Physics of Photosynthesis in Purple Bacteria Klaus Schulten Lecture at UBC, April 2011

Department of Physics Beckman Institute U. Illiois at Urbana-Champaign

Theoretical and Computational Biophysics Group Center for Biomolecular Modeling and Bioinformatics Center for Physics of Living Cells Habitats of Photosynthetic Life Forms

purple bacterium The proteins that make up the chromatophore 10 of photosynthetic bacteria Schematic arrangement of all six protein 1 5 types

hν stoichiometry 200:20:20:10:5:1 20 200 photosynthetic unit ADP ATP

purple bacterium cell energy converter Chromatophore of Purple Bacteria (section of the chromatophore membrane)

cytoplasm ADP ATP H+

Q/QH /Q hν membrane 2 ATPase

RC bc1

LH-I e- LH-II cytochrome c2 H+ periplasm Section of the curved chromatophore membrane illustrating how ATP is produced from captured photons

Chromatophore Structure structure of building blocks (X-ray, NMR, EM) LH2 (27 BChls) LH1-RC (dimer) (64 BChls) bc1 complex Melih Sener ATP synthase

long range order and composition (AFM, EM, LD, gel electrophoresis) (Bahatyrova et al., al., et (Bahatyrova Nature, 2004.)

dynamics/function (spectroscopy) (Arvi Freiberg, (Arvi Freiberg, U. Tartu ) Sener, Olsen, Hunter, Schulten, PNAS, 2007; Sener, Strumpfer, Timney, Freiberg, Hunter, Schulten, Biophys. J., 2010; also to be submitted. Photosynthetic Chromatophore of Purple Bacteria LH2 complex from Rb. sphaeroides

chromatophore RC-LH1 core complex

LH2

chromatophore Structure and mechanism of the photosynthetic reaction center (RC)

chromatophore Role of Thermal Environment on Electron Transfer Rates

hν

e- LH-II LH-I

cytochrome c2 Physicists seek to describe how electron transfer is coupled to the thermal motion of the surrounding protein. RC RC Electron Transfer Process Coupled to the Protein Matrix

Relaxation rate

energy gap from MD energy gap correlation function rms deviation of energy gap

D. Xu and K. Schulten. Chemical Physics, 182: 91--117, 1994. Light Harvesting Proteins of Purple Bacteria Light Harvesting Proteins of Plants Morphology of Light Harvesting Systems in Purple Bacteria spherical lamellar (ﬂat) cylindrical

LH2 LH1-RC

M. Sener, J. Strumpfer, J.Hsin, D. Chandler, S. Scheuring, C. N. Hunter, and Kl. Schulten. Förster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems. ChemPhysChem, 12:518-531, 2011. LH1 - LH2 Mixture Determines Chromatophore Shape simulations suggest that all LH2s can induce curvature

- why are some chromatophores flat?

- arrangement of LH2s with LH1 monomers/dimers may Danielle Chandler be what determines final shape

lamellar (flat) membranes spherical species

Goncalves et al. 2005 Bahatyrova et al. 2004 LH1 monomers break up LH2 domains, LH1 dimers aggregate, leaving larger preventing long-range curvature due to LH2s highly-curved LH2-only domains

We need to simulate large mixed (LH1 + LH2) systems!

D. E. Chandler, J. Gumbart, J. D. Stack, Ch. Chipot, and K. Schulten. Membrane curvature induced by aggregates of LH2s and monomeric LH1s. Biophysical Journal, 97:2978-2984, 2009. Reduced curvature in LH1-LH2 mixed system LH1 monomer surrounded by seven LH2 complexes (LH1 and LH2 from Rps. acidophila, RC from Rb. sphaeroides)

side view after 14 ns

top view very little curvature

LH2s tilt:

curved protein patch calculate tilt angle:

D. Chandler, J. Hsin, Ch. B. Harrison, J. Gumbart, and K. Schulten. Intrinsic curvature properties of photosynthetic proteins in chromatophores. Biophysical Journal, 95:2822-2836, 2008. LH2 Curvature Varies by Species Avg. tilt angle of the six peripheral LH2s Ph. molischianum

