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  • richardmitnick 10:12 am on April 17, 2019 Permalink | Reply
    Tags: , , , , , , , The Baker Lab,   

    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

    Susan Gregg
    UW Medicine

    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.

    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.


    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 9:21 am on May 25, 2017 Permalink | Reply
    Tags: "Unleashing the Power of Synthetic Proteins, , , , The Baker Lab,   

    From Nautilus: “Unleashing the Power of Synthetic Proteins” 



    March 2017
    David Baker, Baker Lab, U Washngton, BOINC Rosetta@home project

    Dr. David Baker

    Rosetta@home project

    The opportunities for the design of synthetic proteins are endless.

    Proteins are the workhorses of all living creatures, fulfilling the instructions of DNA. They occur in a wide variety of complex structures and carry out all the important functions in our body and in all living organisms—digesting food, building tissue, transporting oxygen through the bloodstream, dividing cells, firing neurons, and powering muscles. Remarkably, this versatility comes from different combinations, or sequences, of just 20 amino acid molecules. How these linear sequences fold up into complex structures is just now beginning to be well understood (see box).

    Even more remarkably, nature seems to have made use of only a tiny fraction of the potential protein structures available—and there are many. Therein lies an amazing set of opportunities to design novel proteins with unique structures: synthetic proteins that do not occur in nature, but are made from the same set of naturally-occurring amino acids. These synthetic proteins can be “manufactured” by harnessing the genetic machinery of living things, such as in bacteria given appropriate DNA that specify the desired amino acid sequence. The ability to create and explore such synthetic proteins with atomic level accuracy—which we have demonstrated—has the potential to unlock new areas of basic research and to create practical applications in a wide range of fields.

    The design process starts by envisioning a novel structure to solve a particular problem or accomplish a specific function, and then works backwards to identify possible amino acid sequences that can fold up to this structure. The Rosetta protein modelling and design software identifies the most likely candidates—those that fold to the lowest energy state for the desired structure. Those sequences then move from the computer to the lab, where the synthetic protein is created and tested—preferably in partnership with other research teams that bring domain expertise for the type of protein being created.

    At present no other advanced technology can beat the remarkable precision with which proteins carry out their unique and beautiful functions. The methods of protein design expand the reach of protein technology, because the possibilities to create new synthetic proteins are essentially unlimited. We illustrate that claim with some of the new proteins we have already developed using this design process, and with examples of the fundamental research challenges and areas of practical application that they exemplify:

    This image shows a designed synthetic protein of a type known as a TIM-barrel. Naturally occurring TIM-barrel proteins are found in a majority of enzymes, the catalysts that facilitate biochemical reactions in our bodies, in part because the circular cup-like or barrel shape at their core provides an appropriate space for the reaction to occur. The synthetic protein shown here has an idealized TIM-barrel template or blueprint that can be customized with pockets and binding sites and catalytic agents specific to particular reactants; the eight helical arms of the protein enhance the reaction space. This process can be used to design whole new classes of enzymes that do not occur in nature. Illustration and protein design prepared by Possu Huang in David Baker’s laboratory, University of Washington.

    Catalysts for clean energy and medicine. Protein enzymes are the most efficient catalysts known, far more so than any synthesized by inorganic chemists. Part of that efficiency comes from their ability to accurately position key parts of the enzyme in relation to reacting molecules, providing an environment that accelerates a reaction or lowers the energy needed for it to occur. Exactly how this occurs remains a fundamental problem which more experience with synthetic proteins may help to resolve.

    Already we have produced synthetic enzymes that catalyze potentially useful new metabolic pathways. These include: reactions that take carbon dioxide from the atmosphere and convert it into organic molecules, such as fuels, more efficiently than any inorganic catalyst, potentially enabling a carbon-neutral source of fuels; and reactions that address unsolved medical problems, including a potential oral therapeutic drug for patients with celiac disease that breaks down gluten in the stomach and other synthetic proteins to neutralize toxic amyloids found in Alzheimer’s disease.

