Biomolecular Machines

[Techne]

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. Please post interesting discoveries and perhaps describe the functionality of these 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)

The Replisome: Sliding clamps, clamp-loaders and helicases.​

​

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) [1].

Figure 1: Sliding clamps from the various domains of life.​

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

Great video!

Figure 2: Replication machinery.​

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 3: Structures of PCNA connected to RFC (front))

(Figure 4: Structures of PCNA connected to RFC (side))​

(Figure 5: Structures of PCNA connected to RFC (back))
Helicase: Blue (Figure 6: 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 3-5 above). Interestingly again, their functional and structural architecture are conserved across the three domains of life with low-level sequence similarity [2]. 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 6) 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 [3, 4]. 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 provide a robust way for DNA replication to prevent unnecessary DNA damage and mutation.

References.
1. Vivona JB, Kelman Z. The diverse spectrum of sliding clamp interacting proteins. FEBS Lett. 2003 Jul 10;546(2-3):167-72.
2. Jeruzalmi D, O'Donnell M, Kuriyan J. Clamp loaders and sliding clamps. Curr Opin Struct Biol. 2002 Apr;12(2):217-24.
3. Ha T. Need for speed: mechanical regulation of a replicative helicase. Cell. 2007 Jun 29;129(7):1249-50.
4. Johnson DS, Bai L, Smith BY, Patel SS, Wang MD. Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell. 2007 Jun 29;129(7):1299-309.

 

[Techne]

Something related to the replisome and DNA repair:
DNA Repair: Structure Of The Mre11 Protein Bound To DNA

ScienceDaily (Oct. 2, 2008) — Repairing breaks in the two strands of the DNA double helix is critical for avoiding cancer. In humans and other organisms, a molecular machine called the MRN complex is responsible for finding and signaling double-strand breaks (DSBs), then launching the error-free method of DNA repair called homologous recombination.

Small-angle x-ray scattering confirmed the U-shape of the Mre11 dimer (gray envelope) in solution. Although of lower resolution than crystallography, SAXS was used to establish the orientation of the dimer's components, as shown in ribbon format. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)​

Something related to the movement of cells:
Landmark Discovery Of 'Engine' That Drives Cell Movement

ScienceDaily (Oct. 7, 2008) — How a cell assembles its internal machinery required for cell movement has been revealed for the first time.

The researchers discovered a complex of three proteins that directly regulates the myosin network within a cell, thus generating traction force to propel the cell forward. (Myosin is the most common protein found in muscle cells, and is responsible for the elastic and contractile properties of muscle. A different form of myosin is involved in cell movement.)

This action of the tripartite protein complex may be likened to a spring in a toy motorcar – when the protein complex assembles and moves backwards within the cell, it resembles the wound up "engine" of the toy car that has been pulled backwards.

Subsequent disassembling of the protein complex and the resultant forward movement of the cell can be likened to the released spring which unleashes the earlier stored potential energy to propel the car forward.

Michael Sheetz, Ph.D., who is William R Kenan Jr Professor of Cell Biology at the Department of Biological Sciences, Columbia University, and also Distinguished Visiting Professor at the National University of Singapore, said, "This is an exciting paper because Leung's group has discovered an unexpected step in cell migration and contractility — a complex of three proteins including a form of myosin, that is responsible for assembling most of the other myosin components involved in motile processes. The assembly mechanism has been a major mystery and is critical in a variety of diseases from cardiovascular to aging. Now we have a new tool to understand the bases of these critical processes."

Of the three proteins MRCK, LRAP35a and MYO18A, MRCK was discovered by the GSK-IMCB group 10 years ago, while the other two had hitherto unknown functions. Dr. Leung of IMCB said, "The success of the work relies on the commitment and perseverance of the team. A major contributor, Dr. Ivan Tan, is a home-grown scientist who has been working on this project for many years and he has had several clues as to how the system functions for some time, but it was only recently that the jigsaw puzzle was put together. The system has the potential to unravel other as yet undiscovered mechanisms that coordinate the different 'engines' for proper cell migration."

Emphasis mine.
Hard work with spectacular results .

 

[Techne]

Using Living Cells As Nanotechnology Factories

ScienceDaily (Oct. 8, 2008) — In the tiny realm of nanotechnology, scientists have used a wide variety of materials to build atomic scale structures. But just as in the construction business, nanotechnology researchers can often be limited by the amount of raw materials. Now, Biodesign Institute at Arizona State University researcher Hao Yan has avoided these pitfalls by using cells as factories to make DNA based nanostructures inside a living cell.

The results were published in the early online edition of the Proceedings of the National Academy of Sciences.

Yan specializes in a fast-growing field within nanotechnology -- commonly known as structural DNA nanotechnology -- that uses the basic chemical units of DNA, abbreviated as C, T, A, or G, to self-fold into a number of different building blocks that can further self-assemble into patterned structures.

"This is a good example of artificial nanostructures that can be replicated using the machineries in live cells" said Yan. "Cells are really good at making copies of double stranded DNA and we have used the cell like a copier machine to produce many, many copies of complex DNA nanostructures."

Cells Coordinate Gene Activity With FM Bursts, Scientists Find

ScienceDaily (Oct. 2, 2008) — How a cell achieves the coordinated control of a number of genes at the same time, a process that's necessary for it to regulate its own behavior and development, has long puzzled scientists.

Michael Elowitz, an assistant professor of biology and applied physics at the California Institute of Technology (Caltech), along with Long Cai, a postdoctoral research scholar at Caltech, and graduate student Chiraj Dalal, have discovered a surprising answer. Just as human engineers control devices ranging from dimmer switches to retrorockets using pulsed -- or frequency modulated (FM) -- signals, cells tune the expression of groups of genes using discrete bursts of activation.

Elowitz, who is also a Bren Scholar and an investigator with the Howard Hughes Medical Institute, and his colleagues discovered this process by combining mathematical and computational modeling with experiments on individual living cells. The scientists looked specifically at the molecular changes within simple baker's yeast (Saccharomyces cerevisiae) cells after exposure to excess calcium, which increases in concentration in cells in response to stressful conditions such as high salt levels, alkaline pH, and cell wall damage.

The scientists tracked that response using a protein called Crz1 labeled with a green fluorescent tag. Crz1 is stimulated in response to high calcium levels and activates genes that help protect the cell. The glowing of the fluorescent marker allowed Elowitz and colleagues to visualize the movement of Crz1 as it travelled within the cell from the cytoplasm into the cell nucleus and out again into the cytoplasm. Using time-lapse microscopy, they created "movies" of that movement.

Proteins Have Controlled Motions, Researcher Shows

Most biochemists traditionally believe proteins have many random, uncontrolled movements.

Research conducted by Jernigan, director of the L.H. Baker Center for Bioinformatics and Biological Statistics together with Guang Song, an assistant professor in computer science and graduate student Lei Yang, over a 10-year period shows that not only are protein motions more restricted, but also that these restricted, controlled motions are part of the function of the proteins.

