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  • richardmitnick 10:12 am on April 17, 2019 Permalink | Reply
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    UW Medicine Newsroom: “Protein design named as an Audacious project” 

    U Washington
    University of Washington

    UW Medicine Newsroom

    April 16, 2019

    Leila Gray
    UW Medicine
    leilag@uw.edu
    206.685.0381

    Susan Gregg
    UW Medicine
    sghanson@uw.edu
    206.390.3226

    The Institute for Protein Design at the UW School of Medicine will advance medicine and improve healthcare with an initial $45 million in funding through TED’s The Audacious Project.

    1
    At the Institute for Protein Design, David Baker (left) and Neil King display enlarged 3-D printouts of computer-engineered proteins. ian Haydon/IPD

    The Institute for Protein Design at the University of Washington School of Medicine in Seattle has received a commitment of an initial $45 million in funding through The Audacious Project, a philanthropic collaborative that surfaces and funds critical projects with the potential to create massive global change.

    “This is simply wonderful, and it comes at the best possible time,” said David Baker. He is the the institute’s director, a UW School of Medicine professor of biochemistry, and a Howard Hughes Medical Institute investigator. He also holds the Henrietta and Aubrey Davis Endowed Professorship in Biochemistry.

    “As we get better and better at designing proteins to perform specific tasks,” said Baker, “it has become possible to have bold new approaches to solving some of the most vexing problems in medicine today.”

    The institute will use The Audacious Project funds to pursue the computational design of:

    A universal flu vaccine capable of providing lifetime immunization
    New drug candidates with enhanced abilities to enter the brain
    Advanced protein containers for targeted gene delivery (including the delivery of RNA into cells)
    Smart proteins capable of identifying cancerous or otherwise unhealthy cells
    Self-assembling protein nanomaterials for use in solar energy and nanofabrication

    Please see the Institute for Protein Design fact sheet for more information on the institute and its innovation hub of projects.

    The institute will expand its team of engineers and scientists who will work together to advance their best-in-class Rosetta protein design software. It will also add three new tenure-track professors, five acting instructors, and will support additional postdoctoral fellows, graduate students, and staff scientists from around the world. The funding will also support investments in equipment, supplies, and laboratory space needed to design, build, and characterize millions of synthetic proteins.

    Support leveraged via The Audacious Project was made possible through the generosity of Laura and John Arnold, Steve and Genevieve Jurvetson, Chris Larsen and Lyna Lam, Lyda Hill Philanthropies, Miguel McKelvey, the Clara Wu and Joe Tsai Foundation, Rosamund Zander and Hansjörg Wyss for the Wyss Foundation, and several anonymous donors. The UW School of Medicine hopes these funds will spur more contributions to the Institute for Protein Design.

    Baker said the goal of the initiative is to create the Bell Labs of protein design, referring to the enormous productivity and invention of Bell Telephone Laboratories. There, scientists and engineers invented such technologies as the transistor and the laser, as well as information theory, which underpins the digital age. “We hope to attract some of the best and brightest from around the world to work on what we think is going to be a protein design revolution,” Baker said.

    “We believe that protein-based technologies will play an increasingly transformative role in this space,” said Neil King, an assistant professor of biochemistry at the UW School of Medicine, who leads the institute’s vaccine design efforts. “The Audacious Project will help us realize that vision in a way that simply wouldn’t be possible through traditional grant-based funding.”

    “We created The Audacious Project to give lift-off to some of the world’s most transformative projects — the ones with the potential to revolutionize entire fields,” said Anna Verghese, executive director of The Audacious Project. “The Institute for Protein Design has been a long-standing pioneer in computational protein design. Now, with a solid blueprint in place and support through The Audacious Project, the Institute for Protein Design will venture to accelerate the pace of discovery, disseminate new protein technology, and fundamentally change how drugs, vaccines, fuels, and new materials are made.”

    About the Audacious Project

    The Audacious Project was launched in April 2018, with a mission to foster “collaborative philanthropy for bold ideas.” Housed at TED (the nonprofit devoted to ideas worth spreading) and operated with support from The Bridgespan Group (a leading social impact advisor to nonprofits and NGOs, philanthropists and investors), The Audacious Project brings together some of the most respected organizations and individuals in philanthropy—the Skoll Foundation, Virgin Unite, Dalio Foundation and more. The Audacious Project surfaces and funds critical projects with the potential to create global change. By removing barriers associated with funding, The Audacious Project empowers social entrepreneurs to dream boldly and take on the world’s biggest and most urgent challenges.

    The 2019 projects include: Center for Policing Equity, Educate Girls, Institute for Protein Design at the UW School of Medicine, Salk Institute for Biological Studies, the END Fund, The Nature Conservancy, Thorn and Waterford UPSTART. Learn more or support an existing project at http://www.AudaciousProject.org.