    We have also begun to understand how to design, de novo, scaffolds that are the basis for entire superfamilies of known enzymes (Fig. 1) and other proteins known to bind the smaller molecules involved in basic biochemistry. This has opened the door for potential methods to degrade pollutants or toxins that threaten food safety.

    New super-strong materials. A potentially very useful new class of materials is that formed by hybrids of organic and inorganic matter. One naturally occurring example is abalone shell, which is made up of a combination of calcium carbonate bonded with proteins that results in a uniquely tough material. Apparently, other proteins involved in the process of forming the shell change the way in which the inorganic material precipitates onto the binding protein and also help organize the overall structure of the material. Synthetic proteins could potentially duplicate this process and expand this class of materials. Another class of materials are analogous to spider silk—organic materials that are both very strong and yet biodegradable—for which synthetic proteins might be uniquely suited, although how these are formed is not yet understood. We have also made synthetic proteins that create an interlocking pattern to form a surface only one molecule thick, which suggest possibilities for new anti-corrosion films or novel organic solar cells.

    Targeted therapeutic delivery. Self-assembling protein materials make a wide variety of containers or external barriers for living things, from protein shells for viruses to the exterior wall of virtually all living cells. We have developed a way to design and build similar containers: very small cage-like structures—protein nanoparticles—that self-assemble from one or two synthetic protein building blocks (Fig. 2). We do this extremely precisely, with control at the atomic level. Current work focuses on building these protein nanoparticles to carry a desired cargo—a drug or other therapeutic—inside the cage, while also incorporating other proteins of interest on their surface. The surface protein is chosen to bind to a similar protein on target cells.

    These self-assembling particles are a completely new way of delivering drugs to cells in a targeted fashion, avoiding harmful effects elsewhere in the body. Other nanoparticles might be designed to penetrate the blood-brain barrier, in order to deliver drugs or other therapies for brain diseases. We have also generated methods to design proteins that disrupt protein-protein interactions and proteins that bind to small molecules for use in biosensing applications, such as identifying pathogens. More fundamentally, synthetic proteins may well provide the tools that enable improved targeting of drugs and other therapies, as well as an improved ability to bond therapeutic packages tightly to a target cell wall.

    A tiny 20-sided protein nanoparticle that can deliver drugs or other therapies to specific cells in the body with minimal side effects. The nanoparticle self-assembles from two types of synthetic proteins. Illustration and protein design prepared by Jacob Bale in David Baker’s laboratory, University of Washington.

    Novel vaccines for viral diseases. In addition to drug delivery, self-assembling protein nanoparticles are a promising foundation for the design of vaccines. By displaying stabilized versions of viral proteins on the surfaces of designed nanoparticles, we hope to elicit strong and specific immune responses in cells to neutralize viruses like HIV and influenza. We are currently investigating the potential of these nanoparticles as vaccines against a number of viruses. The thermal stability of these designer vaccines should help eliminate the need for complicated cold chain storage systems, broadening global access to life saving vaccines and supporting goals for eradication of viral diseases. The ability to shape these designed vaccines with atomic level accuracy also enables a systematic study of how immune systems recognize and defend against pathogens. In turn, the findings will support development of tolerizing vaccines, which could train the immune system to stop attacking host tissues in autoimmune disease or over-reacting to allergens in asthma.

    New peptide medicines. Most approved drugs are either bulky proteins or small molecules. Naturally occurring peptides (amino acid compounds) that are constrained or stabilized so that they precisely complement their biological target are intermediate in size, and are among the most potent pharmacological compounds known. In effect, they have the advantages of both proteins and small molecule drugs. The antibiotic cyclosporine is a familiar example. Unfortunately such peptides are few in number.

