Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


You are not connected. Please login or register

Intelligent Design, the best explanation of Origins » Intelligent Design » The amazing design of bacteriophage viruses and its DNA packaging motor

The amazing design of bacteriophage viruses and its DNA packaging motor

View previous topic View next topic Go down  Message [Page 1 of 1]

Admin


Admin
The amazing design of the DNA packaging motor

http://reasonandscience.heavenforum.org/t2134-the-amazing-design-of-bacteriophage-viruses-and-its-dna-packaging-motor

The argument from the DNA’s molecular motor
1. There is a “very fast and powerful molecular motor” that crams the viral DNA tightly into the capsid with the help of five moving parts.
2. The parts of the motor move in sequence like the pistons in a car's engine, progressively drawing the genetic material into the virus's head, or capsid.
3. The motor is needed to insert DNA into the capsid of the T4 virus, which is called a bacteriophage because it infects bacteria.
4. The T4 molecular motor is the strongest yet discovered in viruses and proportionately twice as powerful as an automotive engine. The motors generate 20 times the force produced by the protein myosin, one of the two proteins responsible for the contraction and strength of muscles.
5. Even viruses, which are not even alive by the scientific definition of being able to reproduce independently, show incredible design.
6. If design is what we observe, then there must be a designer.
7. God exists.


According to the United Nations, 2015 is the International Year of Light as well as the International Year of Soils. But, for the marine microbial ecologist Forest Rohwer, 2015 is also the Year of the Phage.  Phages, more formally known as bacteriophages, are viruses that infect bacteria. They are easily as ubiquitous, universal, and essential to life on Earth as light and soil, and yet they are largely unknown.

“The thing that even most biologists don’t get—let alone most of the rest of the world—is that phages are the most diverse things on the planet, and there are more of them than anything else, and we really don’t have a clue” Phages possess a wide array of forms and functions. They are all incredibly small; at just a few nanometres across, they lie on the border of measurability between quantum and classical physics, all but impossible to see without a scanning electron microscope.

Viruses look incredibly well designed. Some bacteriophages look like lunar landing capsules, legs and all.

Viruses are tiny particles that can’t reproduce on their own, but hijack the machinery of truly living cells. But they still have genetic material, long strands of DNA (or sometimes RNA) enclosed in a protein sheath. They are biologically inert until they enter into host cells. Then they start to propagate using host cellular resources. The infected cell produces multiple copies of the virus, then often bursts to release the new viruses so the cycle can repeat. One of the most common types is the bacteriophage (or simply ‘phage’) which infects bacteria. It consists of an infectious tailpiece made of protein, and a head capsule (capsid) made of protein and containing DNA packaged at such high pressure that when released, the pressure forces the DNA into the infected host cell.

How does the virus manage to assemble this long information molecule at high pressure inside such a small package, especially when the negatively charged phosphate groups repel each other? It has a special packaging motor, more powerful than any molecular motor yet discovered, even those in muscles.  ‘The genome is about 1,000 timeslonger than the diameter of the virus. It is the equivalent of reeling in and packing 100 mts of fishing line into a coffee cup, but the virus is able to package its DNA in under five minutes.
Force
A surprising finding  is that the phage packaging motor generates enormous force in order to package DNA. Forces as high as ∼60 pN were measured in phages ϕ29, λ, and T4, thus making the packaging motor one of the strongest force generating biological motors reported to date.  The force is 20–25 times that of myosin, 10 times that of kinesin, or >2 times that of RNA polymerase. Such high forces seem to be essential to pack the viral DNA against the enormous electrostatic repulsive forces (and bending and entropic energies) to confine a highly negatively charged DNA polymer within a limited volume of the capsid

Velocity
The phage packaging motors show high rates of packaging as well as high processivity. The T4 motor can achieve rates as high as ∼2000 bp/sec, the highest recorded to date.

Power
Phage packaging motors generate enormous power, with the T4 motor being the fastest and the most powerful. Even with a high external load force of 40 pN, the T4 motor can translocate DNA at a remarkable speed of ∼380 bp/sec. This is equivalent to a power of 15,200 pN/bp/s, or 5.2 × 10−18 W. Scaling up the nanoscale T4 packaging motor to a macromotor, the motor power density is approximately twice that of a typical automobile engine

The sequence of steps in the head morphogenesis  is as follows:

(i) assembly of the packaging motor on a nascent (unexpanded) empty prohead (Figure A)
(ii) expansion of the capsid after about 10%–25% of the genome is packaged (Figure B)
(iii) packaging until the head is full
(iv) cutting of DNA and dissociation of the motor (Figure C)
(v) assembly of neck proteins to seal the packaged heads (Figure D)

Question : How could natural forces and chemical reactions have come up with such a elaborated mechanism ?

In a specially interesting scientific paper from last year scientists report that  The 30° tilt of the subunits matches perfectly with the 30° transitions that the dsDNA helix exhibits during revolution (360° ÷ 12 = 30°).

Question : how did this precise and finely tuned arrangement emerge ? trial and error ?

In each step of revolution that moves the dsDNA to the next subunit, the dsDNA physically moves to a second point on the channel wall, keeping a 30° angle between the two segments of the DNA strand . This structural arrangement enables the dsDNA to touch each of the 12 connector subunits in 12 discrete steps of 30° transitions for each helical pitch . Nature has created and evolved  a clever machine   that advances dsDNA in a single direction while avoiding the difficulties associated with rotation, such as DNA supercoiling, as seen in many other processes.

