Biomolecular machines

[Teleological]

Welcome to the Molecular Machines​

A thread to lump together all the interesting discoveries regarding the intracellular biomolecular machinery that are crucial for life to exist. Feel free to post interesting discoveries and perhaps describe the functionality of the intracellular biomolecular machines.

Intracellular biomolecular machinery include the following:
1) DNA replication and repair machinery (replisome)
2) DNA transcription machinery and RNA processing and translation machinery (Spliceosomes and ribosomes)
3) Cell cycle signaling network (pRB, e2F, CDKs)
4) Programmed cell death machinery (Apoptosis, autophagy, mitotic catastrophe)
5) Protein processing machinery (Chaperones, ubiquitin-proteasome system)
6) Intracellular signaling networks (protein kinases and phosphatases)
7) Mechanical machines for intracellular shuttling of biomolecules and cellular movement (Microtubule network, kinesin, dynein)
8) Energy production machines (Electron transport chain, F0F1 ATP synthase)

Sliding clamps and the clamp-loading machine.​

​

Sliding clamps are ring-shaped proteins that some refer to as the “guardians” of the genome or others name them as the “ringmasters” of the genome.
Interestingly these clamps are structurally and functionally conserved in all branches of life and crystallographic studies have shown that they have almost superimposable three-dimensional structures, yet these components have very little sequence similarity.
Figure 1: Human sliding clamp
Figure 2: E. coli sliding clamp
Figure 3: Bacteriophage T4 sliding clamp
Figure 4: Sulfolobus solfataricus (Archaeon) sliding clamp

What do they do?​

The picture below is taken from the Molecular Biology Visualization of DNA video (2:14) from the freesciencelectures.com site.

Great video!

The following components can be seen.
Sliding clamps (PCNA in eukaryotes): Green circular shaped
Clamp loader (RFC in eukaryotes): Blue-white component in the middle
(Figure 5: Structures of PCNA connected to RFC (front))
(Figure 6: Structures of PCNA connected to RFC (side))
(Figure 7: Structures of PCNA connected to RFC (back))
Helicase: Blue
(Figure 8: Helicase (front))
DNA polymerase: Dark-blue components attached to the sliding clamps
Primase: Green component attached to helicase
Leading strand: Spinning off to the right
Lagging strand: Spinning off to the top

They are not ringmasters for nothing.
Sliding clamps participate and control events that orchestrate DNA replication events in the following ways:

• Enhancement of DNA polymerase activity.
• Coordinate Okazaki fragment processing.
• Prevention of rereplication
• Translesion synthesis
• Prevents sister-chromatid recombination and also coordinates sister-chromatid cohesion
• Crucial role in mismatch repair, base excision repair, nucleotide excision repair
• Participates in chromatin assembly

Other functions include:

• Epigenetic inheritance
• Chromatin remodeling
• Controls cell cycle and cell death signaling

The true ringmasters.

Clamp loaders are another group of interesting proteins (see video and figures 5-7 above). Interestingly again, their functional and structural architecture are conserved across the three domains of life with low-level sequence similarity. At the replication fork during replication, they load the sliding clamps many times onto the lagging strand (after DNA priming) and only once onto the leading strand. They also act as a bridge to connect the leading and lagging strand polymerases and the helicase. Which brings us to another interesting group of proteins; the helicases.

Helicases are also known to be ring-shaped motor proteins, typically hexamers (see figure 8) and separate double-stranded DNA into single-stranded templates for the replication machinery. Replication occurs at about 1000 base pairs per second due to the highly efficient combination of sliding clamps and the polymerases. Thus, helicases need to unwind DNA at at least that speed. Unwinding DNA too slowly and the replication machinery might break down . Unwind the DNA too fast or untimely and harmful mutations might occur as single-stranded DNA is prone to degradation and cytosine deamination. The speed at which helicase unwinds DNA is no accident though, as it is intrinsically controlled. As helicase is bound to the lagging strand, it unwinds the leading strand in a separate direction. Applying a pulling force on the leading strand leads to a 7-fold increase in the speed of DNA unwinding by helicase. The highly efficient DNA polymerase/sliding clamp combination provides this controlling force on the leading strand. This forms a robust unwinding/polymerization interaction whereby polymerization controls and prevents unwanted DNA unwinding.
Altogether, the replisome machinery provides a robust way for DNA replication to prevent unnecessary DNA damage and mutation. Epigenetic factors are also able to control its efficiency (more later).

