Large scale molecular dynamics simulations of light receptor proteins

Transcription

1 Large scale molecular dynamics simulations of light receptor proteins Jocelyne Vreede Computational Chemistry Van t Hoff Institute for Molecular Sciences University of Amsterdam SARA superday December 1, 2010

2 Temperature erature Light Nutrients etc. DNA Proteins Ions Acid Ethanol etc.

3 Temperature Light Nutrients etc. DNA Proteins Ions H + Ethanol etc.

4 Background: protein structure -NH-CHR-C=O- R O R O R O N C α C N C α C N C α C N C α C N C α C N C α C O O R O R O R

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6 Protection against high-energy light DNA blue light General stress response Negative phototaxis

7 Protein signal transduction Dark state Signaling state

8 Blue light activates the general stress response in Bacillus subtilis Signal perception DNA Communication of signal form sensor to regulator Activation of transcription factors via phosphorylation reactions Transcription of genes that code for general stress response proteins YtvA is a blue-light sensor Avila-Perez, Vreede et al. J Biol Chem 2009

9 YtvA Regulates phosphorylation reactions linker Contains co-factor that senses blue light Molecular simulation Avila-Perez, Vreede et al. J Biol Chem 2009

10 Molecular Dynamics (MD) F i = m i a i = m i d 2 x i (t) dt 2 for i = 1,,N particles The force F i is given by the gradient of the potential V i F i = V (rn ) r i Given the potential, one can integrate the trajectory x(t) of the whole system as a function of time. Leapfrog algorithm: v(t + t/2) = v(t t/2) + t f(t) m r(t + t) =r(t)+v(t + t/2) t!t!t!t Frenkel & Smit Understanding Molecular Simulation 2 nd ed GROMACS 4.0

11 V (r) = movies by S.J. Marrink bonds angles dihedrals i<j k r (r r eq ) 2 + bonds k θ (θ θ eq ) 2 + angles Force field 1 2 ν n(1 + cos(nφ φ 0 ))+ torsions ( ) a ij rij 12 b ij rij 6 + q iq j ɛr ij non-bonded interactions

12 Simulation of YtvA 100 ns on 32 cores takes 11 days Singhal, Hellingwerf, Bolhuis & Vreede in preparation

13 Activation FMN co-factor captures light Co-factor forms covalent bond to protein Salzmann et al. J Phys Chem B 2009

14 Unfolding of linker region In the dark Light activation linker Singhal, Hellingwerf, Bolhuis & Vreede in preparation

15 Singhal, Hellingwerf, Bolhuis & Vreede in preparation New interface

16 Signal transduction in YtvA FMN co-factor captures light Co-factor forms covalent bond to protein Rearrangement in sensor domain lead to formation of interface Interface formation causes unfolding of J" helix and opens up part of core of effector domain Result of ~5000 hrs of simulation on 32 cores Singhal, Hellingwerf, Bolhuis & Vreede in preparation

17 Hoff et al Negative phototaxis

18 Photoactive Yellow Protein blue-light sensor from H. halophila pca Tyr42 Glu46 Thr50 pca Cys69 Absorption of a blue-light photon triggers a cascade of reactions

19 Formation of signaling state H H n s µs m s partial unfolding

20 Multiscale process Molecular simulation

21 Simulating partial unfolding - H Molecular dynamics Force field Nothing happens! GROMACS MD software GROMOS 43a1 force field, SPC water model Coordinates cis-pca from Kort et al. J Biol Chem 2004 Force field parameters pca from Groenhof et al. Proteins 2002

22 Crossing free energy barriers Free energy m s Reaction coordinate room temperature high temperature room temperature

23 Temperature 645K... MD Replica exchange algorithm MD... Hansmann Chem Phys Lett 1997 Sugita & Okamoto Chem Phys Lett K 301K 297K F = "k B T lnp(q) Time P acc = min(1,exp[(" i # " j )(U i # U j )]) " = 1 k B T

24 F = "k B T lnp(q) Free energy profile rmsd α [nm] signaling Vreede et al. Biophys J 2005 Vreede, Hellingwerf & Bolhuis Proteins 2008 d XE com [nm] folded

25 Comparison to experiment protein lifetime signaling state wild type ms Δ 25 -PYP hours Vreede et al. Biophys J 2005 Bernard et al. Structure 2005 Vreede et al. Proteins 2008 Krzeminski et al. Proteins 2009 wild type Δ 25 -PYP

26 Crossing free energy barriers Free energy m s Reaction coordinate

27 Transition path sampling Ensemble of transition paths! relevant reaction coordinates! transition states Dellago, Bolhuis, Geissler Adv Chem Phys 2002 Juraszek & Bolhuis Proc Natl Acad Sci USA 2006

28 Transitions folded signaling

29 Unfolding of helix folded helix unfolded (U " ) Vreede, Juraszek & Bolhuis Proc Natl Acad Sci USA 2010

30 Vreede, Juraszek & Bolhuis Proc Natl Acad Sci USA 2010 Transition paths

31 Reaction coordinates of helix!3 unfolding RMSD! water molecules around Tyr42 Ala44(N) - Pro54(C$) dpa Ala44(O) - Asp48(H) dhb2 Vreede, Juraszek & Bolhuis Proc Natl Acad Sci USA 2010

32 folded signaling

33 Solvent exposure events dxy dxe Vreede, Juraszek & Bolhuis Proc Natl Acad Sci USA 2010

34 Result of months of simulation on huygens

35 Work in progress: Calculation of rate! i-1 k TIS AB = " AB h A! i! i+1 n$1 = " AB % P A (# i+1 # i ) = & A % P A (# i+1 # i ) h A i=1 n$1 i=1 DEISA project ProKin van Erp, Moroni & Bolhuis, J Chem Phys 2003 van Erp & Bolhuis, J Comput Phys 2005

36 Signal transduction: The future Molecular simulation

37 Protein signal transduction Dark state Signaling state Molecular simulation elucidates processes of life at high detail

38 Acknowledgements Computational Chemistry Kushagra Singhal (YtvA) Jarek Juraszek (PYP) Wolfgang Lechner (TIS) Peter Bolhuis Computational Chemistry Laboratory for Microbiology Klaas Hellingwerf SARA Jeroen Engelberts (DEISA project ProKin) lisa, huygens Dutch Computer Facilities (NCF) VENI grant (NWO)