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  • richardmitnick 3:55 pm on July 13, 2017 Permalink | Reply
    Tags: A new three-dimensional snapshot of HIV, , Env trimer, , HIV’s Env is a protein complex made up of three identical mushroom-shaped structures that each contain a stalk-like subunit gp41 and a cap-like region called gp120, , Scripps Institute   

    From Scripps: “TSRI Scientists Capture First High Resolution Image of Key HIV Protein Transitional State” 

    Scripps
    Scripps Research Institute

    July 12, 2017

    A new, three-dimensional snapshot of HIV demonstrates the radical structural transformations that enable the virus to recognize and infect host cells, according to a new study led by scientists at The Scripps Research Institute (TSRI).

    The atomic-scale close-up image reveals an intricate dance between different parts of a key HIV protein complex, known as the envelope (Env) trimer, that takes place just moments before the virus would normally fuse itself to an immune cell’s plasma membrane.

    1
    CD4 and b12 both trap Env in an open, pre-fusion conformation but only CD4 exposes the co-receptor binding site required for entry.

    “One could consider this a ‘missing link’ between HIV’s previously known prefusion and the post-fusion states,” said Andrew Ward, an associate professor at TSRI who led the study.

    The image also gives scientists their clearest glimpse yet at the plastic nature of Env, which constantly shifts between different configurations before latching on to human cells.

    “Several other studies have shown evidence of trimer ‘breathing,’ and here we are able to capture two different conformational states of Env at high resolution,” said study co-first author Gabriel Ozorowski, a senior research associate at TSRI.

    Findings from the study, published online on July 12 in the journal Nature, could provide new potential targets for HIV vaccine designs.

    “By understanding the molecular details of this fusion intermediate state, we can infer how the trimer transitions between states and engineer mutations or molecules to block those transitions,” Ward said.

    An Elusive Target

    HIV, the human immunodeficiency virus, currently infects about 37 million people worldwide. The development of a vaccine that can prevent—as opposed to just manage—HIV infections has been largely stymied by the complex and elusive structure of Env.

    HIV’s Env is a protein complex made up of three identical, mushroom-shaped structures that each contain a stalk-like subunit, gp41, and a cap-like region called gp120. The structures are only loosely connected to one another, enabling the trimer to change shape and making it notoriously difficult to study and target with drugs. In addition, the trimer also frequently mutates its outermost “variable loop” regions to evade immune attack, and its surfaces are coated with complex sugar molecules (called glycans) that obscure potential drug-binding sites.

    But by capturing Env in a configuration that exposes previously unknown patches on the trimer’s surfaces, the snapshot presents interesting new prospects for drug developers.

    “If we can target the newly found pockets with small molecules, then there is the potential to create new fusion inhibitor drugs,” Ward said.

    Help from a Substitute

    The team’s ultra-detailed image of Env is actually a composite picture digitally stitched together from thousands of images taken with a cryo-electron microscope.

    For HIV infection to occur, Env must first bind with two proteins on an immune T cell’s outer surface, a membrane receptor known as CD4, and then to a coreceptor, either CXCR4 or CCR5. For the new study, the scientists created a protein that included a modified form of Env—genetically engineered for stability—that is bound to CD4 and 17b, a human antibody that resembles CXCR4/CCR5 and is used as a stand-in for the coreceptors. The trimer complexes are then embedded into a thin layer of ice and placed under the microscope for imaging.

    “The electron beam is scattered by the protein atoms, leading to detailed two-dimensional images,” said study co-first author Jesper Pallesen, also a senior research associate at TSRI. “We take about 2,000 images, each one containing thousands of complexes frozen in random orientations, and we computationally align them to create a high-resolution, three-dimensional snapshot.”

    A New State

    The new snapshot of Env in its “fusion intermediate” state reveals that upon binding to CD4, the V1 and V2 variable loops of gp120 flip away from the center of the trimer, exposing the coreceptor binding site. CD4 binding also triggers parts of the gp41 “stalk” to rearrange themselves to create a small pocket of space inside the trimer. This pocket acts to stabilize the fusion peptide—an amino acid sequence that anchors itself in the host cell—as it moves from the base of the trimer toward the interior in preparation for membrane fusion.

    Due to its critical role in infection, the fusion peptide region of HIV is particularly resistant to mutation and thus a sought-after drug target. “If you can target this particular stretch of amino acids, then the virus has a hard time escaping,” Pallesen said.

    However, actually hitting this target has proven difficult because the fusion peptide rarely stays still. “Prior to CD4 binding, the fusion peptide is floating and flopping around outside of the trimer,” Ozorowski said. “What we see for the first time in our structure is that when Env binds CD4, the fusion peptide moves closer to the trimer’s interior and adopts a more stable state as it prepares to anchor into the host cell’s membrane.”

    Breathing

    The team also conducted a second antibody-substitute experiment to obtain the clearest picture yet of Env’s shapeshifting abilities. “Because Env is a metastable fusion machine, it has been long understood that it must be a malleable structure,” Ward said.

    Swapping out CD4 for a similarly shaped antibody, b12, the team was able to show that in addition to a “closed” state, in which the CD4 binding site is hidden, and an “open” state that is ready for CD4 binding, Env also contorts into a partially open configuration that accommodates b12 but not CD4.

    “For infection to happen, the trimer must transition from a closed state to an open state that brings the fusion peptide in close proximity to the host cell,” Ozorowski said. “Sampling various states could make it easier for Env to switch from one to the next. We show that despite these different conformations, each one still exhibits some degree of stability.”

    This stable meta-state is yet another path that drug makers can explore. “We can now probe this new conformation to discover new druggable pockets on the surface of Env,” Pallesen said. “So, it opens up yet another arsenal of weapons in the fight against infection.”

