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Author Topic: Structure Of HIV Protein Shell Revealed  (Read 7012 times)

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Offline Inchlingblue

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Structure Of HIV Protein Shell Revealed
« on: June 15, 2009, 12:33:09 PM »
New research by scientists at The Scripps Research Institute and other institutions provides a close-up look at the cone-shaped shell that is the hallmark of human immunodeficiency virus (HIV), revealing how it is held together-and possible ways to break it apart.

Previously, scientists had known that the genetic material within HIV is enclosed within a shell called the capsid, which is formed by a honeycomb arrangement of about 250 hexagonal protein building blocks. For HIV to infect human cells, the virus binds to cell surface receptors, and then the capsid is delivered into the cytoplasm of the cell.

Now, in an advance, online issue of the journal Cell published on June 11, 2009, Professor Mark Yeager and colleagues at The Scripps Research Institute, the University of Virginia, and the University of Utah describe the first high-resolution molecular structure of the hexagonal protein building block, called CA, that makes up the HIV capsid. This detailed description may help scientists identify new ways to block HIV infection.

Bringing Down the Capsid

Since HIV/AIDS was first recognized in 1981, several drugs and drug combinations have allowed infected individuals to live longer and healthier lives. However, resistance to the existing drugs has created an urgent need for novel therapeutic strategies.

Current drugs target critical steps in the virus life cycle. For example, protease inhibitors block the protein cleavages that generate viral components-one of them being the protein CA.

Other possible ways to block infection would be to prevent formation of the capsid by blocking assembly of CA molecules or to find a way to disassemble the capsid once it is made.

"Anything that destabilises the capsid, either by inhibiting assembly or accelerating disassembly should attenuate or even kill the virus," says Owen Pornillos, an investigator in Yeager's lab and first author of the Cell paper.

But to destabilise the capsid, it's necessary to know precisely how it is held together.

Making Crystals

"No one had been able to visualise the CA hexamer at atomic resolution," says Yeager. "Other groups had been able to solve structures of individual regions of CA. But it was not clear from these structures exactly how the CA proteins fit together."

To make the capsid, sets of six CA protein molecules first form hexamers, which then associate with one another to build a honeycomb-like shell comprised of about 250 hexamers. The ends of the shell are closed by insertion of seven and five CA protein pentamers, yielding the characteristic cone-like appearance of the capsid.

In 2007, Yeager's group managed to view the CA hexamers by a type of electron microscopy in which the samples are quick frozen in buffers, which preserves the inherent structure of proteins. That study provided the first glimpse of how CA proteins are arranged in the capsid. (The first author of the 2007 article was Barbie Ganser-Pornillos, Owen Pornillos' wife, who was also involved in the current study.)

In order to view the CA hexamer at even higher resolution, Yeager's group turned to X-ray crystallography. This technique requires growing 3D crystals of a molecule and then scattering a beam of X-rays off the crystals, which are recorded on a detector. Computational methods are then used to interpret the scattering patterns to calculate the position of every atom in the crystallised molecule.

But growing large, 3D crystals of the CA hexamer was no easy feat. The two ends of each CA protein molecule are held together by a "floppy" bridge, which precluded formation of orderly arrays of CA hexamers to form 3D crystals.

To overcome the problem, Pornillos and Yeager turned to molecular biology. They engineered CA proteins that would form sturdy chemical links between them, relying on the 2007 structure as their roadmap to determine exactly where to place the links.

"Our work takes advantage of so-called hybrid methods-molecular biology, biochemistry, electron microscopy, and X-ray crystallography," says Yeager. "These methods are synergistic. The EM results guided the molecular biology to engineer stable CA hexamers that were then amenable to 3D crystallisation and X-ray structure analysis at atomic resolution."

The structure they obtained provided a view of the CA hexamer at an unprecedented resolution of two-Ångstrom (one Ångstrom equals one ten-billionth of a meter).

A Close-Up Look

All proteins are composed of linear chains of amino acids-with one end called the N-terminus and the opposite end the C-terminus-that are folded in three-dimensional shapes. In the CA protein, amino acid chains are twisted into several rods, called a-helices, with extensions-called side chains-that protrude from the main chain to interact with other folded regions of the protein.