The group's findings were recently published in the journal "Structure"

Using as an example a protein from HIV virus, Jernigan conducted his research using a simple model and tested to see how the proteins moved. The large number of reported structures show exactly the motions that are required for their function, and exactly the same motions as computed by Jernigan's model.

"This is one experimental case that is indicative, but there are many others," he said.

Jernigan believes this research is the first step to better understanding proteins and cell behaviors.

"There is the possibility of creating designer drugs with this newly discovered information," he said.

"These are models that conform to the point of view that the structures have been designed to exert very strong control of their motions," he said. "Those motions correspond closely to the motions needed for their function."

For instance, HIV virus protein structures that Jernigan studied did not move randomly, but actually opened and closed to allow access to other structures.

There is a binding site that must open to permit access to the protein and then close again to allow the protein to function, he said.

Because the protein structure opens and closes as part of it function, Jernigan believes that the motion is controlled and part of the function of the protein.

Jernigan's studies used the HIV virus, but he believes that the results are relevant to many other protein structures.

So much control, all the way down to protein motion.

 

[Techne]

Robustness and back-up systems​

New Evidence On The Robustness Of Metabolic Networks

ScienceDaily (Sep. 8, 2008) — Biological systems are constantly evolving in ways that increase their fitness for survival amidst environmental fluctuations and internal errors. Now, in a study of cell metabolism, a Northwestern University research team has found new evidence that evolution has produced cell metabolisms that are especially well suited to handle potentially harmful changes like gene deletions and mutations.

You Can Be Replaced: Immune Cells Compensate For Defective DNA Repair Factor

Genetic instability can lead to multiple problems, including cell death and many forms of cancer. Therefore, it is absolutely critical for cells to have both the means to constantly survey genes for damage and the mechanisms to repair broken DNA. Currently, there are six well characterized classical non-homologous end-joining (C-NHEJ) factors that repair double strand breaks (DSBs) in mammalian cells.Lymphocytes, a type of immune cell, use a kind of genetic shuffling called variable, diversity, joining V(D)J recombination. This gene shuffling occurs during lymphocyte development and helps to produce diverse immune system cells that can recognize all sorts of different foreign substances, called antigens, that might pose a threat to the organism. Previous work in mice has shown that deficiency of C-NHEJ factors results in a severely compromised immune system, because of incomplete V(D)J recombination, along with increased sensitivity to cellular ionizing radiation (IR) and genomic instability.

Preadaptations are good for the future.

Newly discovered mechanics of a molecular machine that transports proteins.​

Channel hopping: protein translocation through the SecA–SecY complex

Newly synthesized proteins are translocated across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane through an evolutionarily conserved protein conducting channel or translocon known as Sec61 in eukaryotes and SecY in prokaryotes. In bacteria, the SecA ATPase is thought to be the motor for translocation through the SecY channel. Two papers by Tom Rapoport and colleagues report the long-awaited structure of the SecA–SecY complex from bacteria. The structure, reveals major conformational changes between both partners and suggests that SecA uses a two-helix finger to push translocating proteins into SecY's cytoplasmic funnel. Crosslinking studies provide further experimental support for this mechanism. In a third paper, Osamu Nureki and colleagues present a crystal structure of SecY bound to an anti-SecY Fab fragment revealing a pre-open state of the channel. Together these three papers provide novel insights into the path taken by a translocating protein. In News and Views, Anastassios Economou takes stock of where this work leaves current knowledge of this 'astonishing cellular nanomachine'

Research articles:
Structure of a complex of the ATPase SecA and the protein-translocation channel
A role for the two-helix finger of the SecA ATPase in protein translocation
Conformational transition of Sec machinery inferred from bacterial SecYE structures

Over 30% of proteins are secreted across or integrated into membranes. Their newly synthesized forms contain either cleavable signal sequences or non-cleavable membrane anchor sequences, which direct them to the evolutionarily conserved Sec translocon (SecYEG in prokaryotes and Sec61, comprising alpha-, bold gamma- and bold beta-subunits, in eukaryotes). The translocon then functions as a protein-conducting channel1. These processes of protein localization occur either at or after translation. In bacteria, the SecA ATPase2, 3 drives post-translational translocation. The only high-resolution structure of a translocon available so far is that for SecYEbold beta from the archaeon Methanococcus jannaschii 4, which lacks SecA. Here we present the 3.2-Å-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermophilus. The structure, solved as a complex with an anti-SecY Fab fragment, revealed a 'pre-open' state of SecYE, in which several transmembrane helices are shifted, as compared to the previous SecYEbold beta structure4, to create a hydrophobic crack open to the cytoplasm. Fab and SecA bind to a common site at the tip of the cytoplasmic domain of SecY. Molecular dynamics and disulphide mapping analyses suggest that the pre-open state might represent a SecYE conformational transition that is inducible by SecA binding. Moreover, we identified a SecA–SecYE interface that comprises SecA residues originally buried inside the protein, indicating that both the channel and the motor components of the Sec machinery undergo cooperative conformational changes on formation of the functional complex.

Exquisite control of biomolecular processes with the aid of nanomachines all the way down to the simplest organisms .

 

[Techne]

Paley’s Watch?​

Cyanobacteria are one of the organisms with the deepest history, with evidence of their remains dating back possibly to about 3.5 billion years ago. So, what is found in some of these simple cells? CLOCKWORK...

A cyanobacterial circadian clockwork.

Cyanobacteria have become a major model system for analyzing circadian rhythms. The temporal program in this organism enhances fitness in rhythmic environments and is truly global--essentially all genes are regulated by the circadian system. The topology of the chromosome also oscillates and possibly regulates the rhythm of gene expression. The underlying circadian mechanism appears to consist of both a post-translational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) and ATP. These three core oscillator proteins have been crystallized and structurally determined, the only full-length circadian proteins to be so characterized. The timing of cell division is gated by a circadian checkpoint, but the circadian pacemaker is not influenced by the status of the cell division cycle. This imperturbability may be due to the presence of the PTO that persists under conditions in which metabolism is repressed. Recent biochemical, biophysical, and structural discoveries have brought the cyanobacterial circadian system to the brink of explaining heretofore unexplainable biochemical characteristics of a circadian oscillator: the long time constant, precision, and temperature compensation.

On the structure of:
Structural Insights into a Circadian Oscillator

An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

A biological clock with all the cogs and gears. The KaiABC clock is a bona fide dynamically oscillating nanomachine that precess unidirectionally and robustly. Present in one of the most primitive, simple organisms...


More on the nanomachinery that governs DNA processing.
Biologists Discover Motor Protein That Rewinds DNA

ScienceDaily (Nov. 2, 2008) — Two biologists at the University of California, San Diego have discovered the first of a new class of cellular motor proteins that “rewind” sections of the double-stranded DNA molecule that become unwound, like the tangled ribbons from a cassette tape, in “bubbles” that prevent critical genes from being expressed.

“When your DNA gets stuck in the unwound position, your cells are in big trouble, and in humans, that ultimately leads to death” said Jim Kadonaga, a professor of biology at UCSD who headed the study. “What we discovered is the enzyme that fixes this problem.”