    About the Institute for Protein Design at the University of Washington School of Medicine

    Proteins perform the vast array of functions in life. At the Institute for Protein Design, established in 2012 in the Department of Biochemistry at the University of Washington School of Medicine in Seattle, researchers use computers to design entirely new proteins from scratch. These custom proteins not only mimic many of the functions of naturally occurring proteins, but they also can perform entirely new functions that natural proteins cannot.

    “For many years, when protein researchers wanted to solve a problem, they looked to nature for a molecule that did something close to what they wanted, then they would try to make small changes to it,” said David Baker, director of the Institute for Protein Design at the University of Washington School of Medicine.

    U Washington Dr. David Baker

    “It’s similar to how our Stone Age ancestors developed their technology: If you wanted to dig a hole, you went looking for a bone that was roughly the right shape, and you sharpened it a bit.”

    Baker added, “What we do at the Institute for Protein Design is, first, determine what shape a protein would need to do a certain task — say, to serve as an enzyme — and then, using the Rosetta computer software developed at the institute, identify the amino acid sequence that will give us a protein that can do that task,” Baker said. The approach allows researchers to move beyond the limitations of proteins that were created by evolution over millions of years of trial and error.

    In recent years, researchers at the institute have developed a mini-protein that can neutralize the flu virus, an enzyme that degrades gluten in the stomach and which is now in clinical trials as a potential treatment for celiac disease, and a first-of-its-kind nanoparticle vaccine candidate for respiratory syncytial virus, oro RSV, which is second only to malaria as a cause of infant mortality worldwide. To date, eight spinout companies have been launched to further develop several of the institute’s engineered, novel proteins ffor clinical and commercial use.

    Institute for Protein Design
    Foldit (Institute’s online protein-folding video game)
    Rosetta@home (Institute’s citizen-science portal)

    David Baker’s Rosetta@home project, a project running on BOINC software from UC Berkeley


    Rosetta@home BOINC project

    See the full article here .

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    About UW Medicine

    UW Medicine is one of the top-rated academic medical systems in the world. With a mission to improve the health of the public, UW Medicine educates the next generation of physicians and scientists, leads one of the world’s largest and most comprehensive biomedical research programs, and provides outstanding care to patients from across the globe.

    The UW School of Medicine, part of the UW Medicine system, leads the internationally recognized, community-based WWAMI Program, serving the states of Washington, Wyoming, Alaska, Montana and Idaho. The school has been ranked No. 1 in the nation in primary-care training for more than 20 years by U.S. News & World Report. It is also second in the nation in federal research grants and contracts with $749.9 million in total revenue (fiscal year 2016) according to the Association of American Medical Colleges.

    UW Medicine has more than 27,000 employees and an annual budget of nearly $5 billion. Also part of the UW Medicine system are Airlift Northwest and the UW Physicians practice group, the largest physician practice plan in the region. UW Medicine shares in the ownership and governance of the Seattle Cancer Care Alliance with Fred Hutchinson Cancer Research Center and Seattle Children’s, and also shares in ownership of Children’s University Medical Group with Seattle Children’s.

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 9:17 am on November 1, 2018 Permalink | Reply
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    From Discover Magazine: “Meet the Biochemist Engineering Proteins From Scratch” 

    DiscoverMag

    From Discover Magazine

    October 30, 2018
    Jonathon Keats

    1
    David Baker. Brian Dalbalcon/UW Medicine

    U Washington Dr. David Baker

    In a sleek biochemistry laboratory at the University of Washington, postdoctoral fellow Yang Hsia is watching yellowish goo — the liquefied remains of E. coli — ooze through what looks like a gob of white marshmallow. “This isn’t super exciting,” he says.

    While growing proteins in bacteria and then purifying them, using blobby white resin as a filter, doesn’t make for riveting viewing, the end product is extraordinary. Accumulating in Hsia’s resin is a totally artificial protein, unlike anything seen in nature, that might just be the ideal chassis for the first universal flu vaccine.

    David Baker, Hsia’s adviser, calls this designer protein a “Death Star.” Imaged on his computer, its structure shows some resemblance to the notorious Star Wars superweapon. Though microscopic, by protein standards it’s enormous: a sphere made out of many interlocking pieces.

    2
    The Death Star artificial protein. Institute for Protein Design

    “We’ve figured out a way to put these building blocks together at the right angles to form these very complex nanostructures,” Baker explains. He plans to stud the exterior with proteins from a whole suite of flu strains so that the immune system will learn to recognize them and be prepared to fend off future invaders. A single Death Star will carry 20 different strains of the influenza virus.

    Baker hopes this collection will cover the entire range of possible influenza mutation combinations. This all-in-one preview of present and future flu strains could replace annual shots: Get the Death Star vaccination, and you’ll already have the requisite antibodies in your bloodstream.

    As Baker bets on designer proteins to defeat influenza, others are betting on David Baker.