    We have recently demonstrated a new computational design method that can generate two broad classes of peptides that have exceptional stability against heat or chemical degradation. These include peptides that can be genetically encoded (and can be produced by bacteria) as well as some that include amino acids that do not occur in nature. Such peptides are, in effect, scaffolds or design templates for creating whole new classes of peptide medicines.

    In addition, we have developed general methods for designing small and stable proteins that bind strongly to pathogenic proteins. One such designed protein binds the viral glycoprotein hemagglutinin, which is responsible for influenza entry into cells. These designed proteins protect infected mice in both a prophylactic and therapeutic manner and therefore are potentially very powerful anti-flu medicines. Similar methods are being applied to design therapeutic proteins against the Ebola virus and other targets that are relevant in cancer or autoimmune diseases. More fundamentally, synthetic proteins may be useful as test probes in working out the detailed molecular chemistry of the immune system.

    Protein logic systems. The brain is a very energy-efficient logic system based entirely on proteins. Might it be possible to build a logic system—a computer—from synthetic proteins that would self-assemble and be both cheaper and more efficient than silicon logic systems? Naturally occurring protein switches are well studied, but building synthetic switches remains an unsolved challenge. Quite apart from bio-technology applications, understanding protein logic systems may have more fundamental results, such as clarifying how our brains make decisions or initiate processes.

    The opportunities for the design of synthetic proteins are endless, with new research frontiers and a huge variety of practical applications to be explored. In effect, we have an emerging ability to design new molecules to solve specific problems—just as modern technology does outside the realm of biology. This could not be a more exciting time for protein design.

    Predicting Protein Structure

    If we were unable to predict the structure that results from a given sequence of amino acids, synthetic protein design would be an almost impossible task. There are 20 naturally-occurring amino acids, which can be linked in any order and can fold into an astronomical number of potential structures. Fortunately the structure prediction problem is now well on the way toward being solved by the Rosetta protein modeling software.

    The Rosetta tool evaluates possible structures, calculates their energy states, and identifies the lowest energy structure—usually, the one that occurs in a living organism. For smaller proteins, Rosetta predictions are already reasonably accurate. The power and accuracy of the Rosetta algorithms are steadily improving thanks to the work of a cooperative global network of several hundred protein scientists. New discoveries—such as identifying amino acid pairs that co-evolve in living systems and thus are likely to be co-located in protein structures—are also helping to improve prediction accuracy.

    Our research team has already revealed the structures for more than a thousand protein families, and we expect to be able to predict the structure for nearly any protein within a few years. This is an important achievement with direct significance for basic biology and biomedical science, since understanding structure leads to understanding the function of the myriad proteins found in the human body and in all living things. Moreover, predicting protein structure is also the critical enabling tool for designing novel, “synthetic” proteins that do not occur in nature.

    How to Create Synthetic Proteins that Solve Important Problems

    A graduate student in the Baker lab and a researcher at the Institute for Protein Design discuss a bacterial culture (in the Petri dish) that is producing synthetic proteins. Source: Laboratory of David Baker, University of Washington.

    Now that it is possible to design a variety of new proteins from scratch, it is imperative to identify the most pressing problems that need to be solved, and focus on designing the types of proteins that are needed to address these problems. Protein design researchers need to collaborate with experts in a wide variety of fields to take our work from initial protein design to the next stages of development. As the examples above suggest, those partners should include experts in industrial scale catalysis, fundamental materials science and materials processing, biomedical therapeutics and diagnostics, immunology and vaccine design, and both neural systems and computer logic. The partnerships should be sustained over multiple years in order to prioritize the most important problems and test successive potential solutions.

    A funding level of $100M over five years would propel protein design to the forefront of biomedical research, supporting multiple and parallel collaborations with experts worldwide to arrive at breakthroughs in medicine, energy, and technology, while also furthering a basic understanding of biological processes. Current funding is unable to meet the demands of this rapidly growing field and does not allow for the design and production of new proteins at an appropriate scale for testing and ultimately production, distribution, and implementation. Private philanthropy could overcome this deficit and allow us to jump ahead to the next generation of proteins—and thus to use the full capacity of the amino acid legacy that evolution has provided us.