Next:
Photosynthesis photosystem II
The bc1-complex for electron transfer from dihydroubiquinone to cytochrome c through the Q-cycle.
The apoptosome
The anaphase promoting complex/cyclosome (APC/C)

 

[nauseous_monkey]

guess who's back.

 

[Teleological]

Very nice article about the photosynthesis photosystem II mechanism and how design principles of the system can be used to engineer similar systems to produce solar fuel.

Solar water-splitting into H2 and O2: design principles of photosystem II and hydrogenases

Architecture of the photosynthetic oxygen evolving center (ribbons style).

2.6 Summary: Principles of photosynthetic water-splitting

From the above text the following seven principles of photosynthetic water splitting can be extracted:

1. The components of the primary photo-reactions as well as the Mn4OxCa cluster are supported by protective components and, once destroyed, automatically replaced by the organism by a specific repair mechanism.
2. A multimeric transition metal complex (Mn4OxCa cluster) is employed to couple the very fast one–electron photochemistry with several orders of magnitude slower four electron water-splitting chemistry.
3. The water-splitting catalyst is located in a sequestered environment; channels exist for substrate entry and product release.
4. The matrix (protein) around the Mn4OxCa cluster is highly important for the coupling of proton and electron transfer reactions. This feature is essential for achieving about equal redox potentials for all oxidation steps that match the oxidizing potential of the light-generated primary oxidant.
5. Point 4 leads to a decoupling of the release of the two products O2 and H+ from the catalytic site.
6. The substrate water molecules are stepwise prepared for O–O bond formation by binding to the Mn4OxCa cluster and by (partial) deprotonation. The concerted oxidation of the activated substrate occurs then either in two 2 e− or one concerted 4 e− reaction step(s). This avoids high energy intermediates.
7. The Mn4OxCa cluster undergoes several structural changes during the Kok cycle, which are probably significant for the mechanism. The surrounding matrix therefore needs to be flexible enough to support such changes.

3.6 Design principles of hydrogenases

For a better understanding of the design principles of native hydrogenases a comparison of the two major hydrogenases is useful.

The two groups of hydrogenases have a completely different genetic background. Whereas the [NiFe] group is widely distributed in prokaryotes (mostly sulfur reducing bacteria), the [FeFe] group is less widely distributed but occurs in both prokaryots and eukaryots (algae, yeast). In fact, the genetic signature of the H-cluster is found in many higher organisms, even in homo sapiens. The [FeFe] hydrogenases are, in general, most active in H2 production while [NiFe] hydrogenases are more tuned to H2 oxidation. Both types are however bidirectional. Organisms employing [NiFe] hydrogenases are found in regions with higher oxygen levels than those using [FeFe] hydrogenase. This is because [FeFe] hydrogenases are extremely oxygen sensitive and will be inhibited irreversibly under O2. [NiFe] hydrogenases are, in general, more oxygen tolerant and some enzymes even evolve H2 under O2.

On the other hand, there are many similarities between the basic structures of the active site in both enzymes:

1. Both enzymes employ a bimetallic center where the chemistry is taking place.
2. Both active sites have a butterfly-shaped core in which the two metals are bridged by SR-ligands.
3. Only one of these metal atoms is redox active (Ni in [NiFe] and Fed in [FeFe] hydrogenase) and they both have a d7 configuration (Ni(III) and Fe(I), respectively) in their active states.
4. In both catalytic sites the Fe atom is kept at a low valence by the strongly donating ligands CN− and CO.
5. The metal-metal distance in both structures is short (2.5–2.9 ), indicating a metal–metal bond.
6. One metal with an open coordination site can be identified in both active states. This is the site where H2 is believed to bind or is being released.
7. The H/D-isotope effect shows that in both cases the H2 splitting is heterolytic
8. In both active sites a sulfur or nitrogen/oxygen ligand probably acts as base to accept or donate the H+.
9. For both enzymes the catalytic activity is often inhibited by O2 and CO.