    After revolutionizing the study of proteins — molecules that perform crucial tasks in every cell of every natural organism — Baker is now engineering them from scratch to improve on nature. In late 2017, the Open Philanthropy Project gave his University of Washington Institute for Protein Design more than $10 million to develop the Death Star and support Rosetta, the software platform he conceived in the 1990s to discover how proteins are assembled. Rosetta has allowed Baker’s lab not only to advance basic science and pioneer new kinds of vaccines, but also to create drugs for genetic disorders, biosensors to detect toxins and enzymes to convert waste into biofuels.

    His team currently numbers about 80 grad students and postdocs, and Baker is in constant contact with all of them. He challenges their assumptions and tweaks their experiments while maintaining an egalitarian environment in which ideas may come from anyone. He calls his operation a “communal brain.” Over the past quarter-century, this brain has generated nearly 450 scientific papers.

    “David is literally creating a new field of chemistry right in front of our eyes,” says Raymond Deshaies, senior vice president for discovery research at the biotech company Amgen and former professor of biology at Caltech. “He’s had one first after another.”

    Nature’s Origami

    When Baker was studying philosophy at Harvard University, he took a biology class that taught him about the so-called “protein folding problem.” The year was 1983, and scientists were still trying to make sense of an experiment, carried out in the early ’60s by biochemist Christian Anfinsen, that revealed the fundamental building blocks of all life on Earth were more complex than anyone imagined.

    The experiment was relatively straightforward. Anfinsen mixed a sample of the protein ribonuclease — which breaks down RNA — with a denaturant, a chemical that deactivated it. Then he allowed the denaturant to evaporate. The protein started to function again as if nothing ever happened.

    What made this simple experiment so striking was the fact that the amino acids in protein molecules are folded in three-dimensional forms that make origami look like child’s play. When the denaturant unfolded Anfinsen’s ribonuclease, there were myriad ways it could refold, resulting in structures as different as an origami crane and a paper airplane. Much as the folds determine whether a piece of paper can fly across a room, only one fold pattern would result in functioning ribonuclease. So the puzzle was this: How do proteins “know” how to refold properly?

    “Anfinsen showed that the information for both structure and activity resided in the sequence of amino acids,” says University of California, Los Angeles, biochemist David Eisenberg, who has been researching protein folding since the 1960s. “There was a hope that it would be possible to use sequence information to get three-dimensional structural information. Well, that proved much more difficult than anticipated.”

    2
    Protein molecules play critical roles in every aspect of life. The way each protein folds determines its function, and the ways to fold are virtually limitless, as shown in this small selection of proteins visualized through the software platform Rosetta, born in Baker’s lab. Institute for Protein Design.

    Baker was interested enough in protein folding and other unsolved mysteries of biology to switch majors and apply to grad school. “I’d never worked in a lab before,” he recalls. He had only a vague notion of what biologists did on a daily basis, but he also sensed that the big questions in science, unlike philosophy, could actually be answered.

    Grad school plunged Baker into the tediousness and frustrations of benchwork, while also nurturing some of the qualities that would later distinguish him. He pursued his Ph.D. under Randy Schekman, who was studying how molecules move within cells, at the University of California, Berkeley. To aid in this research, students were assigned the task of dismantling living cells to observe their internal molecular traffic. Nearly half a dozen of them, frustrated by the assignment’s difficulty, had given up by the time Baker got the job.

    Baker decided to follow his instincts even though it meant going against Schekman’s instructions. Instead of attempting to keep the processes within a cell still functioning as he dissected it under his microscope, Baker concentrated on preserving cell structure. If the cell were a wristwatch, his approach would be equivalent to focusing on the relationship between gears, rather than trying to keep it ticking, while taking it apart.

    “He was completely obsessed,” recalls Deshaies, who was his labmate at the time (and one of the students who’d surrendered). Nobody could stop Baker, or dissuade him. He worked for months until he proved his approach was correct: Cell structure drove function, so maintaining its anatomy preserved the internal transportation network. Deshaies believes Baker’s methodological breakthrough was “at the core of Randy’s Nobel Prize,” awarded in 2013 for working out one of the fundamentals of cellular machinery.

    But Baker didn’t dwell on his achievement, or cell biology for that matter. By 1989, Ph.D. in hand, he’d headed across the Bay to the University of California, San Francisco, where he switched his focus to structural biology and biochemistry. There he built computer models to study the physical properties of the proteins he worked with at the bench. Anfinsen’s puzzle remained unsolved, and when Baker got his first faculty appointment at the University of Washington, he took up the protein-folding problem full time.

    From Baker’s perspective, this progression was perfectly natural: “I was getting to more and more fundamental problems.” Deshaies believes Baker’s tortuous path, from cells to atoms and from test tubes to computers, has been a factor in his success. “He just has greater breadth than most people. And you couldn’t do what he’s done without being somewhat of a polymath.”

    3
    Illustration above: National Science foundation. Illustrations below: Jay Smith

    Rosetta Milestone

    Every summer for more than a decade, scores of protein-folding experts convene at a resort in Washington’s Cascade Mountains for four days of hiking and shop talk. The only subject on the agenda: how to advance the software platform known as Rosetta.