Question : how did this precise and finely tuned arrangement emerge ? trial and error ? since when can  be clever be assigned to something that is not intelligent ?? Should the author of the article not rather honor the inventor of this amazing nano machinery, namely the creator ??

The dramatic divergence of bacteriophage genomes is an obstacle that frequently prevents the detection of homology between proteins and, thus, the determination of phylogenetic links between phages.

Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data.

Convergence, of course,is a common feature of design. It’s also precisely the opposite of “divergence”, which is supposed to be a hallmark of evolution.

Even viruses, which are not even alive by the definition of being able to reproduce independently, show incredible design.  They are too well designed to be accidents.

Proponents of naturalism have to believe in miracles – that super-efficient, compact, powerful motors like this just appeared, arose or emerged (favorite Darwinian miracle-words) from nowhere.

The large packaging subunit gp17 but not the small subunit gp16 exhibited an ATPase activity. 2 Although gp16 lacked ATPase activity, it enhanced the gp17-associated ATPase activity by >50-fold. The gp16 enhancement was specific and was due to an increased catalytic rate for ATP hydrolysis. A phosphorylated gp17 was demonstrated under conditions of low catalytic rates but not under high catalytic rates in the presence of gp16. The data are consistent with the hypothesis that a weak ATPase is transformed into a translocating ATPase of high catalytic capacity after assembly of the packaging machine. The nonstructural terminase complex, constituted by one small subunit and one large subunit, is a key component of the DNA-packaging machine

So both subunits are required for proper functioning of the molecular motor. These subunits do not have any use unless duly embedded in this nano motor. A irreducible complex system must have at least two subunits, who could not have emerged through evolutionary steps. This seems to be the case in this amazing molecular machine as well. Further evidence is the fact that no protein homology exists between different Phages, which is another indication that they are designed and created separately.



According to the United Nations, 2015 is the International Year of Light as well as the International Year of Soils. But, for the marine microbial ecologist Forest Rohwer, a professor at San Diego State University, 2015 is also the Year of the Phage. 9 Phages, more formally known as bacteriophages, are viruses that infect bacteria. They are easily as ubiquitous, universal, and essential to life on Earth as light and soil, and yet they are largely unknown.

“The thing that even most biologists don’t get—let alone most of the rest of the world—is that phages are the most diverse things on the planet, and there are more of them than anything else, and we really don’t have a clue” Phages possess a wide array of forms and functions. They are all incredibly small; at just a few nanometres across, they lie on the border of measurability between quantum and classical physics, all but impossible to see without a scanning electron microscope. Like their hosts, phages are everywhere—in dirt, water, intestines, hot springs, Arctic ice cores.  There are, for example, an estimated 1031—ten million trillion trillion—phages on Earth, more than every other organism, including bacteria, put together. The average teaspoon of seawater contains five times as many phages as there are people in Rio de Janeiro.
We live in a microbial driven world that only exists because Bacteria and Archaea tempered the previously hostile environment on early Earth to create atmospheric conditions that allow eukaryotic life forms to flourish. Bacterial and archaeal encoded enzymes catalyze all the major processes involved in global biogeochemical cycling, playing key roles in the carbon and nitrogen cycles, and producing approximately half of the oxygen in the Earth's atmosphere. 10   Once ignored, it is now becoming increasingly accepted that phages play key roles in the biology of microbes, which themselves impact environments at large. Many previous excellent reviews have highlighted the importance of bacteriophages in specific environments for example.
This is a incredible animation of T4 bacteriophage Virus assembly:





Virus has powerful mini-motor to pack up its DNA 4

Viruses are tiny particles that can’t reproduce on their own, but hijack the machinery of truly living cells. But they still have genetic material, long strands of DNA (or sometimes RNA) enclosed in a protein sheath. Viruses come in many different sizes, shapes and designs, and they operate in diverse ways. They are composed of DNA (or RNA in the case of RNA viruses, including retroviruses) and protein. They are not living organisms because they cannot carry out the necessary internal metabolism to sustain life, nor can they reproduce themselves. They are biologically inert until they enter into host cells. Then they start to propagate using host cellular resources. The infected cell produces multiple copies of the virus, then often bursts to release the new viruses so the cycle can repeat. One of the most common types is the bacteriophage (or simply ‘phage’) which infects bacteria. It consists of an infectious tailpiece made of protein, and a head capsule (capsid) made of protein and containing DNA packaged at such high pressure that when released, the pressure forces the DNA into the infected host cell.


How does the virus manage to assemble this long information molecule at high pressure inside such a small package, especially when the negatively charged phosphate groups repel each other? It has a special packaging motor, more powerful than any molecular motor yet discovered, even those in muscles.  ‘The genome is about 1,000 timeslonger than the diameter of the virus. It is the equivalent of reeling in and packing 100 mts of fishing line into a coffee cup, but the virus is able to package its DNA in under five minutes.. Researchers   analysed the bacteriophage T4—a virus that infects E. coli bacteria, the type that inhabit human intestines.  This motor exerts a force of > 60 piconewtons. This sounds small (6 × 10–11 N), but for its size, it’s twice as powerful as a car engine. So the motor, a terminase enzyme complex, ‘can capture and begin packaging a target DNA molecule within a few seconds.’