    My BOINC

    See the full article here .

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  • richardmitnick 8:45 am on July 22, 2016 Permalink | Reply
    Tags: , , Proteins, , , The Baker Lab, This protein designer aims to revolutionize medicines and materials   

    From Science: “This protein designer aims to revolutionize medicines and materials” 



    David Baker shows off models of some of the unnatural proteins his team has designed and made.

    Jul. 21, 2016
    Robert F. Service

    David Baker appreciates nature’s masterpieces. “This is my favorite spot,” says the Seattle native, admiring the views from a terrace at the University of Washington (UW) here. To the south rises Mount Rainier, a 4400-meter glacier-draped volcano; to the west, the white-capped Olympic Mountain range.

    But head inside to his lab and it’s quickly apparent that the computational biochemist is far from satisfied with what nature offers, at least when it comes to molecules. On a low-slung coffee table lie eight toy-sized, 3D-printed replicas of proteins. Some resemble rings and balls, others tubes and cages—and none existed before Baker and his colleagues designed and built them. Over the last several years, with a big assist from the genomics and computer revolutions, Baker’s team has all but solved one of the biggest challenges in modern science: figuring out how long strings of amino acids fold up into the 3D proteins that form the working machinery of life. Now, he and colleagues have taken this ability and turned it around to design and then synthesize unnatural proteins intended to act as everything from medicines to materials.


    Already, this virtuoso proteinmaking has yielded an experimental HIV vaccine, novel proteins that aim to combat all strains of the influenza viruses simultaneously, carrier molecules that can ferry reprogrammed DNA into cells, and new enzymes that help microbes suck carbon dioxide out of the atmosphere and convert it into useful chemicals. Baker’s team and collaborators report making cages that assemble themselves from as many as 120 designer proteins, which could open the door to a new generation of molecular machines.

    f the ability to read and write DNA spawned the revolution of molecular biology, the ability to design novel proteins could transform just about everything else. “Nobody knows the implications,” because it has the potential to impact dozens of different disciplines, says John Moult, a protein-folding expert at the University of Maryland, College Park. “It’s going to be totally revolutionary.”

    Baker is by no means alone in this pursuit. Efforts to predict how proteins fold, and use that information to fashion novel versions, date back decades. But today he leads the charge. “David has really inspired the field,” says Guy Montelione, a protein structure expert at Rutgers University, New Brunswick, in New Jersey. “That’s what a great scientist does.”

    Baker, 53, didn’t start out with any such vision. Though both his parents were professors at UW—in physics and atmospheric sciences—Baker says he wasn’t drawn to science growing up. As an undergraduate at Harvard University, Baker tried studying philosophy and social studies. That was “a total waste of time,” he says now. “It was a lot of talk that didn’t necessarily add content.” Biology, where new insights can be tested and verified or discarded, drew him instead, and he pursued a Ph.D. in biochemistry. During a postdoc at the University of California, San Francisco, when he was studying how proteins move inside cells, Baker found himself captivated instead by the puzzle of how they fold. “I liked it because it’s getting at something fundamental.”

    In the early 1960s, biochemists at the U.S. National Institutes of Health (NIH) recognized that each protein folds itself into an intrinsic shape. Heat a protein in a solution and its 3D structure will generally unravel. But the NIH group noticed that the proteins they tested refold themselves as soon as they cool, implying that their structure stems from the interactions between different amino acids, rather than from some independent molecular folding machine inside cells. If researchers could determine the strength of all those interactions, they might be able to calculate how any amino acid sequence would assume its final shape. The protein-folding problem was born.

    From DNA to proteins

    The machinery for building proteins is essential for all life on earth. Click on the arrows at the bottom or swipe horizontally to learn more.