    The article, Open and Closed Structures Reveal Allostery and Pliability in the HIV-1 Envelope Spike, also included study co-authors Natalia de Val, Christopher Cottrell, Jonathan Torres, Jeffrey Copps, Robyn Stanfield and Ian Wilson of TSRI; Dmitry Lyumkis of the Salk Institute for Biological Studies; and Albert Cupo, Pavel Pugach and John Moore of the Weill Medical College of Cornell University.

    This work was supported by funds from the Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (grant UM1AI100663) and the National Institutes of Health (grants P01 AI110657 and P50 GM103368).

    See the full article here .

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 1:19 pm on July 7, 2017 Permalink | Reply
    Tags: , , Scripps Institute, The Olson Laboratory,   

    From FAAH at WCG: “FightAIDS@Home Targeting a Key HIV Protein” 

    FAAH
    FightAIDS@home

    By: The FightAIDS@Home research team
    15 Jun 2017

    Summary
    FightAIDS@Home researchers restarted the first phase of the project at the end of 2016, and in just a few months, they have completed approximately 46 percent of their projected work on World Community Grid. Read about their progress on finding compounds that could stop HIV from replicating.

    Background

    FightAIDS@Home is searching for possible compounds to target the protein shell of HIV (called a capsid), which protects the virus. Currently, there are no approved drugs that target this protein shell.

    The virtual docking techniques used in Phase 1 are an approximation of the potential effectiveness of promising compounds. Phase 2 of FightAIDS@Home uses a different simulation method to double-check and further refine the virtual screening results that are generated in Phase 1.

    The research team is examining a library of approximately 1.6 million commercially available compounds to find promising treatment prospects. The team estimates that they will need to carry out roughly 621 million docking computations on World Community Grid to thoroughly test each potential compound. With the help of many volunteers who are supporting this project, they’ve already completed 46 percent of their goal.

    You can keep up with the research team’s progress on their website, which includes frequent updates on their experiments and progress.

    Please read below for a detailed look at the technical aspects of their recent work.

    Insilico search for novel drugs targeting the HIV-1 mature capsid protein

    The importance of the capsid protein

    The capsid protein (CA) plays crucial roles in the HIV replication cycle1. After viral and host cell membrane fusion, the capsid core is released into the cytoplasm. This core, which corresponds to the assembly of ~1200 capsid proteins, contains and protects viral RNA and proteins from degradation. Reverse transcription occurs in the core in a process which is tightly connected to the capsid core disassembly. This leads to the import of the cDNA viral genome into the host cell’s nucleus, where it is integrated into the host DNA to finalize the infection.

    To date, no drugs targeting CA are approved for clinical use. With the goal of identifying novel active molecules which destabilize the capsid core, we set up a high throughput virtual screening (VS) campaign in collaboration with World Community Grid as part of the FightAIDS@Home (FA@H) project.

    1
    Figure 1: PDB 4xfx, the hexamer structure of the native HIV-1 mature capsid protein. (Credit: Pierrick Craveur)

    Targeted structures

    The main target of the docking calculations was the recently solved structure of the CA hexameric assembly2. Four pockets of interest were selected at the surface of the hexamer in order to perform focused dockings, mainly at the CA-CA dimer interfaces. Structural variability surrounding these pockets was analyzed by comparing this X-ray structure from the PDB (4xfx, see Figure 1), and the two full capsid core models assembled by Schulten’s lab3 (3j3q and 3j3y, see Figure 2). Based on that, 36 different conformations were selected as targets for the VS, including the X-ray structure and structures from the models. Each target was set as full rigid and also with a specific combination of residue side chains defined as flexible.

    2
    Figure 2: The 2 models of the capsid core assembly. (Credit: Pierrick Craveur)

    An extended library of ~1.6 million commercially available compounds was used for the screening. Replicate computations were performed for each docking experiment in order to assess the consistency of the results. In total ~621 million docking computations will be performed on World Community Grid. For the time being, ~46% of the computation is completed, with an ending date estimated at the end of 2017 if the computation does not increase in speed. However, in one month we will be able to propose to our collaborators from the HIVE Center a selection of compounds (focusing one of the four pockets) for experimental binding and infectivity assays.

    Other information

    Dedicated web pages (see http://fightaidsathome.scripps.edu/Capsid/index.html) were developed to inform the public and the World Community Grid volunteers as the project advances. The pages contain an overview of the project, details on targets and the selection process, a description of the compound library, an hourly updated status of the computations, and a “people” section where volunteers can appear in the page to be fully part of the project.

    An automatic pipeline has been developed in order to constantly post-process the docking results received from World Community Grid. These post computations involve the High Performance Computing (HPC) cluster from The Scripps Research Institute, and are mainly related to the identification of the interactions between drug candidates and the CA protein. The pipeline ends in filling a MySQL database, which will be made public as soon as it will be stable. In details, 3.3TB of compressed data are estimated to be received from World Community Grid, and 1TB to be generated after post-processing.

    Our team from The Scripps Research Institute of San Diego, which includes Dr. Pierrick Craveur, Dr. Stefano Forli, and Prof. Arthur Olson, really appreciates the essential support this project receives from World Community Grid volunteers around the globe.

    References [Sorry, no links]

    Campbell, E. M. & Hope, T. J. HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nat Rev Microbiol 13, 471-483, doi:10.1038/nrmicro3503 (2015).
    PDB 4xfx : Gres AT, Kirby KA, KewalRamani VN, Tanner JJ, Pornillos O, Sarafianos SG. X-Ray Structures of Native HIV-1 Capsid Protein Reveal Conformational Variability. Science (New York, NY). 2015;349(6243):99-103.
    PDB 3j3q & 3j3y : Zhao G, Perilla JR, Yufenyuy EL, et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 2013;497(7451):643-646.

    See the full article here.