Such a powerful motor must use a lot of energy, and in one second, this one goes through over 300 units of life’s energy currency, ATP (adenosine triphosphate), and this itself is generated by a remarkable molecular motor, ATP synthase. The virus has a complementary motor-enzyme, ATPase, built into its packaging engine, to release the energy of the ATP.And not only is the packing motor powerful, it can change its speed as if it had gears. This is important, because the DNA fed to it from the cell is likely not a straightforward untangled thread. ‘Just as it is good for a car to have brakes and gears, rather than only being able to go 60 miles per hour, the DNA-packaging motor may need to slow down, or stop and wait if it encounters an obstruction.’ A report said: ‘It may permit DNA repair, transcription or recombination—the swapping of bits of DNA to enhance genetic diversity—to take place before the genetic material is packaged within the viral capsid.’








Viral DNA packaging motors are among the most powerful molecular motors known.

1 Single-molecule studies show that the packaging motor is fast and powerful. 2

DNA packaging into a viral capsid is a complex process consisting of initiation, elongation, and termination. It involves orchestrated coordination and sequential action of multiple proteins 1


Force 8
A surprising finding from single-molecule studies is that the phage packaging motor generates enormous force in order to package DNA. Forces as high as ∼60 pN were measured in phages ϕ29, λ, and T4, thus making the packaging motor one of the strongest force generating biological motors reported to date.  The force is 20–25 times that of myosin, 10 times that of kinesin, or >2 times that of RNA polymerase. Such high forces seem to be essential to pack the viral DNA against the enormous electrostatic repulsive forces (and bending and entropic energies) to confine a highly negatively charged DNA polymer within a limited volume of the capsid
Velocity
The phage packaging motors show high rates of packaging as well as high processivity. The T4 motor can achieve rates as high as ∼2000 bp/sec, the highest recorded to date. 

Power
Phage packaging motors generate enormous power, with the T4 motor being the fastest and the most powerful. Even with a high external load force of 40 pN, the T4 motor can translocate DNA at a remarkable speed of ∼380 bp/sec. This is equivalent to a power of 15,200 pN/bp/s, or 5.2 × 10−18 W. Scaling up the nanoscale T4 packaging motor to a macromotor, the motor power density is approximately twice that of a typical automobile engine

The bacteriophage DNA packaging machine  3
Large dsDNA bacteriophages and herpesviruses encode a powerful ATP-driven DNA-translocating machine that encapsidates a viral genome into a preformed capsid shell or prohead.







The key components of the packaging machine are the packaging enzyme (terminase, motor) and the portal protein that forms the unique DNA entrance vertex of prohead. The terminase complex, comprised of a recognition subunit (small terminase) and an endonuclease/translocase subunit (large terminase), cuts viral genome concatemers. The terminase-viral DNA complex docks on the portal vertex, assembling a motor complex containing five large terminase subunits. The pentameric motor processively translocates DNA until the head shell is full with one viral genome. The motor cuts the DNA again and dissociates from the full head, allowing head-finishing proteins to assemble on the portal, sealing the portal, and constructing a platform for tail attachment. A body of evidence from molecular genetics and biochemical, structural, and biophysical approaches suggests that ATP hydrolysis-driven conformational changes in the packaging motor (large terminase) power DNA motion. Various parts of the motor subunit, such as the ATPase, arginine finger, transmission domain, hinge, and DNA groove, work in concert to translocate about 2 bp of DNA per ATP hydrolyzed. Powerful single-molecule approaches are providing precise delineation of steps during each translocation event in a motor that has a speed as high as a millisecond/step. The phage packaging machine has emerged as an excellent model for understanding the molecular machines, given the mechanistic parallels between terminases, helicases, and numerous motor proteins.
Study reveals structure of DNA packaging motor in virus
7

In december 2000, Scientists   solved the three-dimensional structure of the central component of a biological "motor" that powers the DNA packaging system in a virus, providing scientists with their first glimpse of such a motor system. The study describes atom-by-atom how the core of the tiny motor, just millionths of a millimeter in size, is constructed and suggests how it works to translocate, or pack, long stretches of the virus' genetic material into its outer shell during the process of viral replication. "Though other motor systems have been studied in biology, this is the first motor known to translocate genetic material."Viruses are essentially a simple parasite consisting only of an envelope that contains the genetic material ready for transportation from one host to another. They can reproduce only after infecting a host cell. Once inside a cell, the virus manipulates the cell's machinery to produce all the necessary components, including genetic material, to assemble new viruses. It is here that the biological motor is needed to fill newly assembled envelopes with their genetic material The new viruses are then released from the host cell and are free to infect other cells.
The study shows that DNA packaging motor is comprised of three primary parts:
an elongated prohead that serves as the virus shell
a doughnut-shaped connector that is positioned at the entrance to the virus shell and feeds DNA into the shell 
a novel ribonucleic acid (RNA)-enzyme complex that converts chemical energy to mechanical energy needed for packaging.