    One way around the problem is to determine protein structures experimentally, through methods such as x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. But that’s slow and expensive. Even today, the Protein Data Bank, an international repository, holds the structures of only roughly 110,000 proteins out of the hundreds of millions or more thought to exist.

    Knowing the 3D structures of those other proteins would offer biochemists vital insights into each molecule’s function, such as whether it serves to ferry ions across a cell membrane or catalyze a chemical reaction. It would also give chemists valuable clues to designing new medicines. So, instead of waiting for the experimentalists, computer modelers such as Baker have tackled the folding problem with computer models.

    They’ve come up with two broad kinds of folding models. So-called homology models compare the amino acid sequence of a target protein with that of a template—a protein with a similar sequence and a known 3D structure. The models adjust their prediction for the target’s shape based on the differences between its amino acid sequence and that of the template. But there’s a major drawback: There simply aren’t enough proteins with known structures to provide templates—despite costly efforts to perform industrial-scale x-ray crystallography and NMR spectroscopy.

    Templates were even scarcer more than 2 decades ago, when Baker accepted his first faculty position at UW. That prompted him to pursue a second path, known as ab initio modeling, which calculates the push and pull between neighboring amino acids to predict a structure. Baker also set up a biochemistry lab to study amino acid interactions, in order to improve his models.

    Early on, Baker and Kim Simons, one of his first students, created an ab initio folding program called Rosetta, which broke new ground by scanning a target protein for short amino acid stretches that typically fold in known patterns and using that information to help pin down the molecule’s overall 3D configuration. Rosetta required such extensive computations that Baker’s team quickly found themselves outgrowing their computer resources at UW.

    Seeking more computing power, they created a crowdsourcing extension called Rosetta@home, which allows people to contribute idle computer time to crunching the calculations needed to survey all the likely protein folds. Later, they added a video game extension called Foldit, allowing remote users to apply their instinctive protein-folding insights to guide Rosetta’s search. The approach has spawned an international community of more than 1 million users and nearly two dozen related software packages that do everything from designing novel proteins to predicting the way proteins interact with DNA.

    “The most brilliant thing David has done is build a community,” says Neil King, a former Baker postdoc, now an investigator at UW’s Institute for Protein Design (IPD). Some 400 active scientists continually update and improve the Rosetta software. The program is free for academics and nonprofit users, but there’s a $35,000 fee for companies. Proceeds are plowed back into research and an annual party called RosettaCon in Leavenworth, Washington, where attendees mix mountain hikes and scientific talks.

    Despite this success, Rosetta was limited. The software was often accurate at predicting structures for small proteins, fewer than 100 amino acids in length. Yet, like other ab initio programs, it struggled with larger proteins. Several years ago, Baker began to doubt that he or anyone else would ever manage to solve most protein structures. “I wasn’t sure whether I would get there.”

    Now, he says, “I don’t feel that way anymore.”

    What changed his outlook was a technique first proposed in the 1990s by computational biologist Chris Sander, then with the European Molecular Biology Laboratory in Heidelberg, Germany, and now with Harvard. Those were the early days of whole genome sequencing, when biologists were beginning to decipher the entire DNA sequences of microbes and other organisms. Sander and others wondered whether gene sequences could help identify pairs of amino acids that, although distant from each other on the unfolded proteins, have to wind up next to each other after the protein folds into its 3D structure.

    Clues from genome sequences

    Comparing the DNA of similar proteins from different organisms shows that certain pairs of amino acids evolve in tandem—when one changes, so does the other. This suggests they are neighbors in the folded protein, a clue for predicting structure.

    Sander reasoned that the juxtaposition of those amino acids must be crucial to a protein’s function. If a mutation occurs, changing one of the amino acids so that it no longer interacts with its partner, the protein might no longer work, and the organism could suffer or die. But if both neighboring amino acids are mutated at the same time, they might continue to interact, and the protein might work as well or even better.