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    FightAIDS@Home is a project run by the Olson Laboratory that uses distributed computing to contribute your computer’s idle resources to accelerate research into new drug therapies for HIV, the virus that causes AIDS. FightAIDS@Home made history in September 2000 when it became the first biomedical Internet-based grid computing project. FightAIDS@Home was started with Scott Kurowski, founder of Entropia. People all around the World continue to donate their home computer’s idle cycles to running our AutoDock software on HIV-1 protease inhibitor docking problems. With the generous assistance of IBM, we joined World Community Grid in late 2005, and launched FightAIDS@Home on World Community Grid on 21 November, 2005.

    How do I join the FightAIDS@Home Project?

    All you need to do is download and install the free client software. Once you have done this, your computer is then automatically put to work and you can continue using your computer as usual.

     
  • richardmitnick 5:26 am on June 17, 2017 Permalink | Reply
    Tags: , , , Scripps Institute,   

    From Scripps: “Scientists Jump Hurdle in HIV Vaccine Design” 

    Scripps
    Scripps Research Institute

    June 19, 2017 issue
    Madeline McCurry-Schmidt

    1
    The new study shows the structure of an important HIV protein, called the envelope glycoprotein, on a common strain of the virus. (Image courtesy Javier Guenaga.)

    Scientists at The Scripps Research Institute (TSRI) have made another important advance in HIV vaccine design. The development was possible thanks to previous studies at TSRI showing the structures of a protein on HIV’s surface, called the envelope glycoprotein. The scientists used these structures to design a mimic of the viral protein from a different HIV subtype, subtype C, which is responsible for the majority of infections worldwide.

    The new immunogen is now part of a growing library of TSRI-designed immunogens that could one day be combined in a vaccine to combat many strains of HIV.

    “All of this research is going toward finding combinations of immunogens to aid in protecting people against HIV infection,” said TSRI Professor Ian Wilson, Hanson Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at TSRI.

    The research, published recently in the journal Immunity, was led by Wilson and TSRI Professor of Immunology Richard Wyatt, who also serves as Director of Viral Immunology for the International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center at TSRI.

    The new study was published alongside a second study in Immunity, led by scientists at the Karolinska Institute in Stockholm, which showed that the vaccine candidate developed in the TSRI-led study can elicit neutralizing antibodies in non-human primates.

    “Together, the two studies reiterate how structure-based immunogen design can advance vaccine development,” said Wyatt.

    Solving the Clade C Structure

    HIV mutates rapidly, so there are countless strains of HIV circulating around the world. Of these strains, scientists tend to focus on the most common threats, called clades A, B and C.

    Like a flu vaccine, an effective HIV vaccine needs to protect against multiple strains, so researchers are designing a set of immunogens that can be given sequentially or as a cocktail to people so their immune systems can prepare for whatever strain they come up against.

    In 2013, TSRI scientists, led by Wilson and TSRI Associate Professor Andrew Ward, determined the structure of a clade A envelope glycoprotein, which recognizes host cells and contains the machinery that HIV uses to fuse with cells. Because this is the only antibody target on the surface of HIV, an effective HIV vaccine will have to trigger the body to produce antibodies to neutralize the virus by blocking these activities.

    Building on the previous original research, the scientists in the new study set out to solve the structure of the clade C glycoprotein and enable the immune system to fight clade C viruses.

    “Clade C is the most common subtype of HIV in sub-Saharan Africa and India,” explained study co-first author Javier Guenaga, an IAVI collaborator working at TSRI. “Clade C HIV strains are responsible for the majority of infections worldwide.”

    The scientists faced a big challenge: the clade C envelope glycoprotein is notoriously unstable, and the molecules are prone to falling apart.

    Guenaga needed the molecules to stay together as a trimer so his co-author Fernando Garces could get a clear image of the clade C glycoprotein’s trimeric structure. To solve this problem, Guenaga re-engineered the glycoprotein and strengthened the interactions between the molecules. “We reinforced the structure to get the soluble molecule to assemble as it is on the viral surface,” Guenaga said.

    The project took patience, but it paid off. “Despite all the engineering employed to produce a stable clade C protein, these crystals (of clade C protein) were grown in very challenging conditions at 4 degrees Celsius and it took the diffraction of multiple crystals to generate a complete dataset, as they showed high sensitivity to radiation damage,” said Garces. “Altogether, this highlights the tremendous effort made by the team in order to make available the molecular architecture of this very important immunogen.”

    With these efforts, the glycoprotein could then stay together in solution the same way it remains together on the virus itself. The researchers then captured a high-resolution image of the glycoprotein using a technique called x-ray crystallography.

    The researchers finally had a map of the clade C glycoprotein.

    Vaccine Candidate Shows Promise

    In a companion study, the scientists worked with a team at the Karolinska Institute to test an immunogen based on Guenaga’s findings. The immunogen was engineered to appear on the surface of a large molecule called a liposome—creating a sort of viral mimic, like a mugshot of the virus.

    This vaccine candidate indeed prompted the immune system to produce antibodies that neutralized the corresponding clade C HIV strain when tested in non-human primates.

    “That was great to see,” said Guenaga. “This study showed that the immunogens we made are not artificial molecules—these are actually relevant for protecting against HIV in the real world.”

    In addition to Wyatt, Wilson and Guenaga, the study, “Glycine substitution at helix-to-coil transitions facilitates the structural determination of a stabilized subtype C HIV envelope glycoprotein,” included co-first author Fernando Garces, Natalia de Val, Viktoriya Dubrovskaya and Brett Higgins of TSRI; Robyn L. Stanfield of TSRI and IAVI; Barbara Carrette of IAVI; and Andrew Ward of TSRI, IAVI and the Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery (CHAVI-ID) at TSRI.

    This work was supported by the IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD; grants OPP1084519 and OPP1115782), CHAVI-ID (grant UM1 AI00663) and the National Institutes of Health (grants P01 HIVRAD AI104722, R56 AI084817 and U54 GM094586).

    See the full article here .

    YOU CAN HELP IN THE FIGHT AGAINST HIV/AIDS FROM THE COMFORT OF YOUR EASY CHAIR.