The two-Ångstrom structure showed the positioning of these a-helices and, for the first time, the location of the atoms in the side chains. "We could precisely delineate all the chemical interactions that stabilise the hexamer," says Yeager.

The centre of the CA hexamer is formed by 6 N-terminal ends of the CA protein subunits. The C-terminal domains form a "floppy" belt around this central core, connecting adjacent hexamers. The fact that the belt is not held rigidly in place, helps explain how the honeycomb shape of the capsid forms. "The curvature of the capsid is not constant," says Pornillos. "Now we can see in atomic detail how flexibility in CA makes this happen."

The group discovered another set of interactions critical to stabilising the capsid-connections between the N-terminal and C-terminal ends of adjacent CA protein molecules in one hexamer. "Think of the fingers of one hand as the N-terminal domain and the palm as the C-terminal," says Yeager. "Imagine the fingers of one hand being cradled in the palm of the other, and so on as if you had six hands in a ring."

Knowing precisely how and where CA proteins interact gives researchers clues on how to interfere with these connections. One approach is to design small molecules that can insert themselves at strategic positions, impeding capsid assembly or making the capsid less stable.

While finding HIV therapies is a main driver for Yeager's work, he points out that it also provides fundamental insights into biology. "Determining the assembly of a relatively simple structure like the capsid of a virus can help us understand how more complex biological structures inside the cell are organised," he explains.

LINKS (with a picture of HIVs outer shell!):

http://www.scientistlive.com/European-Science-News/Biotechnology/Biotechnology_advance_reveals_HIV_protein_shell_structure/22617/

http://www.sciencedaily.com/releases/2009/06/090612163537.htm
« Last Edit: June 16, 2009, 07:52:53 PM by Inchlingblue »

Offline J220

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Re: Structure Of HIV Protein Shell Revealed
« Reply #1 on: June 15, 2009, 04:53:35 PM »
Wow, this is straight out of star trek...lol let's hope this leads to something good! Thanks for posting.
"Hope is my philosophy
Just needs days in which to be
Love of Life means hope for me
Born on a New Day" - John David

Offline freewillie99

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Re: Structure Of HIV Protein Shell Revealed
« Reply #2 on: June 16, 2009, 10:20:05 AM »
Wow, this is straight out of star trek...

HIV...the final frontier...
Beware Romanians bearing strange gifts

Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #3 on: July 25, 2009, 06:11:35 PM »
There are drugs (compounds) in the pipeline that are classified as "capsid assembly inhibitors," (CAI). This new research revealing the structure of the capsid should help identify more of them.

Here is more info about capsid assembly inhibitors. I found number 3 especially interesting, it basically implies that an effective CAI would mean that having HIV would be a much less burdensome undertaking than it is now, i.e. taking one medication, a CAI, with no concerns about resistance; disabling the virus's capsid weakens the virus and essentially removes its ability to cause damage:

This novel class of antivirals is particularly promising for three reasons:
 
1. The targets are protein-protein contacts between the virus structural proteins, which are crucial for correct assembly of the virus into infectious virions.
2. The protein domain that is targeted is often highly conserved among different viruses within the same family which enables broad range treatment.
3. The molecule inhibits essential interactions between virus structural proteins that are critical for the overall integrity and survival of the virus particle. Hence, even if CAI-induced mutations could occur, such mutations would lead to non-infectious virus particles.


LINK:

http://www.natap.org/2009/newsUpdates/010709_02.htm

In a related note, there have been recent advances in fighting hepatitis C, also by homing in on its capsid:

"In one sense, the ongoing issue with hepatitis C is that there are still so very few drugs to treat the virus and very few tools to study it," Strosberg said. "We set out to develop new tools and to identify a new target - core, the capsid protein. By targeting the interactions of core with itself or other proteins, we could reduce the problem of rapid mutation not only because the core protein mutates significantly less, but also because mutations that would affect the interface between core and itself or other proteins would often be more likely to deactivate the virus, in contrast to mutations in viral enzymes which often lead to increased resistance to drugs."