    The upshot, Sander proposed, was that certain pairs of amino acids necessary to a protein’s structure would likely evolve together. And researchers would be able to read out that history by comparing the DNA sequences of genes from closely related proteins in different organisms. Whenever such DNA revealed pairs of amino acids that appeared to evolve in lockstep, it would suggest that they were close neighbors in the folded protein. Put enough of those constraints on amino acid positions into an ab initio computer model, and the program might be able to work out a protein’s full 3D structure.

    Unfortunately, Sander says, his idea “was a little ahead of its time.” In the 1990s, there weren’t enough high-quality DNA sequence data from enough similar proteins to track coevolving amino acids.

    By the early part of this decade, however, DNA sequences were flooding in thanks to new gene-sequencing technology. Sander had also teamed up with Debora Marks at Harvard Medical School in Boston to devise a statistical algorithm capable of teasing out real coevolving pairs from the false positives that plagued early efforts. In a 2011 article in PLOS ONE, Sander, Marks, and colleagues reported that the coevolution technique could constrain the position of dozens of pairs of amino acids in 15 proteins—each from a different structural family—and work out their structures. Since then, Sander and Marks have shown that they can decipher the structure of a wide variety of proteins for which there are no homology templates. “It has changed the protein-folding game,” Sander says.

    It certainly did so for Baker. When he and colleagues realized that scanning genomes offered new constraints for Rosetta’s ab initio calculations, they seized the opportunity. They were already incorporating constraints from NMR and other techniques. So they rushed to write a new software program, called Gremlin, to automatically compare gene sequences and come up with all the likely coevolving amino acid pairs. “It was a natural for us to put them into Rosetta,” Baker says.

    The results have been powerful. Rosetta was already widely considered the best ab initio model. Two years ago, Baker and colleagues used their combined approach for the first time in an international protein-folding competition, the 11th Critical Assessment of protein Structure Prediction (CASP). The contest asks modelers to compute the structures of a suite of proteins for which experimental structures are just being worked out by x-ray crystallography or NMR. After modelers submit their predictions, CASP’s organizers then reveal the actual experimental structures. One submission from Baker’s team, on a large protein known as T0806, came back nearly identical to the experimental structure. Moult, who heads CASP, says the judge who reviewed the predicted structure immediately fired off an email to him saying “either someone solved the protein-folding problem, or cheated.”

    “We didn’t [cheat],” Sergey Ovchinnikov, a grad student in Baker’s lab, says with a chuckle.

    The implications are profound. Five years ago, ab initio models had determined structures for just 56 proteins of the estimated 8000 protein families for which there is no template. Since then, Baker’s team alone has added 900 and counting, and Marks believes the approach will already work for 4700 families. With genome sequence data now pouring into scientific databases, it will likely only be a couple years before protein-folding models have enough coevolution data to solve structures for nearly any protein, Baker and Sander predict. Moult agrees. “I have been waiting 10 years for a breakthrough,” he says. “This seems to me a breakthrough.”

    For Baker, it’s only the beginning. With Rosetta’s steadily improving algorithms and ever-greater computing power, his team has in essence mastered the rules for folding—and they’ve begun to use that understanding to try to one-up nature’s creations. “Almost everything in biomedicine could be impacted by an ability to build better proteins,” says Harvard synthetic biologist George Church.

    Baker notes that for decades researchers pursued a strategy he refers to as “Neandertal protein design,” tweaking the genes for existing proteins to get them to do new things. “We were limited by what existed in nature. … We can now short-cut evolution and design proteins to solve modern-day problems.”

    Take medicines, such as drugs to combat the influenza virus. Flu viruses come in many strains that mutate rapidly, which makes it difficult to find molecules that can knock them all out. But every strain contains a protein called hemagglutinin that helps it invade host cells, and a portion of the molecule, known as the stem, remains similar across many strains. Earlier this year, Baker teamed up with researchers at the Scripps Research Institute in San Diego, California, and elsewhere to develop a novel protein that would bind to the hemagglutinin stem and thereby prevent the virus from invading cells.