    The Fight AIDS at home (FAAH@home) Phase II project is now running at World Community Grid (WCG) From Scripps Research Institute.


    Scripps

    FAAH Phase II

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the FAAH@home Phase II project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.


    My BOINC

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 8:52 pm on June 1, 2017 Permalink | Reply
    Tags: Assembled arenavirus glycoprotein, , Hemorrhagic fever viruses, , , Scripps Institute, , Tripod Shape Key to Future Vaccine Design, Up to 90 percent fatal in pregnant women,   

    From SLAC: “SLAC X-Ray Beam Helps Uncover Blueprint for Lassa Virus Vaccine” 


    SLAC Lab

    June 1, 2017

    1
    The molecular structure of a Lassa virus protein provides the blueprints for vaccine design. (Ollmann Saphire Lab/The Scripps Research Institute)

    2
    Erica Ollmann Saphire, professor of Immunology and Microbial Science at The Scripps Research Institute, during a visit of the Kenema Government Hospital, Sierra Leone, to study Lassa virus. (Kathryn Hastie/The Scripps Research Institute)

    3
    An antibody from a human survivor (turquoise) is shown inactivating a Lassa virus surface protein. (Ollmann Saphire Lab/The Scripps Research Institute)

    A decade-long search ends at the Stanford Synchrotron Radiation Lightsource, where researchers from The Scripps Research Institute emerge with a clear picture of how the deadly Lassa virus enters human cells.

    SLAC/SSRL

    Before Ebola virus ever struck West Africa, locals were continually on the lookout for another deadly pathogen: Lassa virus. With thousands dying from Lassa every year – and the potential for the virus to cause even larger outbreaks – researchers are committed to designing a vaccine to stop it.

    Now a team of scientists from The Scripps Research Institute (TSRI) has solved the structure of the viral machinery that Lassa virus uses to enter human cells.

    X-ray beams from the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory gave the team the final piece in a puzzle they sought to solve for over 10 years.

    Their study, published today in Science, is the first to show a key piece of the viral structure, called the surface glycoprotein, for any member of the deadly arenavirus family, and the new structure provides a blueprint to design a Lassa virus vaccine.

    “This was a tenacious effort – over a decade – to conquer a global threat,” said Erica Ollmann Saphire, a professor of Immunology and Microbial Science from TSRI and senior author of the new study.

    X-ray data for this study was collected at SLAC and the DOE’s Argonne National Laboratory.

    For the SLAC experiments, the researchers used a station at SSRL, a DOE Office of Science User Facility that has a strong program in biological X-ray crystallography. In this method, scientists prompt biological molecules to align and form a crystal, which they then study with powerful X-rays. The way the X-rays scatter off the crystal reveals the structure of the molecules inside – in 3-D and with atomic detail.

    “I am proud of SSRL’s strong partnership with TSRI and our involvement in this project that utilized the bright X-ray microbeams and high level of automation at Beam Line 12-2 to obtain the necessary data,” said SSRL senior staff scientist Aina Cohen. “This structure provides key information towards engineering an effective vaccine against Lassa, enabling the infected to combat the immunosuppressive traits of this virus, which is estimated to kill tens of thousands of people each year.”

    It Started with a Thesis

    The effort began with TSRI staff scientist Kathryn Hastie, the lead author of the study. In 2007, then a grad student in Ollmann Saphire’s lab, she told her thesis committee she wanted to solve the structure of the assembled arenavirus glycoprotein, something never done before. She hoped to create a map of the target on the virus where antibodies need to attack – a key step in developing a vaccine.

    Such maps can be obtained with X-ray crystallography, but the method depends on having a stable protein. Yet, all the Lassa virus glycoprotein wanted to do was fall apart.

    The problem was that glycoproteins are made up of smaller subunits. Other viruses have bonds that hold the subunits together, “like a staple,” Hastie said. Arenaviruses don’t have that staple; instead, the subunits just floated away from each other whenever Hastie tried to work with them.

    Another challenge was to recreate part of the viral lifecycle in the lab – a stage when Lassa’s glycoprotein gets clipped into two subunits. “We had to figure out how to get the subunits to be sufficiently clipped, which is necessary to make the biologically functional assembly, and also where to put an engineered staple to make sure they stayed together,” Hastie said.

    Partnering with West Africa

    As Hastie tackled those challenges from her lab bench in San Diego, staff at the Kenema Government Hospital in Sierra Leone labored on the front lines of the ongoing fight against Lassa.

    Until the 2014–15 Ebola virus outbreak, Kenema was the only hospital in the world to have a special ward dedicated to treating hemorrhagic fever viruses. Staff at the clinic – from the nurses to the ambulance drivers – are all Lassa survivors, which gives them immunity to the disease. The TSRI scientists have a long-term collaboration with Kenema as part of a research program run by Tulane University that provided them with antibodies from survivors of Lassa fever. These antibodies could inactivate the virus, and they provided lifesaving protection to animal models. These were the kinds of antibodies researchers are hoping to elicit with a future Lassa virus vaccine.

    In 2009, Hastie got to visit Kenema on a trip with Ollmann Saphire.

    “I had been working on the project for two years with very little success at that point,” Hastie said. “Going to West Africa showed me how important it was to keep going.”

    Like Ebola virus, Lassa fever starts with flu-like symptoms and can lead to debilitating vomiting, neurological problems and even hemorrhaging from the eyes, gums and nose. The disease is 50 to 70 percent fatal—and up to 90 percent fatal in pregnant women.

    “Studying Lassa is critically important. Hundreds of thousands of people are infected with the virus every year, and it is the viral hemorrhagic fever that most frequently comes to the United States and Europe,” said Ollmann Saphire. “Kate’s study needed to be done.”

    Tripod Shape Key to Future Vaccine Design

    By creating mutant versions of important parts of the molecule, Hastie engineered a version of the Lassa virus surface glycoprotein that didn’t fall apart. She then used this model glycoprotein as a sort of magnet to find antibodies in patient samples that could bind with the glycoprotein to neutralize the virus.