These features can serve as guidelines for the construction of biomimetic hydrogenase models.

Emphasis mine.

Also, the photosystem II mechanism makes use of quantum mechanical computing principles, leading to an excellent quantum efficiency for water-splitting.

From Nature;Vol 446;12 April 2007: Quantum path to photosynthesis

Elsewhere in this issue, Engel et al. (page 782) take a close look at how nature, in the form of the green sulphur bacterium Chlorobium tepidum, manages to transfer and trap light’s energy so effectively. The key might be a clever quantum computation built into the photosynthetic algorithm.

The process is analogous to Grover’s algorithm in quantum computing, which has been proved to provide the fastest possible search of an unsorted information database.

And in the same issue: Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems

When viewed in this way, the system is essentially performing a single quantum computation, sensing many states simultaneously and selecting the correct answer, as indicated by the efficiency of the energy transfer.

A glimpse into the future of our own designs .

 

[alloytoo]

guess who's back.

woo woo.

 

[Teleological]

The bc1-complex for electron transfer from dihydroubiquinone to cytochrome c through the Q-cycle.​

The bc1-like complexes (Complex III in mitochondria) play a central role in the electron transport chains of respiratory and photosynthetic machinery.

Their function is to carry out a sequence of electron and proton transfer reactions to generate a trans-membrane proton motive force that supplies the energy for ATP synthesizing utilizing the ATP synthase (excellent video, funny clip) machinery. Protons and electrons are supplied by dihydroubiquinone which in turn is generated by complexes I and II of the electron transport chain.

How do the bc1-like complexes carry out their function?
First the structure:

The cyt bc1-complex contains two separate redox chains; High potential and low potential.
The high-potential chain connects the Qo-binding site with the cyt c1 through the Rieske Iron-sulphur-protein (RISP). The RISP is situated on a rotateable arm that is able to connect the cyt c1 component with the Qo-binging site.
The low potential chain connects the Qo-site with the Q1-site through the cyt BL and Cyt BH complexes.

Now the mechanism. A bifurcated electron transfer mechanism:

1) The lipid-soluble dihydroubiquinone molecule binds at the Qo-site and liberates one proton into the intermembrane space and in the process forms a semiubiquinone radical.
2) The RISP swings around to receives an electron from the semiubiquinone and donates it to cyt c1 which in turn donates it to cytochrome c. Cytochrome c plays its part in energy transfer to complex IV of the electron transfer chain.
3) A second proton is liberates into the intermembrane space and an electron is donated to the low potential chain, resulting in the formation of ubiquinone
4) At the Q1-site the electron is donated to ubiquinone to form semiubiquinone, while a proton is donated from the mitochondrial matrix.
5) In order for the formation of dihydroubiquinone at the Q1-site, two dihydroubiquinones must bins at the Qo-site.
6) Thus the end result is the formation of 1 dihydroubiquinone, 2 quinones, 4 intermembrane protons and 2 ferrocyrochrome c proteins and loss of 2 mitochondrial matrix molecules after the binding of 2 dihydroubiquinones at the Qo-site.