    The effort required 80 rounds of designing the protein, engineering microbes to make it, testing it in the lab, and reworking the structure. But in the 4 February issue of PLOS ONE, the researchers reported that when they administered their final creation to mice and then injected them with a normally lethal dose of flu virus, the rodents were protected. “It’s more effective than 10 times the dose of Tamiflu,” an antiviral drug currently on the market, says Aaron Chevalier, a former Baker Ph.D. student who now works at a Seattle biotech company called Virvio here that is working to commercialize the protein as a universal antiflu drug.

    Another potential addition to the medicine cabinet: a designer protein that chops up gluten, the infamous substance in wheat and other grains that people with Celiac disease or gluten sensitivity have trouble digesting. Ingrid Swanson Pultz began crafting the gluten-breaker even before joining Baker’s lab as a postdoc and is now testing it in animals and working with IPD to commercialize the research. And those self-assembling cages that debut this week could one day be filled with drugs or therapeutic snippets of DNA or RNA that can be delivered to disease sites throughout the body.

    The potential of these unnatural proteins isn’t limited to medicines. Baker, King, and their colleagues have also attached up to 120 copies of a molecule called green fluorescent protein to the new cages, creating nano-lanterns that could aid research by lighting up as they move through tissues.

    Church says he believes that designer proteins might soon rewrite the biology inside cells. In a paper last year in eLife, he, Baker, and colleagues designed proteins to bind to either a hormone or a heart disease drug inside cells, and then regulate the activity of a DNA-cutting enzyme, Cas9, that is part of the popular CRISPR genome-editing system. “The ability to design sensors [inside cells] is going to be big,” Church says. The strategy could allow researchers or physicians to target the powerful gene-editing system to a specific set of cells—those that are responding to a hormone or drug. Biosensors could also make it possible to switch on the expression of specific genes as needed to break down toxins or alert the immune cells to invaders or cancer.

    Protein for every purpose

    The ability to predict how an amino acid sequence will fold—and hence how the protein will function—opens the way to designing novel proteins that can catalyze specific chemical reactions or act as medicines or materials. Genes for these proteins can be synthesized and inserted into microbes, which build the proteins.

    2D arrays can be used as nanomaterials in various applications.


    Information can be coded into protein sequences, like DNA.


    Antagonists bind to a target protein, blocking its activation.


    Channels through membranes act as gateways.


    Cages can contain medicinal cargo or carry it on their surfaces.


    Sensors travel throughout the body to detect various signals.


    Baker’s lab is abuzz with other projects. Last year, his group and collaborators reported engineering into bacteria a completely new metabolic pathway, complete with a designer protein that enabled the microbes to convert atmospheric carbon dioxide into fuels and chemicals. Two years ago, they unveiled in Science proteins that spontaneously arrange themselves in a flat layer, like interlocking tiles on a bathroom floor. Such surfaces may lead to novel types of solar cells and electronic devices.

    In perhaps the most thought-provoking project, Baker’s team has designed proteins to carry information, imitating the way DNA’s four nucleic acid letters bind and entwine in the genetic molecule’s famed double helix. For now, these protein helixes can’t convey genetic information that cells can read. But they symbolize something profound: Protein designers have shed nature’s constraints and are now only limited by their imagination. “We can now build a whole new world of functional proteins,” Baker says.

    See the full article here .


    Rosetta@home runs on software from Berkeley Open Infrastructure for Network Computing (BOINC).
    Visit the BOINC website, download and install the BOINC software, attach to the Rosetta@home project. It is that simple. The project will use the available cpu cycles of your computer, tablet or cell phone to “crunch” data for the Baker Lab.

    While you are at the BOINC website, check out some of the other really important projects running at universities and institutions all over the world. They could all use your help and would run simultaneously with no conflicts on your devices.