The discovery represents the first time scientists have identified a motor protein specifically designed to prevent the accumulation of bubbles of unwound DNA, which occurs when DNA strands become improperly unwound in certain locations along the molecule.

“We knew this particular protein caused this disease before we started the study,” said Kadonaga. “That’s why we investigated it. We just didn’t know what it did.”

What this protein, called HARP for HepA-related protein, did astounded Kadonaga and Timur Yusufzai, a postdoctoral fellow working in his laboratory. The two molecular biologists initially discovered that this motor protein burns energy in the same way as enzymes called helicases and, like helicases, attached to the dividing sections of DNA. But while helicases use their energy to separate two annealed nucleic acid strands—such as two strands of DNA, two strands of RNA or the strands of a RNA-DNA hybrid— the scientists found to their surprise that this protein did the opposite; that is, it rewinds sections of defective DNA and thus seals the two strands together again.

As a consequence, the UCSD biologists termed their new enzyme activity an “annealing helicase.”

“We didn’t even consider the idea of annealing helicases before this study started,” said Kadonaga. “It didn’t occur to us that such enzymes even existed. In fact, we never knew until now what happened to DNA when it got stuck in the unwound position.”

Clocks, motors, nanomachines etc. Superbly intelligent biomolecular machinery making life possible.

 

[Techne]

A little about RNA splicing machinery: Possibly the most complex macromolecular machine in the cell​

What is RNA splicing?​

Many human genes (+-94%) contain exons (the DNA sequences that code for amino acids). These exons can be spliced together to form different types of proteins from a single gene.

How is it controlled?​

Extensively and exquisitely controlled.

How common is it in humans?​

Human Genes: Alternative Splicing Far More Common Than Thought

ScienceDaily (Nov. 4, 2008) — Scientists have long known that it's possible for one gene to produce slightly different forms of the same protein by skipping or including certain sequences from the messenger RNA. Now, an MIT team has shown that this phenomenon, known as alternative splicing, is both far more prevalent and varies more between tissues than was previously believed.

Two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.

The researchers found that the type of isoform produced is often highly tissue-dependent. Certain protein isoforms that are common in heart tissue, for example, might be very rare in brain tissue, so that the alternative exon functions like a molecular switch. Scientists who study splicing have a general idea of how tissue-specificity may be achieved, but they have much less understanding of why isoforms display such tissue specificity, Burge said.

Thus, the same gene can result in different functions, depending on the functionality and control of the RNA splicing machinery.

Is it important?​

Humans And Chimps Differ At Level Of Gene Splicing
Not only do we differ genetically, but the way the genes are processed differ.

What happens if the machinery malfunctions?​

Quality control systems are in place.
RNA Biology Finding Makes Waves By Challenging Current Thinking

ScienceDaily (Jan. 23, 2008) — Case Western Reserve University School of Medicine researcher Kristian E. Baker, Ph.D. challenges molecular biology's established body of evidence and widely-accepted model for nonsense-mediated messenger ribonucleic acid (mRNA) decay with a new study. With her collaborator, Ambro van Hoof, Ph.D. of The University of Texas Health Sciences Center, Baker directly tested the "faux 3' UTR" model and proved it could not explain how cells recognize and destroy deviant mRNA. This landmark discovery will redirect mRNA research and expand opportunities for new discoveries in understanding the cells' ability to protect itself from these potential errors.

In all cells, including human, mRNA is a copy of the information carried by a gene on the DNA. Occasionally, mRNA contains errors that can make the information it carries unusable. Cells posses a remarkable mechanism to detect these aberrant mRNAs and eliminate them from the cell -- this process represents a very important quality control system for gene expression. "A significant amount of past research in this area of RNA biology has collected data to support the 'faux 3' UTR' model for mRNA quality control, and, as a result, has shaped present research directions in the field," said Baker. "Our recent findings preclude this explanation and will, undoubtedly, result in a rethinking by many as to how to experimentally approach this important cellular process."

For decades researchers have been puzzled by cells' ability to differentiate between "normal" mRNA and those carrying certain types of mutations. mRNA transports DNA's genetic coding information to the sites of protein synthesis: ribosomes. Cells are able to identify mRNA carrying a mutation and prevent it from reaching the protein synthesis phase. Once identified, the cell destroys the abnormal, mutated mRNA. This naturally occurring process ensures malfunctioning proteins are not produced.

Using a yeast model system, Baker's research offers a better understanding of this mRNA quality control process which closely mimics the process in human cells.

Present in yeast, primitive organisms

But how prevalent is this kind of machinery?​

Visualizing The Machinery Of mRNA Splicing

ScienceDaily (Apr. 8, 2008) — Recent research at Yale provided a glimpse of the ancient mechanism that helped diversify our genomes; it illuminated a relationship between gene processing in humans and the most primitive organisms by creating the first crystal structure of a crucial self-splicing region of RNA.

This work, published in Science, highlights a 16-year quest by Anna Marie Pyle, the William Edward Gilbert Professor of Molecular Biophysics & Biochemistry at Yale, and her research team into the nature of "group II" introns, a particular type of intron within gene transcripts that catalyzes its own removal during the maturation of RNA.

Group II introns are found throughout nature, in all forms of living organisms. Although much has been learned about their structure and how they work through biochemical and computational analysis, until now there have been no high-resolution crystal structures available. The resulting images have provided both confirmation of the earlier work and new information on the three-dimensional structure of RNA and the mechanism of splicing.

"One of the most exciting aspects of this work was that we did not need to do anything disruptive to these molecules to prepare them for structural analysis," said Pyle. "The molecules showed us their structure, their active site and their activity -- all in a natural state. We were even able to visualize their associated ions."

According to Pyle, the crystal structure revealed some unexpected features -- showing two sections that were most implicated as key elements of the active site and strengthening a theory that the process of splicing in humans "shares a close evolutionary heritage" with ancient forms of bacteria.

Forms of this machinery present all the way down to bacteria .



Here is a video describing the process.

 

[Techne]

How 'molecular machines' kick start gene activation revealed

How 'molecular machines' inside cells swing into action to activate genes at different times in a cell's life is revealed today (6 November) in new research published in Molecular Cell. Genes are made of double stranded DNA molecules containing the coded information an organism's cells need to produce proteins. The DNA double strands need to be 'melted out' and separated in order for the code to be accessed. Once accessed, the genetic codes are converted to messenger RNAs (mRNA) which are used to make proteins. Cells need to produce particular proteins at different times in their lives, to help them respond and adapt to changes in their environment.

The "melting out" process is carried out by helicases which is part of the replisome. Exquisitely controlled.
Helicases are also known to be ring-shaped motor proteins, typically hexamers 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.

The new study outlines exactly how a molecular machine called RNA polymerase, which reads the DNA code and synthesizes mRNA, is kickstarted by specialised activator proteins. The scientists have discovered that RNA polymerase uses a tightly regulated internal blocking system that prevents genes from being activated when they are not needed.

