Abstract
In this work, the dynamics of some electron-transfer protein complexes
involved in photosynthesis were investigated theoretically.
Protein association, electron-transfer paths, protonation probabilities,
and the similarity of isofunctional proteins were explored.
For these investigations, several methods were not only combined,
but also further developed.
The coupling between the electron and proton
transfer between the quinones
in the bacterial photosynthetic reaction center was
studied by a continuum electrostatic method.
The existent method was extended in two respects.
Not only the protonation but also the redox state of the
quinones were considered and
conformational variability was allowed in the calculation.
Based on the calculated reaction energies, a
sequence for the electron-transfer and protonation reactions
was proposed.
The analysis of the association of plastocyanin and cytochrome f
was done in several steps.
First, Monte Carlo sampling was used to generate docked
complexes.
The molecular configurations were grouped
into six families by a cluster algorithm.
Then the six configurations having the
lowest energies, one from each family,
were used as starting point of a
molecular dynamics simulation.
Furthermore, the relative binding energy
and relative
electronic coupling between the copper and heme sites in the six
configurations was analyzed.
The blue copper protein plastocyanin and the heme protein cytochrome
c6
differ in composition and in structure, but perform the same function in the
photosynthetic electron-transport chain.
These two proteins are compared on the basis of their electrostatic
potentials in order to understand the structural basis of their
functional equivalence.
On the basis of the alignments of plastocyanin and cytochrome c6
,
the docking and the electron-transfer reactions of these two proteins
with its physiological reaction partner cytochrome f were analyzed.
Ferredoxin and flavodoxin are two isofunctional proteins that differ not
only in structure but also in size.
Nevertheless they perform the same physiological function.
Both molecules are superimposed based on their electrostatic potentials
and their interaction with their reaction partners is discussed.
Two superpositions were found in which both molecules completely
overlap.
The molecules are, however, not concentric in these superpositions,
which is in agreement with recent electron microscopic studies on
photosystem I crosslinked to ferredoxin and flavodoxin.
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