LINK:

http://www.scientistlive.com/European-Science-News/Biotechnology/Key_molecules_inhibit_viral_production/21870/hcv+capsid
« Last Edit: July 27, 2009, 02:28:50 AM by Inchlingblue »

Offline veritas

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Re: Structure Of HIV Protein Shell Revealed
« Reply #4 on: July 26, 2009, 05:05:12 AM »


Inch,

Here's the abstract from Pub Med:

http://www.ncbi.nlm.nih.gov/sites/entrez/19523676

Interesting stuff ==== lipids play a major part (anti-ps anyone---lol)

v

Offline riptide

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Re: Structure Of HIV Protein Shell Revealed
« Reply #5 on: July 26, 2009, 09:08:10 AM »
Inch,

You mentioned that there are drugs already in the pipeline....do you know of any information on those drugs and how they are working out? This really sounds like it could be a great treatment option only having to take possibly one pill with no resistance.

Offline veritas

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Re: Structure Of HIV Protein Shell Revealed
« Reply #6 on: July 26, 2009, 09:33:11 AM »

Everything you wanted to know about capsid assembly inhibitors ----- almost:

http://www.medsci.org/v05p0230.htm

This stuff is amazing !!

v

Offline veritas

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Re: Structure Of HIV Protein Shell Revealed
« Reply #7 on: July 26, 2009, 09:50:37 AM »
http://

Here is one patent with respect to small molecule inhibitors:

http://www.medsci.org/v05p0230.htm

From the patent:

"According to the invention, there is provided a method for treating HIV infection comprising administering a small molecule inhibitor in combination with a therapeutically effective agent selected from the group consisting of chemotherapeutic agents, anti-retroviral inhibitors, cytokines, hydroxyurea, monoclonal antibodies that bind to the GAG proteins"

v

Offline riptide

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Re: Structure Of HIV Protein Shell Revealed
« Reply #8 on: July 26, 2009, 11:15:50 AM »
Please anyone,  break this down into simple english for a simple mind like myself..  From what I gather they have no way to deliver the meds to the capsid??  Its always something! Well I'm sure they'll figure it out in  another 10-20 years.


Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #9 on: July 26, 2009, 02:59:21 PM »
riptide: I disagree it'll take that long, although it certainly is not around the corner. The drugs (compounds at this point) that are in the development pipeline are from Vironova Pharmaceuticals. Achillion is also working on CAIs. These CAIs were being developed before the recent research revealed high-resolution images of the HIV capsid. This new research is likely to speed up development of CAIs, as the link to the abstract supplied by veritas, above, says, "The structures. . .  clarify the molecular basis for capsid assembly inhibition and should facilitate structure-based drug design strategies."  

As the lead article on this post states, "to destabilise the capsid, it's necessary to know precisely how it is held together." This new high-res imaging allows scientists to see just that.  


Vironova describes their CAI:

Vironova has been granted exclusive worldwide rights to two patent families owned by the University of Maryland Baltimore County (UMBC).  The patents cover inventions related to substances and targets for capsid assembly inhibitors (CAI) against the HIV-1 and are based on discoveries made by Professor Michael F. Summers at UMBC and the Howard Hughes Medical Institute. Professor Summers is a world authority in HIV research and will stay in close cooperation with Vironova as the projects progress towards clinical development. The project is in the lead optimization phase where the compound shows excellent efficacy in inhibiting HIV infection in cell culture, is well tolerated and with a known mechanism of action.

LINK:

http://www.vironova.com/webpage.aspx?id=150

LINK:

http://files.shareholder.com/downloads/ACHN/0x0x43521/0a829db3-0079-4d8d-8546-275c70e56457/ACHN_News_2005_5_2_General.pdf


[attachment deleted by admin]
« Last Edit: July 27, 2009, 02:31:50 AM by Inchlingblue »

Offline georgep77

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Re: Structure Of HIV Protein Shell Revealed
« Reply #10 on: July 27, 2009, 04:33:58 PM »
Wow CAIs sounds awesome !!! the thingy about not resistance is just amazing     :o

           Thanks Inchlingblue for the info & links.