    David Baker’s Rosetta@home project, a project running on BOINC software from UC Berkeley


    Rosetta@home BOINC project



    They call it Rosettacon.

    Rosetta has been the single most important tool in the quest to understand how proteins fold, and to design new proteins based on that knowledge. It is the link between Anfinsen’s ribonuclease experiment and Baker’s Death Star vaccine.

    When Baker arrived at the University of Washington in 1993, researchers knew that a protein’s function was determined by its structure, which was determined by the sequence of its amino acids. Just 20 different amino acids were known to provide all the raw ingredients. (Their particular order — specified by DNA — makes one protein fold into, say, a muscle fiber and another fold into a hormone.) Advances in X-ray crystallography, a technique for imaging molecular structure, had provided images of many proteins in all their folded splendor. Sequencing techniques had also improved, benefitting from the Human Genome Project as well as the exponential increase in raw computing power.

    “There’s a right time for things,” Baker says in retrospect. “To some extent, it’s just luck and historical circumstance. This was definitely the right time for this field.”

    Which is not to say that modeling proteins on a computer was a simple matter of plugging in the data. Proteins fold to their lowest free energy state: All of their amino acids must align in equilibrium. The trouble is that the equilibrium state is just one of hundreds of thousands of options — or millions, if the amino acid sequence is long. That’s far too many possibilities to test one at a time. Nature must have another way of operating, given that folding is almost instantaneous.

    Baker’s initial approach was to study what nature was doing. He broke apart proteins to see how individual pieces behaved, and he found that each fragment was fluctuating among many possible structures. “And then folding would occur when they all happened to be in the right geometry at the same time,” he says. Baker designed Rosetta to simulate this dance for any amino acid sequence.

    Baker wasn’t alone in trying to predict how proteins fold. In 1994, the protein research community organized a biennial competition called CASP (Critical Assessment of Protein Structure Prediction). Competitors were given the amino acid sequences of proteins and challenged to anticipate how they would fold.

    The first two contests were a flop. Structures that competitors number-crunched looked nothing like folded proteins, let alone the specific proteins they were meant to predict. Then everything changed in 1998.

    3
    Rosetta’s impressive computational power allows researchers to predict how proteins — long, complex chains of amino acids — will fold; the platform also helps them reverse engineer synthetic proteins to perform specific tasks in medicine and other fields. Brian Dalbalcon/UW Medicine.

    Function Follows Form

    That summer, Baker’s team received 20 sequences from CASP, a considerable number of proteins to model. But Baker was optimistic: Rosetta would transform protein-folding prediction from a parlor game into legitimate science.

    In addition to incorporating fresh insights from the bench, team members — using a janky collection of computers made of spare parts — found a way to run rough simulations tens of thousands of times to determine which fold combinations were most likely.

    They successfully predicted structures for 12 out of the 20 proteins. The predictions were the best yet, but still approximations of actual proteins. In essence, the picture was correct, but blurry.

    Improvements followed rapidly, with increased computing power contributing to higher-resolution models, as well as improved ability to predict the folding of longer amino acid chains. One major leap was the 2005 launch of Rosetta@Home, a screensaver that runs Rosetta on hundreds of thousands of networked personal computers whenever they’re not being used by their owners.

    Yet the most significant source of progress has been RosettaCommons, the community that has formed around Rosetta. Originating in Baker’s laboratory and growing with the ever-increasing number of University of Washington graduates — as well as their students and colleagues — it is Baker’s communal brain writ large.

    Dozens of labs continue to refine the software, adding insights from genetics and methods from machine learning. New ideas and applications are constantly emerging.

    4
    Protein (in green) enveloping fentanyl molecule. Bick et al. eLife 2017.

    The communal brain has answered Anfinsen’s big question — a protein’s specific amino acid alignment creates its unique folding structure — and is now posing even bigger ones.

    “I think the protein-folding problem is effectively solved,” Baker says. “We can’t necessarily predict every protein structure accurately, but we understand the principles.

    “There are so many things that proteins do in nature: light harvesting, energy storage, motion, computation,” he adds. “Proteins that just evolved by pure, blind chance can do all these amazing things. What happens if you actually design proteins intelligently?”

    De Novo Design

    Matthew Bick is trying to coax a protein into giving up its sugar habit for a full-blown fentanyl addiction. His computer screen shows a colorful image of ribbons and swirls representing the protein’s molecular structure. A sort of Technicolor Tinkertoy floats near the center, representing the opioid. “You see how it has really good packing?” he asks me, tracing the ribbons with his finger. “The protein kind of envelops the whole fentanyl molecule like a hot dog bun.”

    A postdoctoral fellow in Baker’s lab, Bick engineers protein biosensors using Rosetta. The project originated with the U.S. Department of Defense. “Back in 2002, Chechen rebels took a bunch of people hostage, and there was a standoff with the Russian government,” he says. The Russians released a gas, widely believed to contain a fentanyl derivative, that killed more than a hundred people. Since then, the Defense Department has been interested in simple ways to detect fentanyl in the environment in case it’s used for chemical warfare in the future.

