentation on theme: "Photoactivation of the Photoactive Yellow Protein chemistry department Imperial Colege London London SW7 2AZ United Kingdom Gerrit Groenhof, Berk Hess,"— Presentation transcript:

1 Photoactivation of the Photoactive Yellow Protein chemistry department Imperial Colege London London SW7 2AZ United Kingdom Gerrit Groenhof, Berk Hess, Marc F. Lensink, Mathieu Bouxin-Cademartory, Sam de Visser Massimo Olivucci, Herman J.C. Berendsen, Alan E. Mark and Michael A. Robb dept. of biophysical chemistry University of Groningen Nijenborg 4, 9747 AG Groningen The Netherlands

2 Photoactive Yellow Protein cytoplasmic photoreceptor cytoplasmic photoreceptor Halorhodospira halophila Halorhodospira halophila negative photo-tactic response to blue light negative photo-tactic response to blue light

3 Photoactive Yellow Protein 125 residues 125 residues chromophore chromophore

4 Photoactive Yellow Protein photocycle photocycle -isomerization (ns) -part. unfolding (  s) -relaxation (ms) -photon absorption

5 - photon absorption induces isomerization of the chromophore inside the protein of the chromophore inside the protein aims to understand how to understand how - isomerization of the chromophore induces structural changes in the protein and leads structural changes in the protein and leads to signalling to signalling - the protein mediates these processes

6 photo-chemistry ground-state vs. excited-state reactivity ground-state vs. excited-state reactivity - transition state - surface crossing - statistics govern rate - dynamics govern rate

7 molecular dynamics nuclei are classical particles nuclei are classical particles potential energy and forces potential energy and forces - Newton’s equation of motion - molecular mechanics forcefield (MM) - numerically integrate e.o.m. - molecular quantum mechanics (QM)

8 quantum mechanics solving electronic Schrödinger equation solving electronic Schrödinger equation potential field for nuclei potential field for nuclei more accurate than forcefield more accurate than forcefield computationally demanding computationally demanding - excited states, transitions between el. states - bond breaking/formation

9 QM/MM hybrid model QM subsystem embedded in MM system QM subsystem embedded in MM system A. Warshel & M. Levitt. J. Mol. Biol. 103: 227-249 (1976)

10 simulation setup QM/MD simulation of PYP QM/MD simulation of PYP - dodecahedron - 5089 water molecules (SPC) - 6 Na+ ions with one protein molecule

11 simulation setup QM subsystem QM subsystem - diabatic surface hopping - chromophore (22 atoms) - CASSCF transitions between ground and excited states - apo protein, water & ions (16526 atoms) - gromos96 force-field MM subsystem MM subsystem accurate ground and excited states of (small) molecules

12 results photo-isomerization photo-isomerization

13 results comparison with experiment comparison with experiment - crystal structure of the intermediate state (pR) R. Kort et al. J. Biol. Chem. 279: 26417-26424 (2004)

14 results unsuccessful photo-isomerization unsuccessful photo-isomerization

15 results comparison with experiment comparison with experiment - fluorescence lifetime - quantum yield ~0.3 (exp. 0.35) ~0.3 ps (exp. 0.43/4.8 ps) - S 1 -S 0 gap oscillations 1.6 and 4.8 10 12 Hz (exp. 1.5 and 4.2 10 12 Hz)

16 results preferential stabilization of S 1 in PYP preferential stabilization of S 1 in PYP

17 - twisted S 1 minimum geometry in PYP results preferential stabilization of S 1 in PYP preferential stabilization of S 1 in PYP - charge distribution in S 0 and S 1

18 results preferential stabilization of S 1 in PYP preferential stabilization of S 1 in PYP - electrostatic interaction with Arginine 52 - conical intersection geometry in PYP

19 results meta-stable pR intermediate (continued) meta-stable pR intermediate (continued)

20 results after photo-isomerization after photo-isomerization - protein remains stable - no signalling, isomerization alone is not sufficient - classical MD simulation (Gromos96)

21 results proton transfer proton transfer - before isomerization - after isomerization proton transfer not possible proton transfer possible from glutamic acid - QM/MM analysis (PM3/Gromos96) QM system

22 results after proton transfer after proton transfer - conformational changes - increased flexibility in N-terminus - agreement with NMR data - classical MD simulation (Gromos96)

23 conclusions isomerization mechanism isomerization mechanism - on S0, strain disrupts H-bond with bb amide - on S1, double bond rotates to 90° - rather, bond stretching causes transtion to S0 - rotation does not cause transition to S0

24 conclusions signal transduction signal transduction - signal transduction in the cell - proton transfer from Glu 46 - partial unfolding - destabilization

25 acknowledgements Jocelyne Vreede & Klaas Hellingwerf Haik Chosrowjan & Noboru Mataga Michael Klene & Valerio Trigari University of Amsterdam Amsterdam, The Netherlands University of Osaka Osaka, Japan King’s College/Imperial College London, United Kingdom

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