                                                                 
Come on Sangamo,  Geovax,  Bionor immuno, ...Make us happy !!!
+ 2008

Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #11 on: July 27, 2009, 05:33:43 PM »
I hope that the new findings showing precisely how the capsid (CA) proteins interact speed up development of CAIs.

Here is another recent article that references Medscape and BMC Retrovirology, I love it that CAIs would render HIV "deformed and noninfectious":

Capsid assembly inhibitors a possible new class of anti-HIV agents

4/21/2009

A metabolite of glycineamide causes infectious HIV-1 particles to become deformed and noninfectious, Swedish researchers report in the BMC journal Retrovirology, which is available online.

"Formation of an HIV-1 particle with a conical core structure (i.e. capsid) is a prerequisite for the subsequent infectivity of the virus particle," Dr. Anders Vahlne of the Karolinska Institute in Stockholm, Sweden, and colleagues explain. Their previous work demonstrated that addition of glycineamide to HIV-1-infected cells induced the production of non-infectious HIV-1 particles with deformed cores.

In the current study, Professor Vahlne's team reports, "We demonstrate that it is not glycineamide itself but a metabolite thereof that displays antiviral activity." They identified the metabolite as alpha hydroxyglycineamide (alpha-HGA).

The investigators were able to chemically synthesize alpha-HGA, which inhibited HIV-1 replication to the same degree as glycineamide.

"Alpha-HGA has an unusually simple structure and a novel mechanism of antiviral action," the researchers say. "Thus, alpha-HGA could be a lead for new antiviral substances belonging to a new class of anti-HIV drugs, i.e. capsid assembly inhibitors."

BMC Retrovirology 2009;6.

Medscape Today


LINKS:

http://www.eatg.org/eatg/Global-HIV-News/Basic-Science/Capsid-assembly-inhibitors-a-possible-new-class-of-anti-HIV-agents

Isolation and characterization of a small antiretroviral molecule affecting HIV-1 capsid morphology

http://www.retrovirology.com/content/6/1/34
« Last Edit: July 27, 2009, 06:56:37 PM by Inchlingblue »

Offline MYSTERY

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Re: Structure Of HIV Protein Shell Revealed
« Reply #12 on: July 27, 2009, 05:51:20 PM »
Its fun to hear all of the exciting science that is taking place, but unfortunately we will probably be dead and gone before any of this stuff comes around to benefit us. However, it will help the generation in 50 years or so. Hopefully.
Atheist don't believe in GOD, but GOD believes in them and loves them. Never let the failure of man conflict with your love of GOD.

Offline xman

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Re: Structure Of HIV Protein Shell Revealed
« Reply #13 on: July 27, 2009, 06:14:07 PM »
Its fun to hear all of the exciting science that is taking place, but unfortunately we will probably be dead and gone before any of this stuff comes around to benefit us. However, it will help the generation in 50 years or so. Hopefully.

I absolutely agree. With all the respect, I can't understand the over excitement about those findings which are many in the HIV research field but that are of no impact on the actual situation of the epidemic. Let's excite about those drugs that are close to approval and not for something ready in a decade or more.

I guess clinical trials on humans aren't even on the distant horizon since no drug or compound is ready to test.
« Last Edit: July 27, 2009, 06:16:12 PM by xman »
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline georgep77

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Re: Structure Of HIV Protein Shell Revealed
« Reply #14 on: July 27, 2009, 06:33:20 PM »
we will probably be dead and gone before any of this stuff comes around to benefit us.
Hell not...Im going to fight !!! and nobody is going to take away my hope...even xman  lol

                                                  :D
Come on Sangamo,  Geovax,  Bionor immuno, ...Make us happy !!!
+ 2008

Offline xman

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Re: Structure Of HIV Protein Shell Revealed
« Reply #15 on: July 27, 2009, 06:44:21 PM »
Hell not...Im going to fight !!! and nobody is going to take away my hope...even xman  lol