    With this latest study she solved the structure of the Lassa virus glycoprotein, bound to a neutralizing antibody from a human survivor.

    Her structure showed that the glycoprotein has two parts. She compared the shape to an ice cream cone and a scoop of ice cream. A subunit called GP2 forms the cone, and the GP1 subunit sits on top. They work together when they encounter a host cell. GP1 binds to a host cell receptor, and GP2 starts the fusion process to enter that cell.

    The new structure also showed a long structure hanging off the side of GP1—like a drip of melting ice cream running down the cone. This “drip” holds the two subunits together in their pre-fusion state.

    Zooming in even closer, Hastie discovered that three of the GP1-GP2 pairs come together like a tripod. This arrangement appears to be unique to Lassa virus. Other viruses, such as influenza and HIV, also have three-part proteins (called trimers) at this site, but their subunits come together to form a pole, not a tripod. The structure is also important because it can be used as a model to conquer related viruses throughout the Americas, Europe and Africa for which no equivalent structure yet exists.

    “It was great to see exactly how Lassa was different from other viruses,” said Hastie. “It was a tremendous relief to finally have the structure.”

    This tripod arrangement offers a path for vaccine design. The scientists found that 90 percent of the effective antibodies in Lassa patients targeted the spot where the three GP subunits came together. These antibodies locked the subunits together, preventing the virus from gearing up to enter a host cell.

    A future vaccine would likely have the greatest chance of success if it could trigger the body to produce antibodies to target the same site.

    Ollmann Saphire explained that Hastie accomplished something unique in structural biology. “The research started from scratch with the native, wild-type viruses in patients in a remote clinic—and went all the way to developing a basis for vaccine design. And the work was done almost entirely by one woman.”

    Moving Forward with a Lassa Vaccine

    The next step is to test a vaccine that will prompt the immune system to target Lassa’s glycoprotein.

    As director of the Viral Hemorrhagic Fever Immunotherapeutic Consortium, Ollmann Saphire is already coordinating with her partners at Tulane and Kenema to bring a vaccine to patients.

    The Coalition for Epidemic Preparedness Innovations, an international collaboration that includes the Wellcome Trust and the World Health Organization as partners, has recently named a vaccine for Lassa virus as one of its three top priorities. “The community is keenly interested in making a Lassa vaccine, and we think we have the best template to do that,” said Ollmann Saphire.

    She added that with Hastie’s techniques for solving arenavirus structures, researchers can now get a closer look at other hemorrhagic fever viruses, which cause death, neurological diseases and even birth defects around the world.

    Ollmann Saphire added that beamlines such as 12-2 at SSRL, which provided the X-ray beam used to finally determine the Lassa virus glycoprotein structure, along with its recent detector upgrades, are essential for ongoing advances in structural biology.

    “This research highlights the power of crystallographic techniques that rely on advanced synchrotron facilities to combat the most challenging biological problems. The support of the DOE’s Office of Science Biological and Environmental Research, the National Institutes of Health and private institutions such as TSRI enables us to make these resources available to the wider biomedical community,” Cohen said.

    In addition to Ollmann Saphire and Hastie, the following authors contributed: Michelle A. Zandonatti of TSRI; James E. Robinson and Robert F. Garry of Tulane University; Lara M. Kleinfelter and Kartik Chandran of the Albert Einstein College of Medicine; and Megan L. Heinrich, Megan M. Rowland and Luis M. Branco of Zalgen Labs.

    5
    The new study included (left to right) first author Kathryn M. Hastie, senior author Erica Ollmann Saphire and co-author Michelle A. Zandonatti of The Scripps Research Institute. (Photo by Madeline McCurry-Schmidt.)

    The study was supported by the National Institutes of Health and an Investigators in Pathogenesis of Infectious Diseases Award from the Burroughs Wellcome Fund. Research funding for the SSRL Structural Molecular Biology Program was provided by the DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here .

    See the Scripps press release here .

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    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
    i1

     
  • richardmitnick 1:54 pm on May 30, 2017 Permalink | Reply
    Tags: , , New antibiotic packs a punch against bacterial resistance, , Scripps Institute   

    From Scripps via phys.org: “New antibiotic packs a punch against bacterial resistance” 

    Scripps
    Scripps Research Institute

    phys.org

    May 29, 2017
    No writer credit found

    1
    A colorized scanning electron micrograph of MRSA. Credit: National Institute of Allergy and Infectious Diseases

    Scientists at The Scripps Research Institute (TSRI) have given new superpowers to a lifesaving antibiotic called vancomycin, an advance that could eliminate the threat of antibiotic-resistant infections for years to come. The researchers, led by Dale Boger, co-chair of TSRI’s Department of Chemistry, discovered a way to structurally modify vancomycin to make an already-powerful version of the antibiotic even more potent.

    “Doctors could use this modified form of vancomycin without fear of resistance emerging,” said Boger, whose team announced the finding today in the journal Proceedings of the National Academy of Sciences.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 2:49 pm on January 31, 2017 Permalink | Reply
    Tags: , Scripps Institute   

    From Scripps: “New Method Could Turbocharge Drug Discovery, Protein Research” 

    Scripps
    Scripps Research Institute

    January 30, 2017
    Mo writer credit

    A team led by scientists at The Scripps Research Institute (TSRI) has developed a versatile new method that should enhance the discovery of new drugs and the study of proteins.

    The new method enables researchers to quickly find small molecules that bind to hundreds of thousands of proteins in their native cellular environment. Such molecules, called ligands, can be developed into important tools for studying how proteins work in cells, which may lead to the development of new drugs. The method can be used even without prior knowledge of protein targets to discover ligand molecules that disrupt a biological process of interest—and to quickly identify the proteins to which they bind.