That is the basic general mechanism, however research is ongoing into how bypass reactions are avoided.
For example:
Why do the electrons flow in only one direction in the low electron transport chains?
Why aren't both electrons donated to the high-potential chain in the first place?
Radical hypotheses have been proposed including (From Cape et al. 2006 Trends Plant Sci. 2006 Jan;11(1):46-55.):

(i) A complex that can either stabilize the intermediate semiubiquinone, rendering it inert and invisible through some unknown mechanism, or that can use the unprecedented tactic of destabilizing its reactive intermediates.
(ii) A kinetic ‘water-park’ that tunes reaction activation enthalpies or entropies to route ‘water’ (electron) flow into productive channels.
(iii) A nano-machine that gates the electron and proton transfer reactions of semiubiquinone according to its recognition of the different redox and/or conformational states of the complex.
(iv) An extraordinary, and unprecedented, double concerted oxidation of dihydroubiquinone that simultaneously distributes two electrons and at least one proton between at least three different acceptors.

Options II and III do not exclude the possibility of quantum mechanics and coulombic interactions playing a role.

All-in-all a brilliant solution for a bifurcated electron transfer mechanism in order to generate a proton motive force from dihydroubiquinone.


Interestingly, the intermediate (semiubiquinone) generated at the Qo-site is believed to be a major contributor to the formation of reactive oxygen species by donating it's free electron to oxygen and thereby resulting in the formation of superoxide. Superoxide formation causes damage to various molecules including DNA, RNA, proteins and lipids.

Semiubiquinone​

Paradoxically though, reactive oxygen specie generation at the Qo-site as a result of semiubiquinone formation is increased during periods of hypoxia (low oxygen). Hypoxia is a major initiator of cancerous growth because it activates various pro-growth signaling pathways. Hypoxia in cells usually occur as a result of poor circulation and delivery of oxygen. Obesity, lack of exercise and poor diet all contribute to these circumstances.

Thus, the bc1-complexes connects bad health choices with higher incidences of cancers and other mitochondrially related diseases through reactive oxygen species formation as a result of hypoxic conditions within various systems of the body.

Exercising and eating right are good for oiling your biomolecular machines.

 

[alloytoo]

Exercising and eating right are good for oiling your biomolecular machines.

Yup, that's how they evolved.

 

[Teleological]

One of the most intriguing group of proteins is a group of proteins that assist in the folding and unfolding of macromolecular structures into the correct 3D-architecture, prevents protein clumping and transport damaged or improperly made proteins to be recycled. The chaperones (a lot of them are also known as heat-shock proteins)

Great video

New Insights Into Hidden World Of Protein Folding

"Folding is one of the key steps for the health of the cell," Frydman said.

Virtually all proteins have to be folded-some in complex configurations-in order to function properly, and many are known to require a molecule called a chaperone to fold them. Frydman estimates that perhaps 10 percent of the proteins needing chaperones must have one that, like TRiC, is part of the subset called chaperonins. Other work done in Frydman's lab has shown that proteins that have very complex folds seem to require chaperonins.

"Many of the proteins that have these complex folds are the most important ones for life," Frydman said. "The proteins that control the cell cycle, tumor suppressers and the proteins that control the shape of the cell are dependent on chaperonins to get to the folded state.

"If the chaperones don't work well, then all these proteins that have been made become toxic," she said.

Protein 'Shocks' Evolution Into Action

“One of the great mysteries of biology is how life could have evolved so rapidly,” says Lindquist. “This research gives at least one plausible explanation for the speed of evolution and for the evolution of complex traits affected by several genes.”

“One stressful event can affect many traits and allow previously unseen genetic variation to be expressed,” says Sangster. “We don’t know yet what is going on at the molecular level—why the HSP90-dependent traits are expressed when the plants are mildly stressed.”

Machines depending in other machines .

Seeing that the structure and functionality of sliding clamps and clamp loaders (not an isolated case btw) are conserved across the three domains of life with very little sequence similarity it seems reasonable that chaperones played a part in conserving the structure and functionality of selected proteins over deep time while retaining flexibility and allowing sequence variability.
This ties in nicely with the robust Universal Optimal codon Code that allows for variation but also buffers against the effects of mutation.

 

[nauseous_monkey]

Teleo, I don't think anyone even reads your long posts anymore.

Maybe we should have a poll.

Who actually reads these damn long edging-on-creationist posts?