                                                  :D

I'm not telling you to not have hope. But it's better to have hope for something likely to benefit you in the short term.
« Last Edit: July 27, 2009, 06:46:33 PM by xman »
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline MYSTERY

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Re: Structure Of HIV Protein Shell Revealed
« Reply #16 on: July 27, 2009, 07:20:39 PM »
I think we all have hope. HAART has saved my life. I would be pushing up some serious Daisey's right now with out it.  ;D...Its just that most of this new treatment that we are looking at are years away and I can't get to excited about it for the near future. But, I find that every little step does help and is needed to improve our situation. But lets face it most of the treatment is not going to get that drastically better in our lifetime. I am 44 years old. HAART is probably going to be as good as it gets for me. I may see some improvements and some new options, but for the most part I will be taking pills till the day I die.

I am with ya georgep77, I am going to fight till the bitter end. I will also reiterate that I am blessed to be healthy and am living a productive life due to the medical advances they have made in the treatment of HIV. GOD willing I intend to live a full life.
« Last Edit: July 27, 2009, 07:26:15 PM by MYSTERY »
Atheist don't believe in GOD, but GOD believes in them and loves them. Never let the failure of man conflict with your love of GOD.

Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #17 on: July 27, 2009, 07:27:09 PM »
It is very difficult to find molecules/compounds that work for fighting any disease, and it is even more difficult, not to mention expensive, to turn those compounds into safe and effective drugs.

Of course the drugs discussed in this thread are years away, in my humble opinion not that many years. What makes the prospect of developing safe and effective CAIs a real and achievable possibility, maybe even in the near future, is the research described in the first post of the thread.

The fact that scientists now have a high resolution, close-up, detailed look of HIV's capsid is a BIG deal. It allows them to see very precisely how it is held together, which is what will make it easier to find molecules that can prevent it from assembling in the first place.

I'm skeptical about the statement in the NATAP link that CAI mutations would render the virus noninfectious. The source is a reliable and reputable one and I've seen it mentioned elsewhere, such as in the lead article of the thread ("Anything that destabilises the capsid, either by inhibiting assembly or accelerating disassembly should attenuate or even kill the virus,") so I'm hoping it's true and accurate.  

 
« Last Edit: July 29, 2009, 03:57:42 PM by Inchlingblue »

Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #18 on: November 13, 2009, 11:29:33 AM »
More research on the HIV capsid that will hopefully lead to compounds that interfere with its assembly and function.

Shape Of Things To Come: Structure Of HIV Coat Could Lead To New Drugs

ScienceDaily (Nov. 13, 2009) — Structural biologists at the University of Pittsburgh School of Medicine have described the architecture of the complex of protein units that make up the coat surrounding the HIV genome and identified in it a "seam" of functional importance that previously went unrecognized. Those findings, reported today in Cell, could point the way to new treatments for blocking HIV infection.
 
The researchers used a combination of nuclear magnetic resonance and cryoEM, which are standard structural biology tools, to see both the overall shape and the atomic details of capsid protein (CA) assembly. It takes about 1,500 copies of CA to make the coat, or capsid, that surrounds the genome of the AIDS virus.
 
"This strategy allowed us to see both the forest and the trees," explained study co-author Peijung Zhang, Ph.D., assistant professor in the Department of Structural Biology, Pitt School of Medicine. "Knowing what the CA protein looks like and how the capsid is built will allow scientists to rationally design therapeutic compounds that interfere with assembly of the protein and affect its function."

Capsid proteins, and particularly the interfaces or seams where one connects to another, are very important for assembling and disassembling the HIV coat, said senior author Angela Gronenborn, Ph.D., chair, Department of Structural Biology, and director, University of Pittsburgh Center for HIV Protein Interactions. The study indicates that these seams provide the flexibility to dismantle the coat efficiently after viral entry into the host and to put it back together when new viruses emerge from the cell.
 

"Our lab experiments show that if we replace a few of the pivotal stitches in the seam by mutation, the resulting viruses are less infectious or even non-infectious," Dr. Gronenborn said. "The capsid, and therefore the virus, can no longer function properly."