    “This ,” said co-lead author Christopher G. Parker, a research associate in the laboratory of TSRI Professor Benjamin F. Cravatt, chairman of the Department of Chemical Biology.

    This research was published ahead of print recently in the journal Cell.

    1
    Authors of the new study included (left to right) TSRI’s Andrea Galmozzi, Christopher Parker, Benjamin Cravatt and Enrique Saez. (Photo by Madeline McCurry-Schmidt.)

    Finding New Partners for Un-targetable Proteins

    About 25,000 proteins are encoded in the human genome, but public databases list known ligands for only about 10 percent of them. Biologists have long sought better tools for exploring this terra incognita.

    The new method involves the development of a set of small, but structurally varied, candidate ligand molecules known as “fragments.” Each candidate ligand is modified with a special chemical compound so that, when it binds with moderate affinity to a protein partner, it can be made to stick permanently to that partner by a brief exposure to UV light. A further modification provides a molecular handle by which scientists can grab and isolate these ligand-protein pairs for analysis.

    For an initial demonstration, the team assembled a small “library” of candidate ligands whose structural features include many that are found in existing drugs. By applying just 11 of them to human cells, the researchers identified more than 2,000 distinct proteins that had bound to one or more of the ligands.

    These ligand-bound proteins include many from categories—such as transcription factors—that previously had been considered “un-ligandable” and therefore un-targetable with drugs. In fact, only 17 percent of these proteins have known ligands, according to the widely used DrugBank database.

    The researchers used further methods to identify, for many ligand-protein interactions, the site on the protein where the coupling occurred.

    The candidate ligands initially used to screen for protein binding partners are generally too small to bind to their partners tightly enough to disrupt their functions in cells. But the team showed that, in multiple cases, that these initial small (“fragment”) ligands could be developed into larger, more complex molecules that display higher-affinity interactions and disrupt their protein partner’s functions.

    A New Type of Functional Screen

    For a final demonstration, collaborating chemists at Bristol-Myers Squibb helped create a library of several hundred slightly more complex candidate ligands. With TSRI colleagues Associate Professor Enrique Saez and co-first author Research Associate Andrea Galmozzi, the team then tested these ligands to find any that could promote the maturation of fat cells (adipocytes)—a process that in principle can alleviate the insulin resistance that leads to type 2 diabetes.

    Traditional functional screens of this type do not pinpoint the proteins or other molecules through which the effect on the cell occurs. But with this new discovery method, the researchers quickly found not only a ligand that strongly promotes adipocyte maturation but also its binding partner, PGRMC2, a protein about which little was known.

    “We found a new ‘druggable’ pathway, and we also seem to have uncovered some new biology—despite the fact that adipocyte maturation and other diabetes-related pathways have been studied a lot already,” Parker said.

    “With this method, we look forward to exploring much more thoroughly the druggability of human proteins and accelerating investigations of protein biology,” Cravatt added.

    In addition to Parker, Cravatt, Saez and Galmozzim authors of the study, “Ligand and Target Discovery by Fragment-Based Screening in Human Cells,” included TSRI’s Yujia Wang, Kenji Sasaki, Christopher Joslyn and Arthur S. Kim; Bruno Correia of Ecole Polytechnique Federal in Lausanne, Switzerland; and Cullen Cavallaro, Michael Lawrence and Stephen Johnson of Bristol-Myers Squibb.

    The work was supported by grants from the National Institutes of Health (DK099810; CA132630; 1S10OD16357), an American Cancer Society Postdoctoral Fellowship and a fellowship from the American Heart Association.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 2:03 pm on January 23, 2017 Permalink | Reply
    Tags: , , , HIVE, , Scripps Institute,   

    From FAAH at WCG: “Virtual Screening of the HIV-1 Mature Capsid Protein” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    faah-1-new

    faah-hive

    Scripps Institute

    This webpage is dedicated to the virtual screening of the HIV-1 capsid protein in her mature form. This project is part of the HIVE Center and the FA@H initiative in collaboration with IBM and their World Community Grid (WCG).

    People involved in the project come from the Olson Lab in The Scripps Research Institute, and from all over the world as volunteers of the WCG. Meet them here.

    FightAidsOlsonLab@home

    For any question about the project or this webpage, please contact
    Dr. Pierrick Craveur : pcraveur@scripps.edu

    Background

    During the maturation of the HIV virus, the HIV-1 capsid protein (CA) assembles with thousands of copies to forms the capsid core [ref 1] with a characteristic conical shape (see Figure 1 and Figure 2C). This core encloses the RNA viral genome. Upon the entry of the HIV in host cells, the capsid core is released into the cytoplasm, and it dissociates in connection with the reverse transcription in a not completely understood process. This leads to the importation of DNA viral genome in the host cell’s nucleus, where it is integrated in the host DNA to finalize the infection.

    2
    Figure 1: The early phase of the HIV-1 replication cycle.
    (credit: Nature Reviews Microbiology 13, 471–483 (2015) | doi:10.1038/nrmicro3503)

    The critical role of CA protein, in early and late stages of the viral replication life cycle, has led to recent efforts on drug development, targeting the mature form of the protein. Currently, none of these molecules are used in clinic, and some face natural polymorphism and resistant mutations [ref 2]. Therefore, continued development of drugs targeting the CA protein is still needed.

    The critical role of CA protein, in early and late stages of the viral replication life cycle, has led to recent efforts on drug development, targeting the mature form of the protein. Currently, none of these molecules are used in clinic, and some face natural polymorphism and resistant mutations [ref 2]. Therefore, continued development of drugs targeting the CA protein is still needed.

    3
    Figure 2: The HIV-1 mature capsid assembly.
    (credit: Pierrick Craveur)

    Different level of the capsid protein structure

    CA protein consist of a sequence of 231 amino acids which folds into 3 different domains (Figure 2A): The N-terminal domain (N-ter), the linker, and the C-terminal domain (C-ter). This protein chain complexes with other chains to form hexamers (Figure 2B) or pentamers; which assemble together to form the fullerene-cone shape of the capsid core (Figure 2C). There are several models of the core assembly, but all are composed of ~200 hexamers, and exactly 12 pentamers.

