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Genomics, revealing the blueprint of whole organisms, motivates
researchers to understand the interplay of many proteins in biological
cells. Integral functional units are systems made up of many molecular
components that self-assemble, recognize and control each other with
the end of performing one overall function. The photosynthetic
membrane of purple bacteria, responsible for absorption and conversion
of light energy into ATP, as well as the purple membrane, responsible
for light-driven pumping of protons in halobacteria, are examples for
integral functional units for which all molecular components are
structurally known already today.
We study the structure-function relationships in such integral
functional units with molecular dynamics and quantum mechanics. In
addition to the conceptual challenge of understanding the interplay
between molecular components, the size of the systems pose severe
computational challenges and often require the development of
theoretical descriptions with resolutions adapted to the size of the
systems.
Understanding how integral molecular machines are assembled and how
they work together is the next step towards arriving at an
understanding of how life comes about through the self-organization of
innate matter.
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ATP synthase is a large multi-protein complex which includes a
transmembrane Fo unit coupled to a solvent-exposed
F1 unit via a central stalk. The stalk rotates within the
surrounding subunits of F1, leading to cyclic
conformational changes in the three catalytic sites in F1
and, thereby, to ATP synthesis. We use steered molecular dynamics to
apply a torque to the central stalk in order to understand the
cooperative interactions that underlie this mechanism. |
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The purple membrane (PM) of halobacterium salinarium consists of
bacteriorhodopsin trimers, lipids and water molecules. Upon light
absorption by the chromophore inside bacteriorhodopsin, protons are
pumped across the PM to the extra-cellular side of the membrane. With
molecular dynamics simulations of the whole PM, we are studying the
influence of the native environment on the protein dynamics.
Figure produced with VMD .
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| The photosynthetic unit of purple bacteria consists of the
photosynthetic reaction center (RC), surrounded by a core
light-harvesting complex, and additional peripheral light-harvesting
complexes. In the RC, light energy is used to pump an electron through the
membrane. The light-harvesting complexes are pigment-protein complexes
which absorb light and funnel the light energy, in form of electronic
excitations, to the RC. We study how the architecture of this
multi-protein system controls the various excitation transfer
processes occuring in this system of multiple pigment-protein
complexes.
Figure produced with VMD .
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