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Why is F1Fo-ATP synthase so
important?
F1Fo-ATP synthase, or ATP synthase for short,
is one of the most abundant proteins in every organism.
It is responsible for synthesizing the molecule adenosine tri-phosphate (ATP, depicted on the right),
the cells’ energy currency. ATP is used to power and sustain
virtually all cellular processes needed to survive and reproduce.
Even when at rest, the human body metabolizes more than half its body weight
in ATP per day, this figure rising to many times the body weight under conditions of physical
activity. |
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What do we know about F1Fo-ATP
synthase?
Researchers have been trying to uncover the "secret" behind
ATP synthase’s very efficient mode of operation
for quite some time. Unfortunately, even after more than 30 years of
study, we still don’t fully understand how
F1Fo-ATPase really works.
The protein consists of two coupled rotary molecular motors, called Fo and F1 respectively, the first one being
membrane embedded and the latter one being solvent exposed.
One of the most important breakthroughs in the field was the
determination of an atomic level X-ray crystal structure for
the F1 part
of ATP synthase. This allowed researchers, for the first time,
to connect biochemical data to the three dimensional
structure of the protein (Abrahams et al.,
Nature 370:621-628, 1994). The X-ray structure beautifully supported
Paul Boyer’s "binding change mechanism" (Boyer, Bioch. Bioph. Acta
215-250, 1993) as the modus operandi for ATP
synthase’s rotational catalytic cycle
and lead to the
1997 Nobel Price in chemistry for Boyer and
Walker.
F1-ATPase in its simplest prokaryotic form (shown schematically on the left)
consists of a hexameric
assembly of alternating α and β subunits arranged in the shape of
an orange. The central cavity of the hexamer is occupied by the central
stalk formed by subunits γ, δ and ε.
Due to a lack of high resolution structures for the Fo
part of ATP synthase, much less is known about this subunit. It is currently
thought that a transmembrane proton gradient drives rotation of the c-subunit
ring of Fo which is then coupled to movement of the central stalk.
The rotation of the latter eventually causes conformational changes in the
catalytic sites located in F1 leading to the synthesis of ATP.
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What are some of the missing pieces in our understanding of F1?
ATP synthase can be separated into its two constituent subunits
F1 and Fo, which can then be studied individually.
Solvated F1 is able to hydrolyze ATP and experiments pioneered
by Noji et al. (Nature 386:299-302, 1997) have shown that ATP
hydrolysis in F1 drives rotation of the central stalk.
However, we don’t know if ATP hydrolysis itself or
rather binding of ATP to the catalytic sites induces rotation.
We would also like to know how the binding pockets
cooperate during steady-state ATP hydrolysis to achieve their
physiological catalysis rates.
It has been suggested that ATP binding and product unbinding
provide the main "power stroke" and that the actual catalytic step inside
the binding pockets is equi-energetic, but, unfortunately, there is currently no consensus
regarding this issue. In any case, since
ATP in solution is a very stable molecule, the catalytic sites have to be
able to lower the reaction barrier toward product formation considerably in order to
cause efficient hydrolysis.
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Computational Study of ATP hydrolysis in F1-ATPase:
Our research focuses on investigating the ATP hydrolysis reaction
and its interaction with the protein environment
in the catalytic sites of F1-ATPase using
computer simulations. To be able to study a chemical reaction
inside the extended protein environment provided by the catalytic
sites we employ combined quantum mechanical/molecular mechanical
(QM/MM) simulations to investigate both the βTP
and βDP catalytic sites. The figure on the
right hand side depicts the quantum mechanically treated region of
the former. Quite surprisingly, our simulations show that there
is a dramatic change in the reaction energetics in going from
βTP (strongly endothermic) to βDP
(approximately equi-energetic), despite the fact that
the overall protein conformation is quite similar.
In both βTP and βDP, the
actual chemical reaction proceeds via a multi-center proton
relay mechanism involving two water molecules. A careful
study of the electrostatic interactions between the protein
environment and the catalytic core region as well as several
computational mutation studies identified the "arginine finger"
residue αR373 as the most significant element involved in
this change in energetics.
Several important conclusions can be drawn from our
simulations: Efficient catalysis proceeds via a multi-center
proton pathway and a major factor for ATPase’s efficiency
is, therefore, the ability to provide the proper solvent enviroment
by means of its catalytic binding pocket. Furthermore,
the sidechain of the arginine finger residue αR373
is found to be a major element in signalling between catalytic
sites to enforce cooperation since it controls the reaction
barrier height as well as the reaction equilibrium of the
ATP hydrolysis/synthesis reaction.
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Recent publications:
ATP hydrolysis in the &betaTP and &betaDP catalytic sites of F1-ATPase.
Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 2004, 87:2954-2967
On
the mechanism of ATP hydrolysis in F1-ATPase.
Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 2003, 85:2253-2266
Acknowledgment
This material is based upon work supported by the National Science
Foundation under Grant No. 0234938. Any opinions, findings, and
conclusions or recommendations expressed in this material are those
of the author(s) and do not necessarily reflect the views of the
National Science Foundation.
 Markus Dittrich QM/MM calculations
Shigehiko Hayashi QM/MM and
excited state calculations.
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