    High Throughput Virtual Screening

    The FightAIDS@Home team is working with World Community Grid to find active compounds which could attach to the CA proteins and mediate the assembly of the capsid core. This computational experiment will be performed using the docking software AutoDock VINA [ref 3].
    Thanks to the volunteers, around 2 million molecules will be screened across ~50 conformations of the capsid protein, and hopefully lead to a reduced selection of molecules. This will be the starting point of a drug discovery process targeting the HIV-1 capsid protein.
    This computational experiment will be performed using the docking software AutoDock VINA [ref 3].
    With the support of our collaborators from the HIV Interaction and Viral Evolution (HIVE), experimental biding assays and infectivity assays will be conducted to determine if the selected compounds could be optimized as a promising drug candidate.

    4
    Figure 3: The four pockets of interest.
    (credit: Pierrick Craveur)

    Four pockets of interest

    Based on X-ray structures of CA protein, models of the core, and computational analysis of their flexibility, four pockets of interest have been selected on the surface of the hexamer assembly (see Figure 3).
    These pockets involve either one monomer (as pocket 2 along the linker domain), at the interface of two monomers (pocket 1 & 4), or at the six-fold interface (pocket 3).
    Mutagenesis experiments revealed that core stability is fine-tuned to allow ordered disassembly during early stage of virus replication cycle [ref 4]. This is why selection of compounds will be done either for molecules which could stabilize or destabilize the hexamer; assuming that both actions could have impacts on the equilibrium of the core.

    References

    Briggs, J. A. and H. G. Krausslich (2011). “The molecular architecture of HIV.” J Mol Biol 410(4): 491-500.
    Thenin-Houssier, S. and S. T. Valente (2016). “HIV-1 Capsid Inhibitors as Antiretroviral Agents.” Curr HIV Res 14(3): 270-282.
    Trott, O. and A. J. Olson (2010). “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.” J Comput Chem 31(2): 455-461.
    Forshey, B. M., U. von Schwedler, et al. (2002). “Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication.” J Virol 76(11): 5667-5677.

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 3:10 pm on January 20, 2017 Permalink | Reply
    Tags: , , , Scripps Institute, Telomere length, TZAP   

    From Scripps: “Scientists Discover Master Regulator of Cellular Aging’ 

    Scripps
    Scripps Research Institute

    January 23, 2017
    Madeline McCurry-Schmidt

    1
    “This protein sets the upper limit of telomere length,” says Associate Professor and senior author Eros Lazzerini Denchi (left), pictured here with study first author Graduate Student Julia Su Zhou Li. (Photo by Madeline McCurry-Schmidt.)

    Scientists at The Scripps Research Institute (TSRI) have discovered a protein that fine-tunes the cellular clock involved in aging.

    This novel protein, named TZAP, binds the ends of chromosomes and determines how long telomeres, the segments of DNA that protect chromosome ends, can be. Understanding telomere length is crucial because telomeres set the lifespan of cells in the body, dictating critical processes such as aging and the incidence of cancer.

    “Telomeres represent the clock of a cell,” said TSRI Associate Professor Eros Lazzerini Denchi, corresponding author of the new study, published in the journal Science [link is below]. “You are born with telomeres of a certain length, and every time a cell divides, it loses a little bit of the telomere. Once the telomere is too short, the cell cannot divide anymore.”

    Naturally, researchers are curious whether lengthening telomeres could slow aging, and many scientists have looked into using a specialized enzyme called telomerase to “fine-tune” the biological clock. One drawback they’ve discovered is that unnaturally long telomeres are a risk factor in developing cancer.

    “This cellular clock needs to be finely tuned to allow sufficient cell divisions to develop differentiated tissues and maintain renewable tissues in our body and, at the same time, to limit the proliferation of cancerous cells,” said Lazzerini Denchi.

    In this new study, the researcher found that TZAP controls a process called telomere trimming, ensuring that telomeres do not become too long.

    “This protein sets the upper limit of telomere length,” explained Lazzerini Denchi. “This allows cells to proliferate—but not too much.”

    For the last few decades, the only proteins known to specifically bind telomeres were the telomerase enzyme and a protein complex known as the Shelterin complex. The discovery TZAP, which binds specifically to telomeres, was a surprise since many scientists in the field believed there were no additional proteins binding to telomeres.

    “There is a protein complex that was found to localize specifically at chromosome ends, but since its discovery, no protein has been shown to specifically localize to telomeres,” said study first author Julia Su Zhou Li, a graduate student in the Lazzerini Denchi lab.

    “This study opens up a lot of new and exciting questions,” said Lazzerini Denchi.

    In addition to Lazzerini Denchi and Li, authors of the study, TZAP: a telomere-associated protein involved in telomere length control, were Tatevik Simavorian, Cristina Bartocci and Jill Tsai of TSRI; Javier Miralles Fuste of the Salk Institute for Biological Studies and the University of Gothenburg; and Jan Karlseder of the Salk Institute for Biological Studies.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 1:59 pm on January 4, 2017 Permalink | Reply
    Tags: , , Proteases, Scripps Florida Scientists Expand Toolbox to Study Cellular Function, Scripps Institute   

    From Scripps: “Scripps Florida Scientists Expand Toolbox to Study Cellular Function” 

    Scripps
    Scripps Research Institute

    January 4, 2017
    No writer credit

    Scientists on the Florida campus of The Scripps Research Institute (TSRI) have developed a new tool for studying the molecular details of protein structure.

    Their new study, published recently in the journal Proceedings of the National Academy of Sciences, explores how evolution can be used to discover new and useful enzyme tools, called proteases. Proteases cleave proteins into smaller peptide pieces that scientists can then analyze to determine the identity of the protein and whether a cell has made chemical changes to the protein that might alter its function.