Using electron microscopy to look at the inner workings of bacterial cells, the researchers discovered that the DNA strand-separating process is kickstarted when RNA polymerase is modified by an activator protein, which the cell sends to the site of the gene that needs to be switched on.

This activator protein jump-starts the RNA polymerase machine by removing a plug which blocks the DNA's entrance to the machine. The activator protein also causes the DNA strands to shift position so that the DNA lines up with the entrance to the RNA polymerase. Once these two movements have occurred and the DNA strands are in position, the RNA polymerase machine gets to work melting them out, so that the information they contain can be processed to produce mRNA, and ultimately allow production of proteins.

Professor Xiaodong Zhang, lead author of the paper from the Department of Life Sciences at Imperial College London, explains the significance of the team's findings, saying:

"Understanding how the RNA polymerase gene transcription 'machine' is activated, and how it is stalled from working when it is not needed, gives us a better insight than ever before into the inner workings of cells, and the complex processes that occur to facilitate the carefully regulated production of proteins."

Professor Martin Buck, Head of Imperial's Division of Biology and one of the paper's co-authors, adds that understanding how this process works in bacteria cells is of particular interest, because it is this gene transcription and protein production process which allows bacterial cells to adapt, respond and thrive despite changes in their environment:

"In other words, this is the process that occurs inside bacteria that makes them so good at survival. Many bacteria cause infection and disease in humans, and are hard to defeat. Bacterial RNA polymerase is a proven target for antibiotics such as rifampicin, against which many bacteria have become resistant. Insights gained form our research will now provide opportunities and strategies for the design of novel antibacterial compounds," he concludes

So machines govern the activity of gene expression, and machines are governed by gene expression through a reasonably optimal genetic code mmmm....:cheers:

 

[Techne]

How long will a reaction take to complete without enzymes?
Well, some reactions will only complete in about 2.3 billion years without them...
Without Enzyme, Biological Reaction Essential To Life Takes 2.3 Billion Years

But enzymes don't just pop into existence, not even under the BEST pre-biotic synthesis scenarios. Enzymes are produced and folded into the correct conformation by.... other enzymes... controlled by.... biomolecular machines and a reasonably optimal genetic code...



More about the efficiency of enzymes:
Biochemistry: Enzymes under the nanoscope

Small-scale interactions of substrates with an enzyme's active site — over distances smaller than the length of a chemical bond — can make big differences to the enzyme's catalytic efficiency.

When Richard Feynman died in 1988, he left behind the following words on his blackboard: "What I cannot create, I do not understand." His message certainly resonates with protein engineers.

Enzymes are guided into their correct 3D configuration by other enzyme complexes known as chaperones (part of the heat-shock protein family). What happens if the configurations are not right? Scientists determined that some enzymes, as in the case of ketosteroid isomerase, are so precisely folded for their particular ligand/substrate that if it the 3d conformation was off by even 10 picometers (10^12 meters) it would lose its efficiency. Firstly, the conformation has to be just right to tightly bind the ligand into the pocket of the protein, then another mechanism (built in property of the enzyme) is responsible the transfer of electrons in order to catalyze and complete the enzymatic reaction. Our current best efforts at designing artificial enzymes are (from the article) “still tens of billions of times smaller than those of many enzymes.”

The ribosome is a super complex of enzymes, a molecular machine responsible for the building of polypeptide chains which in turn are folded into active proteins by chaperone complexes.
Problems do occur, but checks and balances are present. For example:
Side-chain recognition and gating in the ribosome exit tunnel
At the exit tunnel of the ribosome, it is hypothesized that there are gate and latch mechanisms with active valves controlling the exit of polypeptides. The researchers conclude that these mechanisms play a role in the regulation of "nascent chain exit and ion flux". Sort-off like a final checkpoint.


As already seen, without enzymes, reactions that are crucial to life might take billions of years to complete. Small changes (10 picometers) in the 3D structure of an enzyme can also negatively affect the function of an enzyme.
So how are enzymes folded into their active conformation?

Chaperonins: Two-stroke, two-speed, protein machines

Article:
Setting the chaperonin timer: A two-stroke, two-speed, protein machine
From the article:

Protein machines and their man-made, macroscopic counterparts share several common attributes, e.g., concerted, coordinated movements, cyclical operation, and energy transduction. These machines are seldom reversible because each cycle generally involves at least one irreversible step, e.g., the consumption of fuel. Often these machines operate at variable speed, a plethora of timing devices adjusting the cycle speed in response to demand.

An exemplary bipartite protein machine is the chaperonin system, typified by GroEL and GroES from Escherichia coli. GroEL is composed of 2 heptameric rings, stacked back to back, which, in the presence of GroES, operate out of phase with one another in the manner of a 2-stroke, reciprocating motor (1, 2). Driven by the hydrolysis of ATP, the chaperonin proteins function as a biological simulated annealing machine (3, 4), optimizing the folding of their substrate proteins (SPs) whose passage to biologically functional conformations is thus assured.

The picture of the chaperonins that emerges from our work is that of a machine equipped with a timer, the trans ring, poised to respond to the appearance of SP [substrate protein inside the cavity] but otherwise idling in a quiescent state. We note that Nature’s design of this 2-speed protein machine minimizes the hydrolysis of ATP in the absence of SP. However, it maximizes the number of turnovers and minimizes the residence time available to the encapsulated SP to reach the native state, design principles well suited to the operation of an iterative annealing device.

Partial part and dynamics of the system.
Nice video of how it operates

Machines folding machines into place. Beautiful... :cheers:

 

[Techne]

The kinesin motor machine:
Nice pic

How Tiny Cell Proteins Generate Force To 'Walk'

ScienceDaily (Dec. 4, 2008) — MIT researchers have shown how a cell motor protein exerts the force to move, enabling functions such as cell division.

Kinesin, a motor protein that also carries neurotransmitters, "walks" along cellular beams known as microtubules. For the first time, the MIT team has shown at a molecular level how kinesin generates the force needed to step along the microtubules.

Microtubules, quantum physics, and consciousness? They form tracks for neurotransmitters to be transported and can possibly act as quantum computational structures. Also, see the mice below.

The researchers, led by Matthew Lang, associate professor of biological and mechanical engineering, report their findings in the Nov. 24 online early issue of the Proceedings of the National Academy of Sciences.

Because kinesin is involved in organizing the machinery of cell division, understanding how it works could one day be useful in developing therapies for diseases involving out-of-control cell division, such as cancer.

The protein consists of two "heads," which walk along the microtubule, and a long "tail," which carries cargo. The heads take turns stepping along the microtubule, at a rate of up to 100 steps (800 nanometers) per second.

In the PNAS paper, Lang and his colleagues offer experimental evidence for a model they reported in January in the journal Structure. Their model suggests — and the new experiments confirm — that a small region of the protein, part of which joins the head and tail is responsible for generating the force needed to make kinesin walk. Two protein subunits, known as the N-terminal cover strand and neck linker, line up next to each other to form a sheet, forming the cover-neck bundle that drives the kinesin head forward.