    Proteins are ideal molecular sensors. In the natural world, they’ve evolved to bind to specific molecules like a lock and key. The body uses this system to identify substances in its environment. Scent is one example; specific volatiles from nutrients and toxins fit into dedicated proteins lining the nose, the first step in alerting the brain to their presence. With protein design, the lock can be engineered to order.

    For the fentanyl project, Bick instructed Rosetta to modify a protein with a natural affinity for the sugar xylotetraose. The software generated hundreds of thousands of designs, each representing a modification of the amino acid sequence predicted to envelop fentanyl instead of sugar molecules. An algorithm then selected the best several hundred options, which Bick evaluated by eye, eventually choosing 62 promising candidates. The protein on Bick’s screen was one of his favorites.

    “After this, we do the arduous work of testing designs in the lab,” Bick says.

    5
    Cassie Bryan, a senior fellow at Baker’s Institute for Protein Design at the University of Washington, checks on a tube of synthetic proteins. The proteins, not seen in nature, are in the process of thawing and being prepped to test how they perform. Brian Dalbalcon/UW Medicine.

    With another image, he reveals his results. All 62 contenders have been grown in yeast cells infused with synthetic genes that spur the yeasts’ own amino acids to produce the foreign proteins. The transgenic yeast cells have been exposed to fentanyl molecules tagged with a fluorescing chemical. By measuring the fluorescence — essentially shining ultraviolet light on the yeast cells to see how many glow with fentanyl — Bick can determine which candidates bind to the opioid with the greatest strength and consistency.

    Baker’s lab has already leveraged this research to make a practical environmental sensor. Modified to glow when fentanyl binds to the receptor site, Bick’s customized protein can now be grown in a common plant called thale cress. This transgenic weed can cover terrain where chemical weapons might get deployed, and then glow if the dangerous substances are present, providing an early warning system for soldiers and health workers.

    The concept can also be applied to other biohazards. For instance, Bick is now developing a sensor for aflatoxin, a residue of fungus that grows on grain, causing liver cancer when consumed by humans. He wants the sensor to be expressed in the grain itself, letting people know when their food is unsafe.

    But he’s going about things differently this time around. Instead of modifying an existing protein, he’s starting from scratch. “That way, we can control a lot of things better than in natural proteins,” he explains. His de novo protein can be much simpler, and have more predictable behavior, because it doesn’t carry many million years of evolutionary baggage.

    For Baker, de novo design represents the summit of his quarter-century quest. The latest advances in Rosetta allow him to work backward from a desired function to an appropriate structure to a suitable amino acid sequence. And he can use any amino acids at all — thousands of options, some already synthesized and others waiting to be designed — not only the 20 that are standard in nature for building proteins.

    Without the freedom of de novo protein design, Baker’s Death Star would never have gotten off the ground. His group is now also designing artificial viruses. Like natural viruses, these protein shells can inject genetic material into cells. But instead of infecting you with a pathogen, their imported DNA would patch dangerous inherited mutations. Other projects aim to take on diseases ranging from malaria to Alzheimer’s.

    In Baker’s presence, protein design no longer seems so extraordinary. Coming out of a brainstorming session — his third or fourth of the day — he pulls me aside and makes the case that his calling is essentially the destiny of our species.

    “All the proteins in the world today are the product of natural selection,” he tells me. “But the current world is quite a bit different than the world in which we evolved. We live much longer, so we have a whole new class of diseases. We put all these nasty chemicals into the environment. We have new needs for capturing energy.

    “Novel proteins could solve a lot of the problems that we face today,” he says, already moving to his next meeting. “The goal of protein design is to bring those into existence.”

    See the full article here .

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  • richardmitnick 6:52 pm on March 6, 2018 Permalink | Reply
    Tags: , , , Institute for Protein Design, , , U Wasington Medicine News Room   

    From UW Medicine Newsroom: “Scientists create complex transmembrane proteins from scratch” 

    U Washington
    University of Washington

    UW Medicine Newsroom

    March 1, 2018
    Leila Gray
    206.685.0381
    leilag@uw.edu

    The ability to build transmembrane proteins opens the way for custom-designing structures that span living cell membranes and perform new tasks.

    1
    Four computer-designed proteins combine to form a transmembrane tetramer with the top of structure facing the cytoplasm. Institute for Protein Design.

    In the living world, transmembrane proteins are found embedded in the membrane of all cells and cellular organelles. They are essential for them to function normally. For example, many naturally occurring transmembrane proteins act as gateways for the movement of specific substances across a biological membrane. Some transmembrane proteins receive or transmit cell signals. Because of such roles, many drugs are designed to target transmembrane proteins and alter their function.

    Now researcher are looking at designing the transmembrane proteins themselve to perform specific tasks.