    The new protease developed in the study helps shed light on these chemical changes, called post-translational modifications. Post-translational modifications are alterations made to proteins after the proteins are translated from RNA.

    “We have to observe these protein modifications directly through chemical analysis; we can’t read them out of DNA sequence,” explained study senior author Brian M. Paegel, associate professor at TSRI.

    These modifications can dramatically alter a protein’s stability and function, and unregulated modification can lead to disease, such as cancer. Therefore, understanding the nature and location of these modifications can be critical in the early phases of drug discovery.

    Scientists currently rely on a technique called mass spectrometry to study post-translational modifications. Mass spectrometry analyzes peptides to see if their mass changes—a bit like zooming in on that protein to see hidden details. An unexpected change in mass can indicate the occurrence of a post-translational modification.

    Many scientists today use a protease called trypsin to break proteins into peptides. Because there are few other proteases available for mass spectrometry, trypsin has become the workhorse of the field. However, Paegel explained, it’s luck of the draw if trypsin generates a peptide with a modified site. So Paegel and co-workers thought it would be useful to have a new tool that cleaved directly at the modified site.

    To solve this problem, Paegel developed a new trypsin “mutant” using a technique called “directed evolution.” The scientists created many thousands of trypsin mutants and tested each mutant for its ability to cut a protein at modified sites. They discovered a mutant that could cut proteins at citrulline, which is one type of modification.

    Paegel believes this new approach could be useful for mapping a wider range of post-translational modifications, and he hopes to use directed evolution to discover proteases that target many other post-translational modifications. “I think we’re on the brink of an explosion of new tools for mass spectrometry,” he said.

    In addition to Paegel, authors of the study, “Evolution of a mass spectrometry-grade protease with PTM-directed specificity,” were Duc. T. Tran (first author), Valerie Cavett, Vuong Q. Dang and Héctor L. Torres of TSRI.

    This study was supported by a National Institutes of Health’s Director’s New Innovator Award (grant OD008535) and a National Science Foundation Research Experiences for Undergraduates Grant (1359369).

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 8:17 am on September 30, 2016 Permalink | Reply
    Tags: , , , Scientists find evidence that life on Earth didn't only originate from RNA, Scripps Institute   

    From Science Alert: “Scientists find evidence that life on Earth didn’t only originate from RNA” 

    ScienceAlert

    Science Alert

    29 SEP 2016
    FIONA MACDONALD

    1
    NASA Goddard Space Flight Centre/Flickr.

    It’s not as simple as it seems.

    Scientists have just put forward an alternate hypothesis for how life originated on Earth – suggesting that RNA alone didn’t kickstart the process.

    Right now, the leading explanation for how life rose up out of Earth’s primordial soup some 3.8 billion years ago is the ‘RNA world’ hypothesis, which proposes that RNA came first, and eventually created DNA, which went on to form complex life as we know it.

    But now a team of chemists from the Scripps Research Institute in California has found evidence that RNA wouldn’t have been able to sustainably give rise to DNA, leading them to suggest that the two molecules might have actually formed at the same time.

    “Even if you believe in a RNA-only world, you have to believe in something that existed with RNA to help it move forward,” said lead researcher Ramanarayanan Krishnamurthy.

    “Why not think of RNA and DNA rising together, rather than trying to convert RNA to DNA by means of some fantastic chemistry at a prebiotic stage?”

    If you need a bit of a refresher on the RNA world hypothesis, RNA (or ribonucleic acid) is widely known as the “older molecular cousin” of DNA (deoxyribonucleic acid).

    While they share a pretty similar structure – RNA looks like one side of DNA’s ladder – RNA is more brittle and less flexible than DNA, which is most likely why DNA ended up forming our genes.

    But it’s widely believed that RNA, despite its faults, came first, with many scientists suggesting that it was the first self-replicating molecule on Earth.

    The RNA world hypothesis states that RNA self-assembled from ancient Earth’s bubbling hot stew of particles, and went on to turn amino acids into proteins and enzymes. Eventually, those enzymes helped RNA to produce DNA, which led to complex life.

    That’s the short story anyway. Many researchers think that there would have also been cases where RNA nucleotides – the little building blocks of RNA – would have mixed with the backbone that forms DNA, creating mixed ‘chimera’ strands.

    Those chimeras would have been a crucial step in the transition from RNA to DNA, and it’s this step that the chemists behind the latest study have an issue with.

    In their research, they tested whether RNA and DNA could realistically share the same backbone, and showed that, when the two molecules are blended, they were highly unstable.

    “We were surprised to see a very deep drop in what we would call the ‘thermal stability’,” said Krishnamurthy.

    That means these chimeras in the RNA world would have most likely died off in favour of more stable RNA molecules, or failed to self-replicate, he explains.

    This isn’t the first time this has been demonstrated – Nobel laureate Jack Szostak from Harvard University has also shown a loss of function when RNA mixed with DNA.

    Even in today’s cells, if RNA nucleotides accidentally join a DNA strand, enzymes rush in to fix the mistake – and 3.8 billion years ago, RNA wouldn’t have had that self-correct mechanism.

    “The transition from RNA to DNA would not have been easy without mechanisms to keep them separate,” said Krishnamurthy.

    That evidence supports the idea that RNA and DNA actually arose at the same time, potentially from similar ingredients in Earth’s primordial soup, the researchers conclude in Angewandte Chemie.

    They’re not the first team to put forward this idea, but their findings provide new evidence to support this alternate hypothesis for the origins of life.

    If their findings are confirmed, it doesn’t necessarily mean that RNA didn’t give rise to DNA – but it’s likely that DNA evolved, at least in some primitive state, earlier than we’d predicted.

    Unfortunately, without a time machine, it’s unlikely we’ll ever really know what went on back at the dawn of life on Earth. But by trying to figure it out, we might have a better shot of predicting where we might find life elsewhere in the Universe.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

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