"This is the kinesin power stroke," said Lang.

Next, Lang's team plans to investigate how the two kinesin heads communicate with each other to coordinate their steps.

Lead author of the PNAS paper is Ahmad Khalil, graduate student in mechanical engineering. Other MIT authors of the paper are David Appleyard, a graduate student in biological engineering; Anna Labno, a recent MIT graduate; Adrien Georges, a visiting student in Lang's lab; and Angela Belcher, the Germehausen Professor of Materials Science and Engineering and Biological Engineering. This work is a close collaboration with authors Martin Karplus of Harvard and Wonmuk Hwang of Texas A&M.

The research was funded by the National Institutes of Health and the Army Research Office Institute of Collaborative Biotechnologies.

Few videos describing the motor:
Kinesin Transport Protein
Kinesin Explanation

Mice with a few kinesin mutations? Look like there is something wrong with their neurphysiology, almost like they are not interacting with the environment in the correct way?
Kinesin mutations in mice

Ever wondered how cellular machinery causes replication of cells?
Awesome video:
Inside the cell
And it does not even remotely cover the intricate mechanisms controllong the process.

Another video of mitosis:
Mitosis
Active cyclinB/cdc2 plays a part in nuclear envelope breakdown, and destruction of cyclinB and abolition of cdc2 activity allows nuclear envelope formation.

In real life it looks something like this:

 

[Techne]

More machines and clockwork:
Clockwork That Drives Powerful Virus Nanomotor Discovered

Related article:
Biologists Learn Structure, Mechanism Of Powerful 'Molecular Motor' In Virus

ScienceDaily (Dec. 29, 2008) — Peering at structures only atoms across, researchers have identified the clockwork that drives a powerful virus nanomotor.

Because of the motor's strength--to scale, twice that of an automobile--the new findings could inspire engineers designing sophisticated nanomachines. In addition, because a number of virus types may possess a similar motor, including the virus that causes herpes, the results may also assist pharmaceutical companies developing methods to sabotage virus machinery.

Again, taking clues from cellular machinery to design our own optimal nanotechnology.


So we think we have designed GPS systems?
Primary Cilium As Cellular 'GPS System' Crucial To Wound Repair

ScienceDaily (Dec. 25, 2008) — The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations.

What we are dealing with is a physiological analogy to the GPS system with a coupled autopilot that coordinates air traffic or tankers on open sea," says Soren T. Christensen, describing his recent research findings on the primary cilium, the GPS-like cell structure, at the American Society for Cell Biology (ASCB) 48th Annual Meeting, Dec. 13-17, 2008 in San Francisco.

Christensen and his colleagues at the University of Copenhagen in Denmark and the Albert Einstein School of Medicine in the Bronx studied the primary cilia in lab cultures of mice fibroblasts, the cells that along with related connective tissues sculpt the bulk of the mammalian body.

"The really important discovery is that the primary cilium detects signals, which tell the cells to engage their compass reading and move in the right direction to close the wound," Christensen explains.

Purposefully communicating information as a means to an end... wound healing.

The researchers suspect this cellular GPS system plays roles other than wound healing. The primary cilia could serve as a fail-safe device against uncontrolled cell movement, says Christensen. Without chemical stimulation, the primary cilia would restrain cell migration, preventing the dangerous displacement of cells that is associated with invasive cancers and fibrosis, the scientists explain. On the other hand, defective primary cilia might fail to provide correct directional instructions during cell differentiation. This failure could be another link connecting primary cilia to severe developmental disorders, the researchers suggest.

Protruding through the cell membrane, primary cilia occur on almost every non-dividing cell in the body. Once written off as a vestigial organelle discarded in the evolutionary dust, primary cilia in the last decade have risen to prominence as a vital cellular sensor at the root of a wide range of health disorders, from polycystic kidney disease to cancer to left-right anatomical abnormalities.

Faulty Darwinian reasoning leading to faulty conclusions only to be corrected by scientific inquiry...

 

[Techne]

sorry, as life and the rules there of are not based on molecular constructs, but based on rules of how many and energy associate.

The structures that life depend on are representations based on the rules of energy and information. Energy can be argued to supervene on information, and cells can use energy to manipulate information. These processes depend on these structures and functions.

How The Sensory Organs Of Bacteria Function

ScienceDaily (Jan. 17, 2009) — Bacteria can occur almost anywhere on earth and exist under the most varying conditions. If these tiny, microscopic organisms are to survive in these environments, they need to be able to rapidly detect changes in their surroundings and react to them. Scientists at the Johannes Gutenberg University of Mainz are currently investigating how bacteria manage to pass information on their environment across their membranes into their cell nuclei.

"The sixty-four-thousand- dollar question is how signals are transmitted across the cell membrane," explains Professor Gottfried Unden of the Institute of Microbiology and Vinology. Working in collaboration with the Max Planck Institute for Biophysical Chemistry in Göttingen, his research group has demonstrated that structural alterations to membrane-based sensors play a major role in the transfer of signals.

Some bacteria possess more than 100 different sensors that they use to form a picture of their environment. These sensors can show, for example, whether nutrient substrates and/or oxygen are present in the immediate neighborhood of the cell and what the external status of temperature and light is like. These sensors are mainly located in the cell membrane, i.e., the layer separating bacteria cells from the environment. From there they then transmit signals into the cell nucleus.

Thanks to the development of new methods of isolating these sensors and of other innovative techniques, it is now possible to discover how all this works. The researchers in Mainz have also managed to modify a sensor that detects an important bacterial substrate so that it can be analyzed making use of new spectroscopic techniques. "This is the first time that solid-body nuclear magnetic resonance (NMR) spectroscopy has been used to investigate large membrane proteins," stated Professor Unden. In addition to this functional analysis, the structural analysis undertaken by the biophysicist team in Göttingen headed by Professor Marc Baldus has identified important details of the signal transmission process: a stimulus molecule – carbonic acid in this case – binds to a part of the sensor that protrudes from the cell.

This appears to result in dissolution of the ordered structure of that segment of the sensor within the cell that is in non-stimulated status. It seems that it is this plasticity that elicits the subsequent activation of the enzymatic reaction cascade within the cell. This results in the cellular response, which, for example, can take the form of neosynthesis of enzymes or the development of protective mechanisms.

In addition to the new findings on signal transmission published in Nature Structural and Molecular Biology, the microbiologists of Mainz University have discovered a previously unknown and exceptional method of signal detection employed by the same sensor (designated DcuS), which they discuss in an article in the Journal of Biological Chemistry. This shows that bacteria react not only to their extracellular environment, but also to the intracellular situation. It is becoming apparent that it is not the sensors alone that detect stimuli.

A second stimulus detection pathway is represented by the transport system that channels substrates into the cell. Once the substrate – carbonic acid – has been taken up, the transporter notifies the sensor of this. Prof. Unden added, "We have been able to identify that segment of the transporter that is responsible for the control of sensor functioning. The transporter is of fundamental importance for the function of the sensor. Without the transporter, the sensor does not work correctly and is constantly in activated status," explained Professor Unden, who suspects that this function-related feedback on metabolic and transport activity is often more important for a cell than information concerning concentrations only.

