Research Projects - Quantum Biology

Research Projects - Quantum Biology

Many important biological processes taking place in cells are driven and controlled by events that involve electronic degrees of freedom and, therefore, require a quantum mechanical description. An important example are enzymatically catalyzed, cellular biochemical reactions. Here, bond breaking and bond formation events are intimately tied to changes in the electronic degrees of freedom. Key events during photosynthesis in plants and energy metabolism in eucaryotes also warrant a quantum mechanical description - from the absorption of light in the form of photons by the photosynthetic apparatus to electron transfer processes sustaining the electrochemical membrane potential. Because of the importance of sensing light to both plants (for regulating vital functions) and animals (for vision), the interaction between light and biological photoreceptors is widespread in nature, and also requires a quantum mechanical description. A prime example is the protein rhodopsin which is present in the retina of the human eye and plays a key role in vision. Our computational tool are combined quantum mechanical/molecular (QM/MM) simulations, that allow to combine an electronic level description of the active region with a classical model of the environment provided by the remainder of the biomolecular system and solvent. This allows us to study the electronic level processes underlying these systems in their natural cellular environment.

Spotlight - Molecular Motor Scooting along DNA
Molecular Motor Scooting along DNA

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DNA with its famous double helix structure stores the genetic information of all life forms known. In order that this information is read, the double helix needs to be first unwound and separated into single helices or strands. This is achieved by cellular motor proteins called helicases that operate on already separated DNA strands. The helicases specialize in unwinding and separating the DNA double helix by scooting along one of DNA's single strands against the point where the two strands merge into the double helix; pushing against this point unwinds and separates the double helix further. The helicases are driven by energy stored in molecules of ATP which bind to the protein and get released in their so-called hydrolyzed, lower energy, form. Based on atomic resolution structures, researchers have studied now one of the smallest helicases known, PcrA, from the electronic to the functional level carrying out quantum mechanical/molecular mechanical simulations (as described in a first publication), as well as a combination of classical molecular dynamics simulation, using NAMD, and stochastic modeling calculations (described in a second publication). This resulted in an overall explanation of how ATP's hydrolysis powers helicase activity which has been reported in a third publication. The researchers discovered that PcrA moves with two "hands" along single stranded DNA; when ATP binds, one "hand" moves along the DNA; when ADP and Pi (the hydrolysis products of ATP) unbind, the other "hand" moves; through a molecular "trick" both "hands" move in the same direction. Amazingly, the hand movement arises mainly from an increase in random mobility of the hands. i.e., is not enforced. Physicists refer to the underlying mechanism as a ratchet mechanism that was indeed long suspected to drive molecular motors. Interestingly, the helicase motor is very closely related to a wide class of other biological motors, for example the FoF1-ATP synthase (see Mar 2004 and Nov 2004 highlights). For more information visit our helicase research website.

All Spotlights

Papers

From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex. Carsten Olbrich, Thomas L. C. Jansen, Jörg Liebers, Mortaza Aghtar, Johan Strümpfer, Klaus Schulten, Jasper Knoester, and Ulrich Kleinekathoefer. Journal of Physical Chemistry B, 115(26):8609-8621, 2011.

Quest for spatially correlated fluctuations in the FMO light-harvesting complex. Carsten Olbrich, Johan Strümpfer, Klaus Schulten, and Ulrich Kleinekathoefer. Journal of Physical Chemistry B, 115:758-764, 2011.

Förster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems. Melih Sener, Johan Strümpfer, Jen Hsin, Danielle Chandler, Simon Scheuring, C. Neil Hunter, and Klaus Schulten. ChemPhysChem, 12:518-531, 2011.

The effect of correlated bath fluctuations on exciton transfer. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 134:095102, 2011. (9 pages).

Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane. Jen Hsin, Johan Strümpfer, Melih Sener, Pu Qian, C. Neil Hunter, and Klaus Schulten. New Journal of Physics, 12:085005, 2010. (19 pages).

Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Melih Sener, Johan Strumpfer, John A. Timney, Arvi Freiberg, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 99:67-75, 2010.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter Sphaeroides. Melih K. Sener, Jen Hsin, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Chemical Physics, 357:188-197, 2009.

Light harvesting complex II B850 excitation dynamics. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 131:225101, 2009. (9 pages).

From atomic-level structure to supramolecular organization in the photosynthetic unit of purple bacteria. Melih K. Sener and Klaus Schulten. In C. Neil Hunter, Fevzi Daldal, Marion C. Thurnauer, and J. Thomas Beatty, editors, The Purple Phototrophic Bacteria, volume 28 of Advances in Photosynthesis and Respiration, pp. 275-294. Springer, 2008.

Atomic level structural and functional model of a bacterial photosynthetic membrane vesicle. Melih K. Sener, John D. Olsen, C. Neil Hunter, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 104:15723-15728, 2007.

Comparison of the light harvesting networks of plant and cyanobacterial photosystem I. Melih K. Sener, Craig Jolley, Adam Ben-Shem, Petra Fromme, Nathan Nelson, Roberta Croce, and Klaus Schulten. Biophysical Journal, 89:1630-1642, 2005.

When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas Reinhardtii. Markus Dittrich, Peter L. Freddolino, and Klaus Schulten. Journal of Physical Chemistry B, 109:13006-13013, 2005.

ATP hydrolysis in the βTP and βDP catalytic sites of F1-ATPase. Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten. Biophysical Journal, 87:2954-2967, 2004.

Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal mode analysis. Shigehiko Hayashi, Emad Tajkhorshid, Hideki Kandori, and Klaus Schulten. Journal of the American Chemical Society, 126:10516-10517, 2004.

Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:1440-1449, 2003.

A general random matrix approach to account for the effect of static disorder on the spectral properties of light harvesting systems. Melih Sener and Klaus Schulten. Physical Review E, 65:031916, 2002. (12 pages).

Structural determinants of spectral tuning in retinal proteins - bacteriorhodopsin vs sensory rhodopsin II. Shigehiko Hayashi, Emad Tajkhorshid, Eva Pebay-Peyroula, Antoine Royant, Ehud M. Landau, Javier Navarro, and Klaus Schulten. Journal of Physical Chemistry B, 105:10124-10131, 2001.

Kinetics of excitation migration and trapping in the photosynthetic unit of purple bacteria. Thorsten Ritz, Sanghyun Park, and Klaus Schulten. Journal of Physical Chemistry B, 105:8259-8267, 2001.

A model for photoreceptor-based magnetoreception in birds. Thorsten Ritz, Salih Adem, and Klaus Schulten. Biophysical Journal, 78:707-718, 2000.