 

[Teleological]

Why should you care? Maybe someone here likes biochemistry/biology/chemistry and find it interesting. What purpose will such a poll have and why would anyone care to participate in it?
Why don't you rather respond to this thread by posting something you find interesting and relevant to this thread?

 

[nauseous_monkey]

Why should you care? Maybe someone here likes biochemistry/biology/chemistry and find it interesting. What purpose will such a poll have and why would anyone care to participate in it?
Why don't you rather respond to this thread by posting something you find interesting and relevant to this thread?

Point Taken.

Enjoy the 'Ctrl + C' and 'Ctrl + V'

 

[Teleological]

Cool, so to clean up this thread could you please delete posts #2, #8 and #10 and I will delete post #9 and #11. Agreed?

EDIT:

Teleo, I don't think anyone even reads your long posts anymore.

Maybe we should have a poll.

Who actually reads these damn long edging-on-creationist posts?

Why do you say "these damn long edging-on-creationist posts"? Did you read ALL of it to get everything I said?

 

[nauseous_monkey]

Cool, so to clean up this thread could you please delete posts #2, #8 and #10 and I will delete post #9 and #11. Agreed?

EDIT:

Why do you say "these damn long edging-on-creationist posts"? Did you read ALL of it to get everything I said?

Leave the censorship to the politicians and religious leaders.

I have not read your posts, from previous experience they are all heavy in religious barking. Can't say I care much for theists trying to manipulate science to get their superstitious messages across.

 

[Teleological]

Leave the censorship to the politicians and religious leaders.

You said nothing worth censoring, it is purely for aesthetical purposes. If you say something worth censoring, I won't censor it .

I have not read your posts, from previous experience they are all heavy in religious barking.

Well now, what a candid confession. Yet, here you are, posting in a thread were you did not read anything. Some might say you are just trolling or posting for personal reasons. Mmmm...

Can't say I care much for theists trying to manipulate science to get their superstitious messages across.

Just like atheists try to manipulate science to suit their metaphysical bias? You have no evidence to support your metaphysical bias. If we did not exist at all I would consider your evidence. But what would be the point then. Take it to the PD section please.
Please, for aesthetical purposes, delete all your posts here, they look silly, and please give some interesting input. Thank you.

 

[nauseous_monkey]

Just like atheists try to manipulate science to suit their metaphysical bias? You have no evidence to support your metaphysical bias. If we did not exist at all I would consider your evidence. But what would be the point then.

You can use as many emoticons as you want, doesn't make your claim any more credible.

Metaphysical

Atheists have never swung any science in any direction. In science we can only talk about real actual factual things. You are playing about in the kiddies pool of rationality... pretty soon maybe you will allow yourself to be promoted to the adult pool where we don't try and convert people all the time through scientific terminology without any real meaning.

Show me one scientist that has gone about his work as to prove that God does not exist intentionally.

 

[Teleological]

I can only ask you nicely to make posts that are relevant to this particular topic. It is not difficult really.

 

[nauseous_monkey]

I can only ask you nicely to make posts that are relevant to this particular topic. It is not difficult really.

I win that round, then ey

 

[Teleological]

Your entertainment value just shot up two points.

 

[nauseous_monkey]

Your entertainment value just shot up two points.

Awesome!

I guess my efforts are in vain anyway... I mean I can't expect someone called Teleological to stop believing in God.

 

[Teleological]

I guess my efforts are in vain anyway... I mean I can't expect someone called Teleological to stop believing in God.

I guess you can say some people are just immune to stupid metaphysics and not prone to acts of sadistic lobotomy.
So nauseous_monkey, are you going to contribute anything meaningful to this thread. Stop trolling for the last time please!
Thank you.

 

[nauseous_monkey]

I guess you can say some people are just immune to stupid metaphysics and not prone to acts of sadistic lobotomy.
So nauseous_monkey, are you going to contribute anything meaningful to this thread. Stop trolling for the last time please!
Thank you.

Read my Blog.