    “Our results pave the way for the design of multispan membrane proteins that could mimic proteins found in nature or have entirely novel structure, function and uses,” said David Baker, a University of Washington School of Medicine professor biochemistry and director of the UW Institute of Protein Design who led the project.

    U Washington Dr. David Baker

    David Baker’s Rosetta@home project, a project running on BOINC software from UC Berkeley

    But understanding how transmembrane proteins are put together and how they work has proved challenging. Because they act while embedded within the cellular membrane, transmembrane proteins have proven to be more difficult to study than proteins that operate in the watery solution that make up the cells’ cytoplasm or in the extracellular fluid.

    In the new study, Lu and his coworkers used a computer program, developed in the Baker lab and called Rosetta, that can predict the structure a protein will fold into after it has been synthesized. The architecture of a protein is crucial because a protein’s structure determines its function.

    A protein’s shape forms from complex interactions between the amino acids that make up the protein chain and between the amino acids and the surrounding environment. Ultimately, the protein assumes the shape that best balances out all these factors so that the protein achieves the lowest possible energy state.

    The Rosetta program used by Lu and his colleagues can predict the structure of a protein by taking into account these interactions and calculating the lowest overall energy state. It is not unusual for the program to create tens of thousands of model structures for an amino acid sequence and then identify the ones with lowest energy state. The resulting models have been shown to accurately represent the structure the sequence will likely assume in nature.

    Determining the structure of transmembrane proteins is difficult because portions of transmembrane proteins must pass though the membrane’s interior, which is made of oily fats called lipids.

    In aqueous fluids, amino acid residues that have polar sidechains – components that can have a charge under certain physiological conditions or that participate in hydrogen bonding — tend to be located on the surface of the protein where they can interact with water, which has negatively and positively side charges to its molecule. As a result, polar residues on proteins are called hydrophilic, or “water-loving.”

    Non-polar residues, on the other hand, tend to be found packed within the protein core away from the polar aqueous fluid. Such residues are called hydrophobic or “water-fearing.” As a result, the interaction between the water-loving and water-fearing residues of the protein and the surrounding watery fluids helps drive protein folding and stabilizes the protein’s final structure.

    In membranes, however, protein folding is more complicated because the lipid interior of the membrane is non-polar, that is, it has no separation of electrical charges. This means to be stable the protein must place nonpolar, water-fearing residues on its surface, and pack its polar, water-loving residues inside. Then it must find a way to stabilize its structure by creating bonds between the hydrophilic residues within its core.

    The key to solving the problem, said Lu, was to apply a method developed by Baker lab to design the transmembrane portion so that the polar, hydrophilic residues fit in such a way that enough would form hydrongen bonds– that can tie the protein together from within

    “Putting together these ‘buried hydrogen bond networks’ was like putting together a jig-saw puzzle,” Baker said.

    With this approach, Lu and his colleagues were able to manufacture the designed transmembrane proteins inside bacteria and mammalian cells by using as many as 215 amino acids. The resulting proteins proved to be highly thermally stable and able to correctly orient themselves on the membrane. Like naturally occurring transmembrane proteins, the proteins are multipass, meaning they traverse the membrane several times, and assemble into stable multi-protein complexes, such as dimers, trimers and tetramers.

    “We have shown that it is now possible to accurately design complex, multipass transmembrane proteins that can be expressed in cells. This will make it possible for researchers to design transmembrane proteins with entirely novel structures and functions,” said Lu.

    This work was supported by the Howard Hughes Medical Institute, National Institutes of Health (R01GM063919), the Raymond and Beverly Sackler fellowship, and the National Research Foundation of Korea (NRF- 2016R1A6A3A03007871).

    The research is reported in the March 1 issue of the journal Science. Peilong Lu, a senior fellow in the Baker lab, is the paper’s lead author.

    See the full article here .

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    About UW Medicine

    UW Medicine is one of the top-rated academic medical systems in the world. With a mission to improve the health of the public, UW Medicine educates the next generation of physicians and scientists, leads one of the world’s largest and most comprehensive biomedical research programs, and provides outstanding care to patients from across the globe.

    The UW School of Medicine, part of the UW Medicine system, leads the internationally recognized, community-based WWAMI Program, serving the states of Washington, Wyoming, Alaska, Montana and Idaho. The school has been ranked No. 1 in the nation in primary-care training for more than 20 years by U.S. News & World Report. It is also second in the nation in federal research grants and contracts with $749.9 million in total revenue (fiscal year 2016) according to the Association of American Medical Colleges.

    UW Medicine has more than 27,000 employees and an annual budget of nearly $5 billion. Also part of the UW Medicine system are Airlift Northwest and the UW Physicians practice group, the largest physician practice plan in the region. UW Medicine shares in the ownership and governance of the Seattle Cancer Care Alliance with Fred Hutchinson Cancer Research Center and Seattle Children’s, and also shares in ownership of Children’s University Medical Group with Seattle Children’s.