Their findings show that the connector is made up of 12 protein subunits that may serve as "cylinders" in the motor system to pull long chains of DNA through the center of the doughnut-shaped system.Five identical enzymes, called ATPases, are positioned around the connector, just outside the opening in the virus shell. The enzymes break down the cell's chemical fuel, called ATP, to produce the energy needed to power the motor.The researchers postulate that successive chemical reactions produced by the ATP cause the phi29 connector to oscillate and rotate, pulling the DNA into the shell two base pairs at a time."Our results suggest that the prohead and connector comprise a rotary motor, with the head and ATPase complex acting as a stator and the DNA acting as a spindle.Rotary-type motor systems are found in two other biological systems, he says, noting that such a motor is used to produce the rotation of flagella of E. coli. "The flagella rotate, and when they rotate synchronously, the bacterium can swim quite rapidly towards a source of food, or carbohydrates, along a concentration gradient."The enzyme that manufactures ATP, called ATP synthase, also operates as a rotary motor to produce ATP or to pump protons.
The DNA-packaging motor appears to differ from these two known rotary motors, because its apparent spindle, the viral DNA, is translocated or moved to a new position.
This motor system appears to be novel mechanistically.

Did God make pathogenic viruses?  6 
 
bacteria are at the basis of our life-support system. They supply our fertile soil and atmospheric gases. They cleanse our water supply, play a role in stabilising the atmospheric nitrogen concentration, regulate the acidity or alkalinity of the soil environment, and thus generally ensure that our world is liveable.

The view now emerging of the normal relationship between viruses and genes is not so much a host/invader relationship, but a relationship more akin to bees carrying pollen from flower to flower, thus causing cross-fertilisation. Viruses carry not only their own genes, but also those of other creatures as well, especially those of bacteria.21 Although bacteria pass genetic information to each other using several processes such as pili transfer (see below), viral transfer is now known to be critically important. viruses convert all bacteria into one giant, global ‘superorganism’, and that viruses ‘possess a remarkable mechanism for the creation and exchange of genetic material’. The traditional understanding that viruses are alien invaders competing against humans in a life or death struggle for the cell’s manufacturing facility is now understood to be oversimplified, if not incorrect. It is usually not expedient for a virus to kill its host, since this may cause the death of the virus. Viruses must have a reservoir of host species in which they can live permanently otherwise they would soon go extinct.
The dramatic divergence of bacteriophage genomes is an obstacle that frequently prevents the detection of homology between proteins and, thus, the determination of phylogenetic links between phages. 1      common descent bye bye ?
 
1) http://www.pnas.org/content/111/42/15096.short
2) http://cel.webofknowledge.com/InboundService.do?SID=2DypYOwSdUP2rHMIiEw&product=CEL&UT=WOS%3A000261767000027&SrcApp=Highwire&Init=Yes&action=retrieve&SrcAuth=Highwire&Func=Frame&customersID=Highwire&IsProductCode=Yes&mode=FullRecord
3) http://www.ncbi.nlm.nih.gov/pubmed/22297528
4) https://creation.com/images/pdfs/tj/j22_1/j22_1_15-16.pdf
6) http://creation.com/did-god-make-pathogenic-viruses
7) http://www.purdue.edu/uns/html4ever/001206.Rossmann.DNAmotor.html
8 )   http://teaguesterling.com/dna/motor-protein.pdf
9)    http://www.newyorker.com/tech/elements/phage-killer-viral-dark-matter
10 ) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109452/



Last edited by Admin on Thu Dec 03, 2015 10:48 pm; edited 20 times in total

View user profile http://elshamah.heavenforum.com

2 T4 portal protein (gp20) assembly on Sun Aug 02, 2015 2:24 pm

Admin


Admin
T4 portal protein (gp20) assembly 1
full text


The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains.  2

They are the most numerous biological entity on earth, with an estimated number of 10^31 tailed phages in the biosphere. They are arguably very ancient as a group, with some estimates placing their ancestors before the divergence of the Bacteria from the Archaea and Eukarya

The dramatic divergence of bacteriophage genomes is an obstacle that frequently prevents the detection of homology between proteins and, thus, the determination of phylogenetic links between phages. For instance, sequence similarity between Siphoviridae major tail proteins (MTPs), which have been experimentally demonstrated to form the phage tail tube, is often not detectable 3

Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. 4

Convergence, of course,is a common feature of design. It’s also precisely the opposite of “divergence”, which is supposed to be a hallmark of evolution. 5




Picture above. (a) 3D density map of T4 portal protein assembly at 3.6 Å resolution with each subunit colour-coded. Shown are the top view (left)
 and side view (right). (b) Ribbon diagram of the gp20 atomic model with each subunit colour-coded. Shown are the top view (left)
 and side view (right).







Picture above  (a) Charge distribution on the outer surface of dodecameric gp20. Blue and red colours correspond to 10 kT e− positive and negative potential,
respectively. (b) Charge distribution on the inner surface of dodecameric gp20. (c) Ribbon drawing of the gp20 monomer structure with each
domain colour-coded.



Picture above (a,b) Cryo-EM density map of the T4 prolate head (gp23: cyan; gp24:magenta; Soc: pink; Hoc: yellow).
(c) Bottom view of the prolate head, showing the gap between gp20 and the capsid. (d) Fit of the gp20 and gp23
structures into the cryo-EM map of the T4 prolate head. (e) A model of the T4 head assembly. A dodecameric portal is
assembled on the inner membrane of E. coli with the assistance of the phage-coded chaperone gp40 and the E. coli chaperone YidC58.
The portal assembly acts as an initiator for head assembly, leading to co-polymerization of the major capsid protein gp23
and scaffolding proteins.