So, bacteria forms a picture of their surroundings so they can adequately respond to the environment.

And cells seem to count as well.

How Do Cells Count? Scientists Take A Step Further In Unraveling Mystery Of How Cells Control Number Of Centrosomes

ScienceDaily (Jan. 12, 2009) — In the 13th January print edition of the journal Current Biology, IGC researchers provide insight into an old mystery in cell biology, and offer up new clues to understanding cancer. Inês Cunha Ferreira and Mónica Bettencourt Dias, working with researchers at the universities of Cambridge, UK, and Siena, Italy, unravelled the mystery of how cells count the number of centrosomes, the structure that regulates the cell’s skeleton, controls the multiplication of cells, and is often transformed in cancer.

This research addresses an ancient question: how does a cell know how many centrosomes it has? It is equally an important question, since both an excess or absence of centrosomes are associated with disease, from infertility to cancer.

Each cell has, at most, two centrosomes. Whenever a cell divides, each centrosome gives rise to a single daughter centrosome, inherited by one of the daughter cells. Thus, there is strict control on progeny! By using the fruit fly, the IGC researchers identified the molecule that is responsible for this ‘birth control policy’ of the cell – a molecule called Slimb. In the absence of Slimb, each mother centrosome can give rise to several daughters in one go, leading to an excess of centrosomes in the cell.

In recent years, Monica’s group has produced several important findings relating to centrosome control: they identified another molecule, SAK, as the trigger for the formation of centrosomes. When SAK is absent, there are no centrosomes, whereas if SAK is overproduced, the cell has too many centrosomes. These results were published in the prestigious journals Current Biology and Science, in 2005 and 2007. Now, the group has discovered the player in the next level up: Slimb mediates the destruction of SAK, and in so doing, ultimately controls the number of centrosomes in a cell.

Monica explains, ‘We carried out these studies in the fruit fly, but we know that the same mechanism acts in mice and even in humans. Knowing that Slimb is altered in several cancers opens up new avenues of research into the mechanisms underlying the change in the number of centrosomes seen in many tumours’.

Mónica first became interested in centrosomes and in SAK when she was an Associate Researcher at Cambridge University, UK, and has pursued this interest at the IGC, where she has been group leader of the Cell Cycle Regulation laboratory since 2006. Inês Cunha Ferreira travelled with Monica from Cambridge, and is now in her second year of the in-house PhD programme. Two other PhD students in the lab also contributed to this research, Ana Rodrigues Martins and Inês Bento.

Sensing, counting and manipulating information in order to control succesful self-replication. Exquisitely controlled .

New Protein Function Discovered Related article: New Protein Function Discovered; Sheds Light On Intricate Mechanics Of Cell Division

ScienceDaily (Jan. 9, 2009) — A group of Dartmouth researchers has found a new function for one of the proteins involved with chromosome segregation during cell division. Their finding adds to the growing knowledge about the fundamental workings of cells, and contributes to understanding how cell function can go wrong, as it does with cancerous cells.

The researchers studied a protein called NOD, distantly related to the motor proteins that power diverse cellular activities, including intracellular transport, signaling, and cell division. They used X-ray crystallography to determine its structure, and then they used enzyme kinetics to find out how it performed. While this protein is found in fruit flies, the results are helpful in determining how related proteins work in humans.

Nucleotide-binding Oligomerization Domain (NOD)

"This study on NOD provided evidence for a new way a kinesin motor could function," said Jared Cochran, a postdoctoral fellow at Dartmouth and the lead author on the study. "Rather than moving on its own, it hitches a ride on the ends of microtubules which results in a dynamic cross-linking between the arms of chromosomes and the cell's growing spindle of microtubules. If NOD doesn't function properly, then the two cells end up with either both or none of that particular chromosome, which is lethal [to the cell and the organism] in most cases."

"Before this study, it had been shown that kinesin motors either walked along their microtubule tracks or functioned to break microtubules apart," says Jon Kull, the senior author on the paper, associate professor of chemistry at Dartmouth, and a 1988 Dartmouth graduate. "This work describes a novel mode for kinesin function, in which NOD does not walk, but rather alternates between grabbing on to and letting go of the end of the growing filament, thereby tracking the end as it grows. The diversity of function of these proteins is remarkable."

Original article:
ATPase Cycle of the Nonmotile Kinesin NOD Allows Microtubule End Tracking and Drives Chromosome Movement

 

[Techne]

but in light of NEW material to share what is occuring in research, can be observed in the photosynthesis developments

perhaps read this

http://www.sciforums.com/showthread.php?t=89452

Yes, photosynthesis coupled with quantum mechanics is a fascinating subject.
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

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 .

 

[Walter L. Wagner]

Techne:

Thanks for the fascinating links and information.

 

[Techne]

And quantum physics and consciousness? Think there could be a link?

Quantum physics and Consciousness. Are they connected? The microtubule connection.

Research into the brain-body-mind problem is ongoing and one way of attempting to understand it is to try and describe consciousness in terms of material particles and fields interacting between inputs, internal states, and outputs without any intrinsic meaning. Terms such as “feeling”, “intention”, “knowing” and “choice” are thus not viewed as primary causal factors of consciousness, but a byproduct of these blind interactions.

Quantum physics has not been at the forefront to attempt to describe consciousness as the neurocomputational model of laterally connected input layers of the brain’s neurocomputational architecture is viewed as the most credible explanation for consciousness. One problem that quantum mechanics face is the effect of quantum decoherence (The Role of Decoherence in Quantum Mechanics) and failures to measure it. Essentially, quantum states are believed to be too sensitive and fragile to disruption by thermal energy to affect the macroscopic nature of proteins and other macromolecular structures.

The Penrose-Hameroff orchestrated objective reduction (orch. OR) model provides a basis to connect consciousness with quantum mechanics. Microtubules are integral in this theory.

Connecting quantum mechanics, aromatic ring pi-bonds, protein formation, microtubules and consciousness.

The “quantum physics” and “aromatic ring pi bond” connection.
An aromatic (aromaticity) compound is composed of a conjugated planar ring system with delocalized pi electron clouds. Benzene is an example of an aromatic compound (Figure 1). In benzene (and other aromatic compounds) the double bonds are shorter than the single bonds, causing the carbon atoms to be pulled and pushed between two states and thus vibrate between two states (Figure 2). The pi electrons are also delocalized above and below the carbon ring (Figure 1). Aromatic compounds are thus described to be resonating and are best described quantum mechanically.

The “aromatic ring pi bond” and “protein formation” connection.
4 amino acids contain aromatic rings: tyrosine, phenylalanine, tryptophan and histidine (Figure 3). Histidine, however has 6 delocalized electrons but not a benzene ring and is hydrophilic (more polar).