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 9:51 am on October 2, 2017 Permalink | Reply
    Tags: , , Institute for Protein Design, , ,   

    From U Washington Medicine: “Mini-protein rapid design opens way to new class of drugs” 

    U Washington

    University of Washington

    September 27, 2017
    Leila Gray
    206.685.0381
    leilag@uw.edu

    Scientists at the Institute for Protein Design have created a way to generate thousands of different mini-protein binders as possible drug candidates. The proteins can be custom tailored to specific therapeutic targets. Recently, a set of these proteins were successfully tested in mice against the flu, and another group of these binders was able to protect brain cells against the botulism neurotoxin.

    1
    Artist impression of designed mini-protein binders targeting Influenza hemagglutinin to effectively bind and neutralize the virus. Cognition Studio, Daniel-Adriano Silva, Lance Stewart

    These computer-designed proteins, which did not previously exist in nature, combine the stability and bioavailability of small molecule drugs with the specificity and potency of larger biologics. They would not require refrigeration, and they likely would be simple for patients to take.

    “These mini-protein binders have the potential of becoming a new class of drugs that bridge the gap between small molecule drugs and biologics. Like monoclonal antibodies, they can be designed to bind to targets with high selectivity, but they are more stable and easier to produce and to administer,” said David Baker, who led the multi-institutional research project. He is a professor of biochemistry at the University of Washington School of Medicine and director of the UW Institute for Protein Design.

    Dr. David Baker, Baker Lab, U Washington

    Baker and his colleagues report their findings in article published online Sept. 27 by the journal Nature.

    Aaron Chevalier, Daniel-Adriano Silva and Gabriel J. Rocklin were the lead authors and were all senior fellows at the UW Institute for Protein Design at the time of the project.

    The method used a computer platform, called Rosetta, developed by Baker and colleagues at the University of Washington. They designed thousands of short proteins, about 40 amino acids in length, that the Rosetta program predicted would bind tightly to the molecular target.

    Rosetta@home project, a project running on BOINC software from UC Berkeley


    Rosetta@home BOINC project

    BOINC

    My BOINC

    Because of their small size, these short proteins tend to be extremely stable. They can be stored without refrigeration. They also are more easily administered than large protein drugs, such as monoclonal antibodies.

    Previously, such short, protein-binder drugs were typically re-engineered versions of naturally occurring proteins. These, however, tended not to be significantly better than monoclonal antibodies.

    Because these mini-proteins binders are original designs, they can be tailored to fit their targets much more tightly and are simpler to modify and refine.

    In this study, the researchers sought to design two sets of these proteins: one set that would prevent the influenza virus from invading cells and another that would bind to and neutralize a deadly nerve toxin from botulism. This toxin is considered a potential bioweapon.

    The computer modeling identified the amino-acid sequences of thousands of short proteins that would fit into and bind to the influenza and botulinum targets. The researchers created short pieces of DNA that coded each of these proteins, grew the proteins in yeast cells, and then looked at how tightly they bound to their targets. The targets were Influenza H1 hemagglutinin and botulinum neurotoxin B.

    All told, the method allowed them to design and test 22,660 proteins in just a few months. More than than two-thousand of them bound to their targets with high affinity.

    Evaluation of the best candidates found that the anti-influenza proteins neutralized viruses in cell culture and other designed proteins prevented the botulinum toxin from entering brain cells.

    A nasal spray containing one of the custom-designed proteins completely protected mice from the flu if administered before or as much as 72 hours after exposure.. The protection that the treatment provides equaled or surpassed that seen with antibodies, the researchers report.

    Testing of a subset of the proteins showed that they were extremely stable and, unlike antibodies, did not become inactivated by high temperatures. The small proteins also triggered little or no immune response, a problem that often renders larger protein drugs ineffective.

    Funding for the study came from Life Sciences Discovery Fund Launch grant (9598385), Doctorado en Ciencias Bioquiacutemicas UNAM (R56AI117675), Molecular Basis of Viral Pathogenesis Training Grant (T32AI007354-26A1), Investigator in the Pathogenesis of Infectious Disease award from the Burroughs Wellcome Fund and NIH (1R01NS080833), CoMotion Mary Gates Innovation Fellow; Shenzhen Science and Technology Innovation Committee (JCYJ20170413173837121), Hong Kong Research Grant Council (C6009-15G and AoE/P-705/16), PAPIIT UNAM (IN220516), CONACyT (254514) and Facultad de Medicina UNAM (AI091823, AI123920,AI125704), NIAID grant (1R41AI122431) (1R21AI119258), and Life Sciences Discovery Fund grant (20040757).

    See the full article here .

    Please help promote STEM in your local schools.

