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Biomolecular Machines

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StevoMuso
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« Reply #15 on: May 11, 2010, 22:31:30 PM »

Nice post thanks Teleo. Interesting read.
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Teleological
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« Reply #16 on: July 05, 2010, 18:32:11 PM »

The exact mechanism of complex III of the electron transport chain is currently under investigation (as mentioned here).

Meanwhile, research into the mechanisms of electron transfer of complex I are yielding interesting results:
Nanomachines in the Powerhouse of the Cell: Architecture of the Largest Protein Complex of Cellular Respiration Elucidated

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ScienceDaily (July 2, 2010) — Scientists of the University of Freiburg and the University of Frankfurt have elucidated the architecture of the largest protein complex of the cellular respiratory chain.They discovered an unknown mechanism of energy conversion in this molecular complex. The mechanism is required to utilize the energy contained in food.



The structural model of mitochondrial complex I provides new insights in energy conversion at nanoscale. A molecular coupling device links pump modules in the membrane arm of the huge enzyme complex. (Credit: Image courtesy of Albert-Ludwigs-Universität Freiburg)

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After ten years of research work, the x-ray crystallographic analysis of the huge and most complicated protein complex of the mitochondrial respiratory chain was successful. The complex contains more than 40 different proteins, marks the entry to cellular respiration and is thus also called mitochondrial complex I. The results are published in the current online-edition of the journal Science.

A detailed understanding of the function of complex I is of special medical interest. Dysfunction of the complex is implicated in several neurodegenerative diseases such as Parkinson´s disease or Alzheimer´s disease, and also with the physiological processes of biological aging, in general. The work of Prof. Carola Hunte of the Freiburg Institute for Biochemistry and Molecular Biology and the Freiburg excellence centre BIOSS (Centre for Biological Signalling Studies) in cooperation with Prof. Ulrich Brandt, Professor for Molecular Bioenergetics and member of the excellence centre „Macromolecular Complexes" and Dr. Volker Zickermann of his research group is a major step forward to this understanding.

The energy metabolism takes place in the so-called powerhouses of the cell, the mitochondria. They transduce the energy taken up as food into adenosine triphosphate, in short ATP, which is the universal energy currency of life. A chain of five complicated molecular machines in the mitochondrial membrane are responsible for the energy conversion. The production of ATP in mitochondria requires so many steps, as it is in principal a Knallgasreaction. In a laboratory experiment, hydrogen and oxygen gas would react in an explosion and the energy contained would be released as heat. In biological oxidation, the energy will be released by the membrane bound protein complexes of the respiratory chain in a controlled manner in small packages. Comparable to a fuel cell, this process generates an electrical membrane potential, which is the driving force of ATP synthesis. The total surface of all mitochondrial membranes in a human body covers about 14.000 square meter. This accounts for a daily production of about 65 kg of ATP.

The now presented structural model provides important and unexpected insights for the function of complex I. A special type of „transmission element," which is not known from any other protein, appears to be responsible for the energy transduction within the complex by mechanical nanoscale coupling. Transferred to the technical world, this could be described as a power transmission by a coupling rod, which connects for instance the wheels of a steam train. This new nano-mechanical principle will now be analysed by additional functional studies and a refined structural analysis.


Original article:
Functional Modules and Structural Basis of Conformational Coupling in Mitochondrial Complex I

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Proton-pumping respiratory complex I is among the largest and most complicated membrane protein complexes. Its function is critical for efficient energy supply in aerobic cells and malfunctions are implicated in many neurodegenerative disorders. Here, we report the x-ray crystallographic analysis of mitochondrial complex I. The positions of all iron-sulfur clusters relative to the membrane arm were determined in the complete enzyme complex. The ubiquinone reduction site resides close to 30 Å above the membrane domain. The arrangement of functional modules suggests conformational coupling of redox chemistry with proton pumping and essentially excludes direct mechanisms. We suggest that a ~60 Å long helical transmission-element is critical for transducing conformational energy to proton-pumping elements in the distal module of the membrane arm.
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Rigil Kent
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« Reply #17 on: July 05, 2010, 19:20:59 PM »

Is a "biomolecular machine" the same thing as an enzyme?

Mintaka
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« Reply #18 on: July 05, 2010, 21:04:41 PM »

Is a "biomolecular machine" the same thing as an enzyme?

Mintaka
Depends on your definition of machine and enzyme I guess.
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Rigil Kent
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« Reply #19 on: July 05, 2010, 21:17:30 PM »

An enzyme is a catalyst, usually (if not always)a protein. A machine is an assembly that moves so that a mechanical job can be done. So I'm curious why the array above would be classed as a machine instead of an enzyme.