Rb. sphaeroides

Rps. acidophila Ph. molischianum: 11.2º → R = 344 Å Rb. sphaeroides: 12.9º → R = 318 Å Rps. acidophila: 8.6º → R = 488 Å Radius of a spherical chromatophore: 150 - 400 Å LH2 Curvature Partially Driven by Electrostatics

Curvature is reduced by removal of conserved cytoplasmic charged residues!

molischianum

Ph. molischianum wild-type

acidophila

Ph. molischianum modified

D. Chandler, J. Hsin, Ch. B. Harrison, J. Gumbart, and K. Schulten. Intrinsic curvature properties of photosynthetic proteins in chromatophores. Biophysical Journal, 95:2822-2836, 2008.

NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC http://www.ks.uiuc.edu/ Jen Hsin

Fitting RC-LH1-PufX dimer into an EM Map

resolution = 25 Å

NIH Resource for Macromolecular Modeling and Bioinformatics resolution = 25 Å Beckman Institute, UIUC http://www.ks.uiuc.edu/ Molecular Dynamics Flexible Fitting (MDFF) Simulation

• In an MDFF simulation, RC-LH1-PufX dimer atoms are steered into high-density regions of the EM map; • 5 ns of MDFF, followed by a 29 ns of equilibration was performed.

• The entire lipid patch became arched • Curvature is anisotropic • Lipid patch is “twisted”

NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC http://www.ks.uiuc.edu/ Membrane Curvature Analysis R (Å) Evolution of membrane geometry during the 34 ns MDFF+equilibration trajectory: 460

500

540

580

620

• Radius of curvature within range of experimental value • “Twisting” of the membrane quantified -- axis of maximum curvature slanted

J. Hsin, J. Strumpfer, M. Sener, P. Qian,NIH Resource C. N. for Hunter, Macromolecular and ModelingK. Schulten. and Bioinformatics Energy transfer dynamics Beckmanin an Institute,RC-LH1- UIUC http://www.ks.uiuc.edu/ PufX tubular photosynthetic membrane. New Journal of Physics, 12:085005, 2010. Local Curvature Properties and Long-Range Order * Helical stacking of RC-LH1-PufX explained through local curvature properties

Direct stacking Off-set stacking Surfaces not complimentary Surfaces complimentary Tubular vesicle w/ off-set stacking Helical arrangement observed

J. Hsin, J. Strumpfer, M. Sener, P. Qian,NIH Resource C. N. for Hunter, Macromolecular and ModelingK. Schulten. and Bioinformatics Energy transfer dynamics Beckmanin an Institute,RC-LH1- UIUC http://www.ks.uiuc.edu/ PufX tubular photosynthetic membrane. New Journal of Physics, 12:085005, 2010. Cylindrical, helical Stacking of (RC-LH1) Dimers explained Through Local Bending Tubular vesicle, w/ off-set stacking, helical arrangement as observed

Qian et al., 2008

NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC http://www.ks.uiuc.edu/ Light Absorption and Emission Excitonic dynamics in LH2 Exciton States in B850 band of BChls of LH2

LH2 Exciton States in B850 band of BChls of LH2 Absorption of Sun Light Inﬂuenced by Thermal Motion

Zhang et al., JPC B104,3683 (2000) Ioan Kosztin and Klaus Schulten. Molecular dynamics methods for bioelectronic systems in photosynthesis. In Thijs Aartsma and Joerg Matysik, editors, Biophysical Techniques in Photosynthesis II, volume 26 of Janosi et al., JCP 124, (2006) Advances in Photosynthesis and Respiration, pp. 445-464. Springer, Dordrecht, 2008.