LINK:

http://www.sciencedaily.com/releases/2009/11/091112121559.htm
 
« Last Edit: November 13, 2009, 11:40:21 AM by Inchlingblue »

Offline xman

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Re: Structure Of HIV Protein Shell Revealed
« Reply #19 on: November 13, 2009, 02:36:35 PM »
But how could this approach cure us or even eradicate the virus from our bodies?
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #20 on: November 13, 2009, 02:45:31 PM »
But how could this approach cure us or even eradicate the virus from our bodies?

If a way is found to disrupt the HIV capsid, it could make the virus non-infectious. All of this research into the capsid brings us closer to being able to disrupt it.

Since the capsid is a "highly structured" region, it would be difficult for HIV to become resistant to a compound that disrupted the capsid.

Offline sensual1973

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Re: Structure Of HIV Protein Shell Revealed
« Reply #21 on: November 13, 2009, 02:54:28 PM »
selling dreams again
God grant me the serenity to accept the things i can not change.

Offline georgep77

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Re: Structure Of HIV Protein Shell Revealed
« Reply #22 on: November 13, 2009, 05:40:42 PM »
selling dreams again
The Big Pharma is going to buy this research and bury it in the north pole !
They need to sell HAART for another 25 years    8)
Come on Sangamo,  Geovax,  Bionor immuno, ...Make us happy !!!
+ 2008

Offline GNYC09

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Re: Structure Of HIV Protein Shell Revealed
« Reply #23 on: November 14, 2009, 10:00:15 AM »
selling dreams again

selling despair again

Offline Inchlingblue

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Re: Structure Of HIV Protein Shell Revealed
« Reply #24 on: January 19, 2011, 08:45:23 PM »
More progress in mapping HIV's capsid:

Scientists Map Key Structure HIV Uses to Infect Cells

Details on gene-delivering 'capsid' could point the way to new drugs

WEDNESDAY, Jan. 19 (HealthDay News) -- U.S. scientists say they've finished the first detailed description of the complete protein package within the human immunodeficiency virus (HIV) thought to be essential to its ability to infect human cells.


HIV uses this protein package, a cone-shaped container called a "capsid," to transport its genetic material into the host cell, after binding with receptors on the cell's surface.

After gaining entry, the capsid releases its genetic cargo into the cell, helping HIV to hijack the cell's machinery to replicate its own genes and proteins, according to a news release from The Scripps Research Institute in La Jolla, Calif.

As new viruses form, the genetic material is incorporated into round, immature capsids that HIV uses to flee from the cell. Each round capsid then reconfigures itself into its characteristic cone shape so it can help the virus move on and infect other cells in a similar fashion.

However, if any part of this capsid rearrangement were to be blocked, it would render HIV no longer infectious, the scientists said. And that could point the way to new drugs aimed at fighting HIV/AIDS.

Much more work will need to be done before that kind of research can begin, stressed senior study author Dr. Mark Yeager, a Scripps Research professor and staff cardiologist and chair of the Molecular Physiology and Biological Physics Department at The University of Virginia School of Medicine.

"We don't have the full story yet, but we have volume one," Yeager said in the Scripps news release.

The findings appear in the Jan. 19 issue of the journal Nature.

Yeager's team noted that the capsid structure of HIV differs greatly from that of many other viruses. For example, the capsid of the poliovirus has a rigid, symmetrical structure, while the HIV capsid is more flexible and can take on slightly varied shapes. Yeager, along with Owen Pornillos and Barbie Ganser-Pornillos, a husband-and-wife team working in his lab, spent years figuring out the precise atomic structure behind capsid formation.

They now plan to use computer programs to hunt for weak spots in the capsid's structure that might offer promising targets for drug development.



LINK:

http://health.usnews.com/health-news/family-health/sexual-and-reproductive-health/articles/2011/01/19/scientists-map-key-structure-hiv-uses-to-infect-cells


KILL that capsid!

Offline lmdo

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Re: Structure Of HIV Protein Shell Revealed
« Reply #25 on: January 20, 2011, 01:26:56 AM »
Thanks for the little tease Inch!
Inch by inch ,getting closer....
Promising stuff

 


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