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    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 11:19 am on September 16, 2016 Permalink | Reply
    Tags: , , , , Hyperstable peptides, Institute for Protein Design,   

    From U Washington: “Super-stable peptides might be used to create ‘on-demand’ drugs” 

    U Washington

    University of Washington

    09.14.2016
    Michael McCarthy

    1
    An artist’s conception of a peptide created at the UW Medicine Institute for Protein Design. The backbone structure is shown in pink, and the molecular surface is blue. White indicates the crossbonds that stabilize the peptide’s shape. Vikram Mulligan

    2

    Scientists at the University of Washington’s Institute for Protein Design have shown it is possible to create small, hyperstable peptides that could provide the basis for developing powerful new drugs and diagnostic tests.

    “These super stable peptides provide an ideal molecular scaffold on which it should be possible to design ‘on demand’ a new generation of peptide-based drugs,” said UW Medicine protein engineering pioneer David Baker, who oversaw the research project. He is a UW professor of biochemistry.

    David Baker
    David Baker

    In a study, which appears in the journal Nature, the researchers demonstrate that not only is it possible to design peptides that fold into a wide variety of different conformations, but also that it is possible to incorporate functional groups of chemicals not normally found in peptides.

    3
    Illustrations of designed peptides with different configurations of two structures: tightly wound ribbons and flat, arrow-shaped ribbons.

    Both of these abilities could give designers even greater flexibility to create drugs that act on their molecular targets with high precision. Such drugs should not only be more potent but would also be less likely to have harmful side effects.

    Most drugs work by binding to a key section of a protein in a way that alters how the protein functions, typically by stimulating or inhibiting the protein’s activity. For the binding to occur, the drug must fit into the target site on the protein as a key fits into a lock. How close the lock-and-key fit is can often determine how well the medication works.

    Currently, most prescription drugs are either made of small molecules or much larger proteins. Both classes of drugs have advantages and disadvantages.

    Small molecule drugs, for example, tend to be easy to manufacture, tend to have a long shelf life, and are often easily absorbed. But they often don’t fit the targeted “lock” as selectively as could be hoped. This imperfect fit can result in off-target binding and side-effects that diminish their effectiveness. Protein drugs, on the other hand, often fit their target receptors very well but they are difficult to manufacture, are more unstable, and lose their potency if they are not kept refrigerated. Because of their size and instability, they need to be injected into patients.

    Peptide drugs fall in between these two classes. They are small, so they have many of advantages of small molecule drugs. But they are made of a chain of amino acids, the same components that make up proteins, so they have the potential to achieve the precision of larger protein drugs.

    The power of some tiny peptides can be observed in venomous creatures. A number of poisonous insects and sea creatures produce small peptide toxins. Those are some of the most potent pharmacologically active compounds known. Their potency is among the reasons why medical scientists are interested in tapping into beneficial uses of peptides.

    In the new study, Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, senior fellows in the Baker lab, and their colleagues, developed computational methods that are now incorporated in the computer program called Rosetta.

    rosetta-screensaver
    rosettahome
    Rosetta@home, a project running on BOINC software from UC Berkeley
    BOINC WallPaper

    These methods are being used to design peptides ranging from 18 to 47 amino acids in length in 16 different conformations, called topologies.

    Originally developed by Baker and his earlier team, Rosetta uses advanced modelling algorithms to design new proteins by calculating the energies of the biochemical interactions within a protein, and between the protein and its surroundings. Because a protein will assume the shape in which the sum of these interaction energies is at its minimum, the program can calculate which shape a protein will most likely assume in nature.

    The peptides were made hyperstable by designing them to have interior crosslinking structures, called disulfide bonds, which staple together different sections of the peptide. Additional stabilization was secured by tying the two ends of the peptide chain together, a process called cyclization. The resulting constrained peptides were so stable that they were able to survive temperatures to 95 °C, nearly boiling. This survival feat would be impossible for antibody drugs.

    The researchers also showed that the design of these peptides could include amino acids not normally found in proteins. Amino acids have a property called handedness or chirality. Two amino acids can be made of the same atoms but have different arrangements, just as our hands have the same number of fingers but have two mirror-image configurations, right and left. This handedness keeps the right hand from fitting properly into a left-handed glove and vice versa.

    In nature, perhaps due to a chance event billions of years ago, amino acids in living cells are all left-handed. Right-handed amino acids are very rare in naturally occurring proteins. Nevetheless, the researchers were able to insert right-handed amino acids in their designed peptides.

    “Being able to include other types of amino acids allows us to create peptides with a much wider variety of conformations,” said Baker, “and being able to use right-handed amino acids essentially doubles your palette.”

    “By making it possible to create peptides that include ‘unnatural’ amino acids, this approach will allow researchers to explore peptide structures and function that have not been explored by nature through evolution,” Baker said.

    Today’s edition of Nature also has a special supplement, Insight The Protein World. Baker, Po-Ssu, and Scott E. Boyken authored the review article, The coming of age of de novo protein design.

    Also see coverage of the Nature hyperstable peptide design paper in Hutch News by the Fred Hutchinson Cancer Research Center.

    The National Institutes of Health provided partial support for this work through grants P50 AG005136, T32-H600035., GM094597, GM090205, and HHSN272201200025C. Additional funding was provided by The Three Dreamers.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
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