B850 B800 Fluorescent Resonant Energy Transfer (FRET) Dissipative Quantum Dynamics

HTOTAL = H SYSTEM + H BATH + H INTERACTION

ρ(t) = exp −i Ldt ρ(0) ( ∫ ) BATH E.g. N=2 n = (0,0) (1,0) (0,1) ⎛ ⎞ ⎡ ⎤ ∂t ρnv = − iL + n jγ j ρnv − i K j ,ρv + (2,1) (1,1) (1,2) ⎜ ∑ ⎟ ∑ n j ⎝ j ⎠ j ⎣ ⎦

* −i n j η j K j ρnv − − ρv − K jη j ∑ n j M j ( ) Tanimura, Kubo (1989) J Phys. Soc. Jpn.

Hierarchy LH2 Excitation Transfer

exp(−kt) 70% of Transfer Rate

Single Exponential Boltzmann Simulation

ρ ≈ exp −βε / Z trelax << ttransfer αα ( α ) Generalized Förster Theory: 10.2 ps Dissipative Quantum Dynamics: 9.5 ps Generalized Förster theory is good for inter-complex transfer Excitation transfer through ﬂuorescent resonant energy transfer (FRET) in photosynthetic light harvesting

Architecture of the Vesicle Low light configuration (100 microeinstein): High light configuration (1500 microeinstein): B850:B875 ratio → 1.9:1.0 B850:B875 ratio → 1.3:1.0 LH2:RC ratio → 2.8:1 LH2:RC ratio → 2:1 LH1RC dimers: 26 LH2s: 107 avg. lifetime: 50 ps q. yield: 95% avg. lifetime: 43 ps q. yield: 96%

Sener et al., PNAS, 2007.

NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC http://www.ks.uiuc.edu/ Inter-Complex Transfer Times Calculations of the inter-complex transfer times distance dependence for LH2-LH2, Slow Medium Fast LH1-LH1 and LH2-LH1 using Förster theory.

50 ps limit:

17 Å 21 Å

23 Å

NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC http://www.ks.uiuc.edu/ Inter-Complex Transfer Times Permit Quinone Passage

Protein separation limits for 50 ps transfer time: LH2-LH2: 17 Å LH1-LH1: 21 Å LH2-LH1: 23 Å

quinone passage

M. Sener, J. Strumpfer, and K. Schulten. in preparation.

NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC http://www.ks.uiuc.edu/ Photosynthetic Apparatus of Purple Bacteria

H+ ADP ATP cytoplasm

Q/QH2/Q hν ATPase

bc1

RC LH-II LH-I periplasm e- H+ cytochrome c2

RC - Photosynthetic Reaction Center LH – Light Harvesting Complex Undocking of cytochrome c2 Studied by Molecular Dynamics

cytochrome c2 undocking

bc1

RC LH-II LH-I cytochrome c2 Mechanism of the bc1 Complex in the Photosynthetic Unit

two path- Iron Sulfur ways for Protein (ISP) Qo Q oxidation o head rotation 2Fe2S can redirect of Qo - e nd site 2 electron

2Fe2S cyt c1 cyt c1 www.ks.uiuc.edu Mechanisms of Rotatory Molecular Motor that Converts Voltage (proton gradient) into ATP Synthesis Photosynthetic Unit of Purple Bacteria Module that converts sun light into chemical energy (ATP) Light in H+ ADP ATP out

Q/QH2/Q hν ATPase

bc1

RC LH-II LH-I e- H+ cytochrome c2 Acknowledgments Melih Sener, UIUC Beckman Jen Hsin, UIUC Physics Danielle Chandler, UIUC Physics

JC Gumbart, UIUC Beckman Danielle Chandler Jen Hsin Chris Harrison, UIUC Beckman John Stack, UIUC Physics Ana Damjanovic, John Hopkins U. Melih Sener Ioan Kosztin, U. Missouri Thorsten Ritz, UC Irvine Johan Strumpfer Dong Xu, U. Missouri Xiche Hu, U. Neil Hunter, U. Sheffield John Ohlsen, U. Sheffield Hu et al., Q. Rev. Biophys., (2002); Arvi Freiberg, U. Tartu Zaida Luthey-Schulten, UIUC NSF