Picture above The upper row (a–d) shows the different portal protein subunits with their wing, stem, clip and crown domains coloured
green, blue, purple and orange, respectively (PDB IDs of portals: φ29: 1FOU, SPP1: 2JES, P22: 3LJ4). The lower row
(e–h) shows the portal assemblies docked into their respective phage capsids (cyan). The T4 portal structure was fitted
into the 10 Å resolution EM map of the prolate head. Similarly the other portal structures were docked into their capsid
structures (PDB IDs: φ29: 1YXN, P22: 2XYZ, SPP1: 4AN5).



Picture above (a) Fitting of the T4 portal protein (purple) and gp17 (tan) into the 35 Å cryo-EM reconstruction of the procapsid+gp17
(EMD-1572 accession number). (b) Residues involved in the interaction between gp20 (purple) and gp17 (tan) are shown
as sticks. (c) The surface charge of gp20 and gp17 around the interface area showing electrostatic interactions. The view
orientation is the same as in panel (b).



The different portal protein subunits with their wing, stem, clip and crown domains are coloured green, blue, purple and orange, respectively.

Relaxation and repulsion helps viruses pack DNA 6

The molecular motor that folds and packs DNA into a virus is at its most efficient when the DNA shows some self-repulsion. That is the surprising finding of researchers based in the US – it was previously thought that such repulsion would act as an obstacle in the packing process. The team also found that pausing the motor and allowing it to relax increased the rate of the whole packaging process. In addition to providing new insights into how viruses function, the work could benefit biotechnologies that enclose long polymers into nanoscale devices.

After invading its host cell, a virus reprogrammes the cell's nucleus to duplicate it.


Question : How was the virus programmed to re-programme the cell's nucleus ? trial and error ? Had the function of reprogramming not have to be fully operating since the beginning, otherwise the virus would not be able to replicate ? 

As it replicates, a strand of DNA is pulled from an infected host cell and squeezed into a protein shell – known as a prohead – which then carries the DNA to infect other cells. In some species, the prohead is produced first, leaving only a small hole at one end through which a powerful molecular motor pushes the DNA in and then packs it at very high densities.

Question : How did it emerge the function to pack the dna at very high densities ? trial and error ?

The motor has to overcome three forces: the electrostatic self-resistance that comes into play because DNA is negatively charged; the mechanical resistance of DNA to bending; and the entropic resistance of DNA to be crowded on itself.

Question: How did the motor emerge this function of overcome the three forces ? trial and error ? 





1) http://www.nature.com/ncomms/2015/150706/ncomms8548/full/ncomms8548.html
full text pdf: http://www.nature.com/ncomms/2015/150706/ncomms8548/pdf/ncomms8548.pdf
2) http://www.nature.com/ncomms/2014/140617/ncomms5173/full/ncomms5173.html
3) http://mmbr.asm.org/content/75/3/423.full.pdf
4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1208326/
5) http://www.uncommondescent.com/intelligent-design/in-other-words-phylogenetic-reconstruction-is-sheer-fantasy/
6) http://physicsworld.com/cws/article/news/2014/jun/25/relaxation-and-repulsion-helps-viruses-pack-dna



Last edited by Admin on Sun Aug 02, 2015 7:57 pm; edited 7 times in total

View user profile http://elshamah.heavenforum.com

Admin


Admin
Bacteriophage lambda replication cycle



CYTOPLASMIC 1

Adsorption: The phage attaches to target cell adhesion receptors through its tail fibers.
The baseplate of the virion attaches to the entry receptor.
Ejection of the viral DNA into host cell cytoplasm by long flexible tail ejection system.
Transcription and translation of early genes.
Replication of genomic DNA by theta replication.
Replication of genomic DNA by rolling circle.
Transcription and translation of late genes.
Assembly of empty procapsids and viral genome packaging.
Mature virions are released from the cell by lysis.





1) http://viralzone.expasy.org/all_by_species/512.html



Last edited by Admin on Sun Aug 02, 2015 7:39 pm; edited 3 times in total

View user profile http://elshamah.heavenforum.com

Admin


Admin
Handy Motor Found in Virus   3
 
the captioned artist   shows five gp17 protein structures.  These structures are protein subdomains embedded in the ring-shaped motor mechanism.  The capsid, or viral container, acts like a hard plastic shell, protecting the DNA inside.  Two rings on the opening hold the motor in place.  The gp17 subdomains take turns grasping the DNA and shoving it in.  Another analogy is that they work like pistons operating in sequence.  Using ATP energy pellets, they take advantage of electrostatic forces to gently but firmly transfer the DNA strand into the interior, where it coils in an orderly fashion.  The mechanism generates 20 times the force used by myosin, the motor in muscle.

 The virus they studied is a bacteriophage – a virus that infects and destroys bacteria.  The cutaway diagram of the capsid shows the DNA wound neatly into a fabric-like pattern.  The researchers hope some day not only to understand viruses better, but to use their tricks for nanotechnology.  Someday man-made motors like these could deliver medicines to patients or power nano-sized machines.  First, though, they need to do basic research on how the viral motor works.  “This particular motor is very fast and powerful,” they said.