When peptide chains fold to form proteins, the structure is stabilized and dynamically regulated in the intracellular aqueous phase. Polar side groups face outwardly and react with the polar aqueous milieu, while non-polar regions face inwardly (Protein folding). Aromatic amino acids are more non-polar and thus coalesce more readily in the centre of a protein. When aromatic amino acids coalesce it allows London force van der Waals interactions between the non-polar electron clouds of the aromatic rings, causing quantum resonation of the coalesced non-polar aromatic rings (Figure 4).

The “protein formation” and “microtubule” connection.
Microtubules are long, hollow, cylindrical, filamentous, tube-shaped protein polymers consisting of alpha and beta tubulin dimers and form part of the cytoskeleton (Figure 5, Figure 6, Figure 7). Microtubules play important roles in cell signaling, cell division and mitosis, vesicle and mitochondrial transport and play crucial roles in the development and maintenance of cells and cell shape. Microtubules are highly dynamic cytoskeletal fibres and are capable of two types of dynamics:
1) Treadmilling and
2) Dynamic instability
Microtubules polymerize (rescue/elongate) at the positive (+) end and depolymerize (catastrophe/shorten) at the negative (-) end. During treadmilling, polymerization and depolymerization occur at equal rates and thus the microtubules do not change in length but changes position 4-dimensionally.
During dynamic instability, either the (+) end polymerizes quicker than the (-) end can depolymerize resulting in total elongation of the microtubule, or the (-) end depolmerizes quicker than the (+) end can polymerize resulting in total shortening of the microtubule. In the Inner Life of the Cell video this behavior can be witnessed at time approx 1.07-1.11min (rescue) and 1.11-1-15 (catastrophe).

Figure 8 shows the structure of the alpha- and beta-tubulin dimers and the prevalence of aromatic amino acids (1sa0.pdb). At a higher resolution (Figure 9) it is clear that the aromatic amino acids are close enough to each other (< 2nM) to allow for London van der Waals (Figure 10) interactions. When tubulins polymerize during dynamic instability (rescue) they form tube-like structures (Figure 7). Quantum level resonance as a result of quantum level dipole oscillations (London van der Waals forces) within hydrophobic pockets result in functional protein vibrations which depend on quantum effects (Figure 11). The quantum effect on a single tubulin protein conformation is superposed and exists in both states simultaneously and acts as a qubit (as in quantum computer). Thus, the elegant formation of microtubules (Figure 7 and Figure 12) can in theory constitute a quantum computer (more detail).

The “microtubule” and “consciousness” connection.
Microtubules extend throughout dendrites and axons (neural cells) and play crucial roles in controlling synaptic strengths responsible for learning and cognitive functions through mechanical signaling, communication as well as cytoskeletal scaffolding (cell movement).

In a nutshell, the Penrose-Hameroff orch OR model proposes that quantum effects are relayed through pi-bonds in hydrophobic pockets within microtubules to the macroscopic structure of the brain, resulting in consciousness. Microtubules are thus viewed as protein quantum computers relaying the information locked in Planck scale. Fascinating!

Of course the detail of this model is much more in depth and the following documents and web pages illustrate it beautifully. Enjoy!!!

1) Quantum consciousness
2) The Brain Is Both Neurocomputer and Quantum Computer
3) That's life! The geometry of pi electron resonance clouds.
4) Quantum computation in brain microtubules? The Penrose-Hameroff "Orch OR" model of consciousness
5) Microtubules - Nature's Quantum Computers?

 

[Techne]

Putting cytosine deamination to work: How the immune system exploits the optimal properties of the genome for antibody diversification and immune function.​

The effect of cytosine deamination on a random pool of amino acids and how it might facilitate evolution has been described. The optimal features of the genetic code are exploited by the vertebrate immune system by "putting cytosine deamination to work". Antibody diversification is crucial in limiting the frequency of environmentally acquired infections and thereby increasing the fitness of the organism. Initial diversification of antibodies is achieved by assembling variable (V), diversity (D) and joining (J) gene segments (V(D)J recombination) by non-homologous recombination. Further diversification is carried out by somatic hypermutation (SHM) and Class Switch Recombination. Central to the initiation to these diversification processes is the activation-induced cytosine deaminase (AID) protein. AID deaminates cytosine to uracil in single stranded DNA (ssDNA - arising during gene transcription) and is dependent on active gene transcription of the various antibody genes. The induced mutation is resolved by at least 4 pathways (Figure 1):
1) Copying of the base by high-fidelity polymerases during DNA replication.
2) Short-Patch Base Excision Repair (SP-BER) by uracil-DNA glycosylase removal and subsequent repair of the base.
3) Long-Patch Base Excision Repair (LP-BER)
4) Mismatch repair (MMR)

Link to big picture

Figure 1: Activation induced cytosine deamination and the pathways involved in resolving the induced mutation. 1) Normal DNA replication results in a C:G→T:A transition. 2) Successful SP-BER resolves the mutation, however the recruitment of error-prone translesion polymerases results (e.g. REV1) in transversions (REV1; C:G→G:C) and transition. 3) LP-BER can also resolve the mutation, however recruitment of low-fidelity polymerases (e.g. Pol n) also causes transition and transversion mutations. 4) MMR repair can also resolve the mutation, however the recruitment of low-fidelity polymerases through this pathway is a major cause of A:T transitions.​

AID causes somatic hypermutation and its activity is limited to the certain genetic regions of the immune system. When the system runs unchecked, mutations might be introduced into proto-oncogenes, resulting in possible cancerous growth. The system is controlled (Figure 2). The activity and gene expression of AID is controlled. The type of error-repair pathway and the subsequent recruitment of various low-fidelity polymerases determine the type of mutations after the repair process and these also seem to be controlled. Current research focuses on the mechanisms of control of downstream repair pathways and why this system is selectively targeted to the small region of antibody genes.

Figure 2: Controlled variability of somatic hypermutation.​

Thus, the immune system exploits the properties the genetic code for the purpose of controlled variability. This system is not only limited to vertabrate. Cytosine deamninases are found in bacteria as well. Error-prone repair systems are also present together with an optimal code.

References:
Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman MF et al. The biochemistry of somatic hypermutation. Annu Rev Immunol. 2008;26:481-511.

Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20.

Goodman MF, Scharff MD, Romesberg FE. Abstract AID-initiated purposeful mutations in immunoglobulin genes. Adv Immunol. 2007;94:127-55.

Basu U, Chaudhuri J, Phan RT, Datta A, Alt FW. Regulation of activation induced deaminase via phosphorylation. Adv Exp Med Biol. 2007;596:129-37

 

[Techne]

How Cells Handle Broken Chromosomes"]How Cells Handle Broken Chromosomes

ScienceDaily (Feb. 12, 2009) — Scientists from the Max Planck Institute of Biochemistry discovered a novel cellular response towards persistent DNA damage: After being recognized and initially processed by the cellular machinery, the broken chromosome is extensively scanned for homology and the break itself is later tethered to the nuclear envelope.

Thus the researchers uncovered a surprising feature of how DNA strand breaks can be handled. Their unexpected findings have important implications for the understanding of DNA repair mechanisms.