ETA: Maybe the proton pump? If protons are relocated through the membrane, I s'pose that could count as a mechanical effort. Nifty.

Mintaka
« Last Edit: July 05, 2010, 21:39:16 PM by Mintaka » Logged
Mefiante
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« Reply #20 on: July 05, 2010, 21:41:30 PM »

Is a "biomolecular machine" the same thing as an enzyme?
No, as strongly hinted at in this and several related threads, it’s any material component that does stuff we can’t presently give a reasonably complete account of, one that is somewhat baffling or marvellous, and which is part of a living organism.  (Conveniently, it also doubles as a hidey-hole for incorporeal deities who occasionally fiddle with the workings of the material world, making sure that things go right.  Cf. “Deus ex machina” – “a … device whereby a seemingly inextricable problem is suddenly and abruptly solved with the contrived and unexpected intervention of some [miracle, prompting us in genuflection to exclaim, ‘Wow, how great art Thou!’].”  I kid you not.)

'Luthon64
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« Reply #21 on: July 05, 2010, 21:51:00 PM »

Very interesting - thanks Luthon. The Ghost in the Enzyme, huh?

Mintaka
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« Reply #22 on: July 06, 2010, 07:56:57 AM »

An enzyme is a catalyst, usually (if not always)a protein. A machine is an assembly that moves so that a mechanical job can be done. So I'm curious why the array above would be classed as a machine instead of an enzyme.

ETA: Maybe the proton pump? If protons are relocated through the membrane, I s'pose that could count as a mechanical effort. Nifty.

Mintaka
Yeah, complex I is a proton pump composed of many subunits (46 last time I checked), several of them containing iron-sulphur clusters as well as a flavin mononucleotide (FMN) prosthetic group which act as enzymes.
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« Reply #23 on: August 04, 2010, 08:14:52 AM »

More machines Smiley

Cells Use Water in Nano-Rotors to Power Energy Conversion
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ScienceDaily (Aug. 3, 2010) — Researchers from the Max Planck Institute of Biophysics in Frankfurt, and Mount Sinai School of Medicine in New York have provided the first atomic-level glimpse of the proton-driven motor from a major group of ATP synthases, enzymes that are central to cellular energy conversion.


Quote
The study, by Dr. Thomas Meier, his PhD student Laura Preiss and Dr. Özkan Yildiz of the Max-Planck Institute, and Drs. Terry Krulwich and David Hicks of Mount Sinai, revealed a water molecule in the critical rotor element of a bacterial nano-motor that shares common features with the rotors of ATP synthases from human mitochondria and from diverse bacteria, including pathogens such as Mycobacterium tuberculosis, in which the ATP synthase is a drug target. The paper publishes in the online, open access journal PLoS Biology.

ATP synthases are among the most abundant and important proteins in living cells. These rotating nano-machines produce the central chemical form of cellular energy currency, ATP (adenosine triphosphate), which is used to meet the energy needs of cells. For example, human adults synthesize up to 75 kg of ATP each day under resting conditions and need a lot more to keep pace with energy needs during strenuous exercise or work. The turbine of the ATP synthase is the rotor element, called the c-ring. This ring is 63 Å in diameter (6.3 nm, or 6.3 millionths of a millimeter) and completes over 500 rotations per second during ATP production.

The researchers from Frankfurt and New York were able to grow three-dimensional protein crystals of the unusually stable rotor ring from a Bacillus that can grow under extremely low-proton (alkaline) conditions. The molecular architecture of this turbine was determined using X-ray crystallography. The researchers were surprised by the results and excited by the promise they hold for future mechanistic insights into the structure and function of ATP synthases.

Dr. Meier states: "We did not expect a water molecule to be a key player in this group of rotors. This atomic structure gives us a new and much better framework for understanding how these proton-driven nano-machines work, how they capture the protons that fuel rotation and how they hold on to them through rotation. The results join other recent examples of the usefulness of unusual organisms, such as this 'extremophilic' bacillus, in providing insights into fundamental life processes and we look forward to further collaborative work on different forms of this rotor. Further basic research into the structural and mechanistic details of ATP synthase nano-machines will impact both nanotechnology and medicine and, perhaps, areas in which nanotechnology converges with medicine."

This work was supported in parts by the Cluster of Excellence "Macromolecular Complexes" at the Goethe University Frankfurt (DFG Project EXC 115), the DFG Collaborative Research Center 807 (to TM), and a research grant GM28454 from the National Institute of General Medical Sciences (to TAK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


And here are few videos to illustrate how this nano-machine operates:
F1 ATP synthase

Molecular Mechanism of ATP synthesis

grt video of atp synthase
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