 Even viruses, which are not even alive by the definition of being able to reproduce independently, show incredible design.  They are too well designed to be accidents.  Why do so many viruses cause disease and death?  Actually, only a small fraction are harmful; most cause no harm and some are beneficial.
       Some creationists speculate that they all had a beneficial function originally: keeping bacteria in check or delivering genetic instructions to animals encountering a new environment.  Proponents of naturalism have to believe in miracles – that super-efficient, compact, powerful motors like this just appeared, arose or emerged (favorite Darwinian miracle-words) from nowhere.  Second, they have to deny that anything is evil or out of order.  In Darwin’s world, whatever is, is right.  A logical consequence is that it is vain to seek cures for disease.  So what if millions of humans die in a pandemic?  It just shows that viruses are more fit.
       If miracles and apathy don’t motivate you to swallow the evolutionary line, then look at the mechanism from a design perspective and figure out what it’s there for.  Basic research can reveal the mechanism.  Philosophy and theology can elucidate its purpose.  Engineering can look for applications.  Who needs Darwin, the guy who sits around telling miracle stories?

     The Purdue team obviously didn’t act like “nothing in biology makes sense except in the light of evolution.”  They had no need of that hypothesis.  The E-word failed to materialize in the press release or any of the writeups on other sites.  “Viruses, start your engines!” EurekAlert began its version.  “Researchers find what drives one of nature’s powerful, nanoscale motors.”
If design is what you observe, then design will lead to the right explanation, which may lie outside the capabilities of science.

We Are Filled with Viruses  2

Viruses have a bad connotation.  We immediately think of the ones that cause disease: “I’ve got a virus,” you say when feeling under the weather.  Actually, you have trillions of them all the time, even in the best of health.  A single gram of stool sample can have 10 billion of them! What does that mean?  Scientists are only beginning to find out.
   One thing it means is that they can’t be all bad.  Elizabeth Pennisi reported in Science this week about work at the University of British Columbia and Washington University to explore the human virome.1  She began her report,
   In the past decade, scientists have come to appreciate the vast bacterial world inside the human body.  They have learned that it plays a role in regulating the energy we take in from food, primes the immune system, and performs a variety of other functions that help maintain our health.  Now, researchers are gaining similar respect for the viruses we carry around.
Bacteria have been easier to count than the tiny viruses.  Many of our internal viruses are bacteriophages that invade and kill bacteria.  This suggests they play a role in keeping the brakes on bacterial infections.  “For every bacterium in our body, there’s probably 100 phages,” Pennisi wrote.  The number of virus species identified in stool samples of healthy adults varied from 52 to 2773.  “The viromes varied significantly from one individual to the next; they were even more diverse than the bacterial communities within the same individuals,” Pennisi reported.  “But each person’s viral community remained stable over the course of the year.”  That is, unless they go on a different diet or eating regimen; then the viromes change.  But people who eat the same foods tend to converge on virus profiles.  Researchers also found that infants with fevers had more viruses than healthy infants.
We are full of viruses, in other words, but we don’t know what they all do.  This is “a true frontier” of research, with much to learn. “Ultimately, those viruses are incredibly important in driving what’s going on” one scientist from the University of British Columbia said.  It’s not enough to know your bacteria; you have to know the viruses that interact with them.  1.  Elizabeth Pennisi, “Microbiology: Going Viral: Exploring the Role Of Viruses in Our Bodies,” Science, 25 March 2011: Vol. 331 no. 6024 p. 1513, DOI: 10.1126/science.331.6024.1513.
It’s always been intriguing that viruses look incredibly well designed. Some bacteriophages look like lunar landing capsules, legs and all.  Scientists have learned that some viruses have shells like hard plastic  and pack their DNA into their capsids with motors generating remarkable force, in an orderly manner .  They are also extremely effective in finding their target cells, inserting their DNA, and commandeering the genetic machinery to make copies of themselves.
Phages are not considered transitional forms between molecules and life.  Intelligent design would describe their design and predict that they have functions, but would be at a loss to explain harmful viruses.  It takes Biblical creation to explain that they were probably designed for good originally, but some became harmful because of the Fall due to sin. Sometimes a single mutation can turn a beneficial bacterium into a disease-causing terror; the same could be true with viruses.
Maybe they were intended to be regulators of bacteria.  Maybe they were designed to convey information to the body about new environments, and were equipped to copy themselves to spread the word so that the body could be prepared.  Who knows?  This is, after all, a frontier of research.  For philosophers, it’s noteworthy that we are stumbling onto a reality right around us – right within us – about which we have been largely oblivious, with the potential to dramatically change our understanding of nature.
Given that an athlete running the high hurdles in the peak of health is carrying around trillions of viruses, intuition suggests that most of what they do for us is good.  The scientific research appears poised to find many beneficial functions for our viral passengers.  It happened with bacteria; it took society a long time to change the emotional response from “germs... uggh!” with the householder running to get the antibacterial spray, to an appreciation of the many good things bacteria do for us.  Now we look differently upon our bacterial passengers.  We have learned they outnumber our own cells, and are learning that our viral passengers outnumber the bacteria 100 to one.  Expect amazing things to be discovered about these tiny, mysterious machines.
Insights into the Structure and Assembly of the Bacteriophage ϕ29 Double-Stranded DNA Packaging Motor 1


Bacteriophage ϕ29 is an excellent model system for exploring motor assembly and for mechanistic studies of DNA packaging . Like other dsDNA phages, ϕ29 is assembled via a well-defined morphogenetic pathway that includes the formation of the prohead, the assembly of a packaging motor complex on the head, ATP-driven translocation, and motor disassembly at the completion of packaging. Unlike the other well-studied dsDNA phages, ϕ29 has an additional essential motor component, an oligomeric ring of RNA (termed pRNA), that binds to proheads and bridges the connector and ATPase components











Mechanism of One-Way Traffic of Hexameric Phi29 DNA Packaging Motor with Four Electropositive Relaying Layers Facilitating Antiparallel Revolution   4

The bacteriophage phi29 DNA translocation motor contains three coaxial rings: a dodecamer channel, a hexameric ATPase ring, and a hexameric pRNA ring. The viral DNA packaging motor has been believed to be a rotational machine. However, we discovered a revolution mechanism without rotation.