The central molecule for life is DNA, which constitutes the genetic blueprint of our organism. However, this precious molecule is constantly threatened by miscellaneous damage sources. DNA damage is a cause of cancer development, degenerative diseases and aging. The most dangerous and lethal type of DNA-damage is the DNA double strand break (DSB). A single DSB is enough to kill a cell or cause chromosomal aberrations leading to cancer. Therefore, cells have evolved elaborate DNA repair systems that are fundamental for human health.

DSBs can be repaired by error-prone non-homologous end joining, a pathway in which the DSB ends are simply fused together again. The alternative repair pathway, called homologous recombination, is mostly error-free and needs homologous DNA sequences to guide repair. A vast amount of research, by many scientists around the world, has provided us with a detailed picture of how the DNA damage is recognized and finally repaired. However, so far little was known, how homologous sequences are found and how cells react when DNA breaks persist.

Now, scientists around Stefan Jentsch, head of the Department of Molecular Cell Biology, were able to shed light on these questions, as they report in the upcoming issue of Molecular Cell.

The scientists modified a yeast strain in which a DSB can be induced and followed over time. Moreover, they managed to label the DNA-break for microscopic studies. Using high-resolution digital imaging, they observed after a few hours a directed movement of the break to the nuclear envelope. Jentsch and colleagues speculate that this tethering to the nuclear envelope could be a safety measure of cells to prevent erroneous and unwanted recombination events, which can have catastrophic consequences like cancer development or cell death.

Marian Kalocsay and Natalie Hiller, who conducted the study as part of their PhD-thesis research, then set out to unravel the molecular details of how a persistent DSB is recognized, processed and – at last - relocated to the nuclear envelope.

Using a high resolution method – the so called chip-on-chip technique - which allowed to investigate repair factor recruitment to DNA in unprecedented details, the researchers made a surprising observation: In an apparent attempt to find homology and repair the DSB, a protein called Rad51 (or “recombinase”) begins within one hour to accumulate and to spread bi-directionally from the break, covering after a short time the entire chromosome – a much larger area than supposed before. “Intriguingly, Rad51 spreading only occurs on the chromosome where the break resides and does not “jump” to other chromosomes”, says Kalocsay. As to the researchers knowledge, this is the first in vivo description of ongoing chromosome-wide homology search, which is the most mysterious event in DSB repair. Therefore, this finding has important implications for the understanding of DNA repair by homologous recombination.

Furthermore, Kalocsay and Hiller identified a novel important player in the DNA-damage response that is essential for Rad51 activation as well as for the relocation of DSBs to the nuclear envelope: the histone variant H2A.Z. In early stages of DNA repair it is incorporated into DNA near the DSBs and is essential there for the initiation of the following repair mechanisms. Later on, the attachment of the small modifying protein SUMO to H2A.Z plays an important role in the tethering of the break to the nuclear envelope. “Moreover, cells lacking H2A.Z are severely sensitive to DSBs, thus revealing H2A.Z as an important and novel factor in DSB-repair”, explains Hiller.

Can't wait for the molecular simulation for this mechanism.


Viruses often get a bad rap. No one knows the origins of viruses though.
Exogenous accidents or endogenous retroviruses gone wild. The second one sounds more plausible.
Research On Viral Origins Suggests New Definition Of Virus May Be Needed

ScienceDaily (Feb. 16, 2009) — The strange interaction of a parasitic wasp, the caterpillar in which it lays its eggs and a virus that helps it overcome the caterpillar’s immune defenses has some scientists rethinking the definition of a virus.

In an essay in the journal Science, Donald Stoltz, a professor of microbiology and immunology at Dalhousie University, in Halifax, Nova Scotia, and James Whitfield, a professor of entomology at the University of Illinois, report that a new study also appearing in Science shows how the diverse ways in which viruses operate within and among the organisms they encounter may not be fully appreciated.

Indeed. Consider the following functions of endogenous retroviruses and related elements (as already mentioned here).
1) Independent envelope genes from unrelated ERV families regulate trophoblast differentiation and syncytia formation during synepitheliochorial placentation. Are there examples of Eutheria that are capable of reproduction without ERVs?
Humans (primates): HERV-W and HERV-FRD
Mice (Rodentia): Syncytin-A and -B
Sheep (Artiodactyla): enJSRV

2) Retroelement formatting of the genome [1].
System architectures formatting by retroelements and other repeat elements possibly have an effect on morphological, physiological and reproductive function.

3) LTRs play a fundamental role in gene expression
Independently acquired LTRs have assumed regulatory roles for orthologous genes [2].
An LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression [3].
LTR class I endogenous retrovirus (ERV) retroelements impact considerably on the transcriptional network of human tumor suppressor protein p53 (guardian of the genome) [4].

4) Role in autoimmunity [5].
Disease associations have been established, however there is as yet no proven definite causative association between HERVs and disease.
a) Human endogenous retroviruses can encode superantigenic activity
b) Transcriptional activation. HERVs may act as insertional mutagens or cis-regulatory elements causing activation, inhibition, or alternative splicing of cellular genes involved in immune function.
c) Molecular mimicry. Production of neo-antigens by modification of cellular components.
d) Epitope spreading.
e) Activation of innate immunity through pattern recognition receptors.

[1] von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res. 2005;110(1-4):108-116.

[2] Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, et al. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet. 2007 Jan 12;3(1):e10.

[3] Dunn CA, Medstrand P, Mager DL. An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12841-12846.

[4] Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18613-18618.

[5] Colmegna I, Garry RF. Abstract Role of endogenous retroviruses in autoimmune diseases. Infect Dis Clin North Am. 2006 Dec;20(4):913-929.


This study just contributes to more fascinating functions of these retroviral elements.

The study, from a team of researchers led by the Université François Rabelais, in Tours, France, found that the genes that encode a virus that helps wasps successfully parasitize caterpillars are actually integrated into the wasps’ own chromosomes. These genes, which they show to be related to those from another known group of viruses, are an indivisible part of the wasp’s genetic heritage; they are passed down from one generation to another of parasitoid wasps.

“Many virology texts won’t even mention polydnaviruses,” Whitfield said. “The issue we bring up is: Do we want to call these viruses? And if not, why not? Because they certainly started out as viruses. And if so, then we have to change the definition of viruses to somehow specify what it is that a virus has to contain, and what it has to do, to be considered a virus.”

ERV research at present is rich with speculations and it is a fertile ground for new and exciting ideas regarding their importance and functionality. (previously thought to randomly integrated junk)

 

[Walter L. Wagner]

Techne:

I appreciate your excellent posts.

Your post on quantum consciousness has previously been addressed in other threads, but it's good to have it summarized anew. It rather reminds me of a question I posed in 1975:

"What property of an electron in one's brain is it that allows it to become aware of the fact that it is an electron?"

The origins of viruses also remain obscure. Clearly, they require a fully developed cell in order to replicate. Ones which have become part of a cell genome, in my estimation, should no longer be called a virus; but that is a technicality. In plants, many viruses are routinely incorporated into the genome and cause beneficial effects. Are they still viruses?

Keep up the good posts!