One-way traffic of dsDNA translocation is facilitated by five factors:

(1) ATPase changes its conformation to revolve dsDNA within a hexameric channel in one direction;
(2) the 30° tilt of the channel subunits causes an antiparallel arrangement between two helices of dsDNA and channel wall to advance one-way translocation;
(3) unidirectional flow property of the internal channel loops serves as a ratchet valve to prevent reversal;
(4) 5′–3′ single-direction movement of one DNA strand along the channel wall ensures single direction; and
(5) four electropositive layers interact with one strand of the electronegative dsDNA phosphate backbone, resulting in four relaying transitional pauses during translocation.


The discovery of a riding system along one strand provides a motion nanosystem for cargo transportation and a tool for studying force generation without coiling, friction, and torque. The revolution of dsDNA among 12 subunits offers a series of recognition sites on the DNA backbone to provide additional spatial variables for nucleotide discrimination for sensing applications.




Illustration of the phi29 DNA packaging motor structure. Side view (A) and bottom view (B). The 30° tilt of the helix of the connector subunit and its antiparallelism with the dsDNA helix is depicted (A). The three coaxial rings: pRNA hexamer, ATPase hexamer, and connector dodecamer in the phi29 DNA packaging motor are depicted (B).



Illustration showing the antiparallel configuration between connector subunit and DNA helix. External view (A) and internal view (B) of the antiparallel configuration of connector and DNA as dsDNA revolves through the connector. One-twelfth of a dsDNA helix is 30° (C), which is the angle dsDNA revolves to advance between two adjacent connector subunits (D). The contact at every 30° for twelve 30° transitions resulted in translocation of one helical turn of the dsDNA through the connector (B).

The 30° Tilting of Channel Subunits Causes an Antiparallel Arrangement between Two Helices Resulting in Revolution in a Single Direction
A cone-shaped central channel is encircled by 12 copies of the protein connector subunit gp10 and serves as a pathway for dsDNA translocation. The wider C-terminal end, 13.6 nm in diameter, is buried inside the procapsid. The narrower N-terminal end is 3.6 nm in diameter and allows dsDNA to enter. The connector is a one-way valve that only allows dsDNA to move into the procapsid unidirectionally All 12 gp10 subunits are tilted at a 30° angle and encircle the channel in a configuration that runs antiparallel to the dsDNA helix residing in the channel. The antiparallel arrangement between the two helices of the connector subunit, and the helix of the dsDNA, can be visualized in an external view (Figure A), with dsDNA potentially making contact at each connector subunit (Figure above). The antiparallelism exhibited by the helices argues against a bolt and screw rotation model since a screw thread and the corresponding whorl should match. The 30° tilt of the subunits matches perfectly with the 30° transitions that the dsDNA helix exhibits during revolution (360° ÷ 12 = 30°).  Question : how did this precise and finely tuned arrangement emerge ? trial and error ? In each step of revolution that moves the dsDNA to the next subunit, the dsDNA physically moves to a second point on the channel wall, keeping a 30° angle between the two segments of the DNA strand (Figure above). This structural arrangement enables the dsDNA to touch each of the 12 connector subunits in 12 discrete steps of 30° transitions for each helical pitch . Nature Nature, or the creator of the natural world ?? has created and evolved evolved ??!!  a clever machine since when can to be clever be assigned to something that is not intelligent ?? Should the author of the article not rather honor the inventor of this amazing nano machinery, namely the creator ??  that advances dsDNA in a single direction while avoiding the difficulties associated with rotation, such as DNA supercoiling, as seen in many other processes. For reference, the Earth rotates around its own axis every day, but revolves around the sun every 365 days.



Figure above. Structure of the phi29 DNA packaging motor, showing the four lysine rings scattered inside the inner wall of the connector. Side view (A) and top view (B) of the connector, showing K200 (magenta) and K209 (yellow). The 229 (cyan) with 246 (red) show the boundary of the connector inner flexible loops that harbor the other two lysines. Due to the flexibility of the loop, the crystal structure of this loop is not available, and the known boundary of the loop was used to show the location. Side (C) and top views (D) of the detailed scheme of DNA revolution through the connector are shown. In this figure, the related position of the dsDNA and the connector subunit are displayed as three-dimensional and viewed at different angles; the position of the dsDNA is different between two channel subunits, even though the DNA itself does not rotate.

1) http://jvi.asm.org/content/88/8/3986.full
2) http://creationsafaris.com/crev201103.htm
3) http://creationsafaris.com/crev200812.htm#20081230b
4) http://pubs.acs.org/doi/full/10.1021/nn4002775



Last edited by Admin on Tue Jan 05, 2016 5:32 pm; edited 14 times in total

View user profile http://elshamah.heavenforum.com

Admin


Admin
A Promiscuous DNA Packaging Machine from Bacteriophage T4 1

Complex viruses are assembled from simple protein subunits by sequential and irreversible assembly. During genome packaging in bacteriophages, a powerful molecular motor assembles at the special portal vertex of an empty prohead to initiate packaging. The capsid expands after about 10%–25% of the genome is packaged. When the head is full, the motor cuts the concatemeric DNA and dissociates from the head. These viruses encode powerful machines to package their genomes tightly inside an icosahedral-shaped capsid “head.” Packaging requires precise orchestration of a series of steps: assembly of an empty prohead, concatemer cutting and attachment of the motor-DNA complex to the portal vertex, ATP-fueled DNA translocation until the head is full, DNA cutting to terminate packaging, detachment of the motor, and sealing of the packaged head by “neck” assembly. The virion consists of a head into which the genome is packaged, and a tail that delivers the genome into the bacterial cell. A capsid of precise dimensions is first assembled, often with a single type of protein subunit polymerizing around a protein scaffold

A capsid of precise dimensions is first assembled, often with a single type of protein subunit polymerizing around a protein scaffold (Figure below). A cone-shaped dodecameric portal initiates assembly and remains at the special five-fold vertex of the isometric capsid (prehead), facilitating all subsequent transactions: DNA entry, tail attachment, and DNA ejection . The scaffold is removed, creating an empty space inside the capsid (prohead or procapsid) for encapsidating the viral genome (Figure A below).

A packaging ATPase motor, also known as the “terminase,” recognizes and cuts the concatemeric viral DNA and docks at the narrow protruding end of the prohead portal, inserting the DNA end into the ∼3.5-nm portal channel. The packaging machine thus assembled drives DNA translocation utilizing the free energy of ATP hydrolysis (Figure B).

After filling the head (“headful” packaging), the motor cuts the DNA and dissociates from the DNA-full head (Figure C) [10]. The neck and tail proteins assemble on the portal, completing the infectious virus assembly (Figure D).

A fundamental feature of virus assembly is “sequential assembly” in which “simple” components assemble in a strict sequence to generate a complex nanomachine with unique biological properties. Each assembly step generates a new site or conformational state to which the next component binds with exquisite specificity, essentially irreversibly . A series of such steps, as documented by elegant studies in phage T4  and numerous other viruses, leads to rapid and high-fidelity assembly of a complex infectious virion. In phage T4, this process assembles virions approaching a theoretical infection efficiency of 1.

The sequence of steps in the head morphogenesis of phage T4 , as well as in other phages and dsDNA viruses (e.g., herpes viruses), is as follows:

(i) assembly of the packaging motor on a nascent (unexpanded) empty prohead (Figure A)
(ii) expansion of the capsid after about 10%–25% of the genome is packaged (Figure B)
(iii) packaging until the head is full
(iv) cutting of DNA and dissociation of the motor (Figure C)
(v) assembly of neck proteins to seal the packaged heads (Figure D)


Conformational changes in the portal are reported to drive these sequential irreversible transitions (Figure 1; different colors of portal represent different conformational states)




A packaging ATPase motor, also known as the “terminase,” recognizes and cuts the concatemeric viral DNA and docks at the narrow protruding end of the prohead portal, inserting the DNA end into the ∼3.5-nm portal channel . The packaging machine thus assembled drives DNA translocation utilizing the free energy of ATP hydrolysis. After filling the head (“headful” packaging), the motor cuts the DNA and dissociates from the DNA-full head. gp17 contains all the enzymatic activities necessary for DNA packaging: ATPase, nuclease, and translocase

The large packaging subunit gp17 but not the small subunit gp16 exhibited an ATPase activity. 2 Although gp16 lacked ATPase activity, it enhanced the gp17-associated ATPase activity by >50-fold. The gp16 enhancement was specific and was due to an increased catalytic rate for ATP hydrolysis. A phosphorylated gp17 was demonstrated under conditions of low catalytic rates but not under high catalytic rates in the presence of gp16. The data are consistent with the hypothesis that a weak ATPase is transformed into a translocating ATPase of high catalytic capacity after assembly of the packaging machine. The nonstructural terminase complex, constituted by one small subunit and one large subunit, is a key component of the DNA-packaging machine 



So both subunits are required for proper functioning of the molecular motor. These subunits do not have any use unless duly embedded in the nano motor. A irreducible complex system must have at least two subunits, who could not have emerged through evolutionary steps. This seems to be the case in this nano motor as well. Further evidence is the fact that no protein homology exists between different Phages, which is another indication that they are designed and created separately. 1  



1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039672/
2) http://www.jbc.org/content/275/47/37127.full

View user profile http://elshamah.heavenforum.com

Admin


Admin
A Cornucopia of Evidence for Intelligent Design: DNA Packaging of the T4 Virus 1

http://www.reasons.org/articles/a-cornucopia-of-evidence-for-intelligent-design-dna-packaging-of-the-t4-virus

Researchers have taken long-term interest in the T4 virus, particularly because of the way the DNA double helix is packed extremely tightly within the viral head. As the DNA presses against the capsid walls, it generates high pressure (about ten times that of a bottle of champagne). This high pressure serves a functional purpose by driving the viral DNA into the host cell during the injection process.







1) http://www.reasons.org/articles/a-cornucopia-of-evidence-for-intelligent-design-dna-packaging-of-the-t4-virus

View user profile http://elshamah.heavenforum.com

Sponsored content


View previous topic View next topic Back to top  Message [Page 1 of 1]

Permissions in this forum:
You cannot reply to topics in this forum