    BOINC WallPaper

    The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition

  • richardmitnick 8:43 pm on June 13, 2012 Permalink | Reply
    Tags: , , , , The Baker Lab, ,   

    From Berkeley Lab: “Berkeley Lab Scientists Help Define the Healthy Human Microbiome” 

    Berkeley Lab

    Computing, bioinformatics, and microbial ecology resources play key role in mapping our microbial make-up

    June 13, 2012
    Dan Krotz

    You’re outnumbered. There are ten times as many microbial cells in you as there are your own cells.

    The human microbiome—as scientists call the communities of microorganisms that inhabit your skin, mouth, gut, and other parts of your body by the trillions—plays a fundamental role in keeping you healthy. These communities are also thought to cause disease when they’re perturbed. But our microbiome’s exact function, good and bad, is poorly understood. That could change.

    The bacterium, Enterococcus faecalis, which lives in the human gut, is just one type of microbe studied in NIH’s Human Microbiome Project. (Courtesy: United States Department of Agriculture)

    A National Institutes of Health (NIH)-organized consortium that includes scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has for the first time mapped the normal microbial make-up of healthy humans. [Human Microbiome Project (HMP) is a United States National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (i.e. their microbial flora). Launched in 2008, it is a five-year project, best characterized as a feasibility study, and has a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects is to test if changes in the human microbiome are associated with human health or disease. This topic is currently not well-understood.]

    The research will help scientists understand how our microbiome carries out vital tasks such as supporting our immune system and helping us digest food. It’ll also shed light on our microbiome’s role in diseases such as ulcerative colitis, Crohn’s disease, and psoriasis, to name a few.”

    See the full article here.

    For those interested – and you should be interested – the Human Protein Folding Project (HPF2) at the Bonneau Lab, New York University, is a participant in the HMP project. HPF2 is a project in Public Distributed Computing under the aegis of the World Community Grid (WCG), running on software from the Berkeley Open Infrastructure for Network Computing (BOINC) and using the project products of the rosetta@home project from the Baker Lab, University of Washington.

    That is a pretty long sentence. What it means is, if you visit WCG, or BOINC, and download the BOINC agent software for Windows, Linux, or Mac, you can attach to the HPF2 project and process data for HMP. While you are at it, look around at WCG website, there are about a dozen very worthwhile projects all aimed at curing illnesses and solving fundamental problems for mankind. Also, at the BOINC website the are a vast variety of projects in Biology, Chemistry, Physics, Mathematics, and Astronomy.

    Here are some pretty pictures.

    So, you know, when you see graphics, these are serious guys. Give them (us) a look.

    My BOINC stats.

  • richardmitnick 9:32 am on December 6, 2011 Permalink | Reply
    Tags: , , , , The Baker Lab, ,   

    From the New York Times: “Computer Scientists May Have What It Takes to Help Cure Cancer” – Another Blown Opportunity to boost BOINC 

    December 5, 2011

    This is copyright protected, so just a couple of hints.
    “The war against cancer is increasingly moving into cyberspace. Computer scientists may have the best skills to fight cancer in the next decade — and they should be signing up in droves….An inspirational example is the Foldit game — developed by the computer scientist Zoran Popovic at the University of Washington.

    Very nice, great article, but, huge gap. No mention of the roots of Dr Popovic’s successful adventure.

    Dr Popovic worked with The Baker Laboratory, the locus of rosetta@home, a project which runs on BOINC software from UC Berkeley. Rosetta@home has currently 37,456 “users” on 60162 “hosts”. The project does currently 58 TeraFLOPS of data per 24 hour period.

    On the one hand, you can certainly visit the Foldit web site to participate. If, on the other hand, you are not fond of games, you can visit the BOINC web site, download and install the small piece of software, and attach to the Rosetta project. You will receive small packs of data called “work units” or “WU’s” to “crunch”. As each WU is finished, your computer will return the results and you will receive more work.

    Rosetta software is also used by World Community Grid (WCG) project Human Proteome Folding. This project is based at New York University in the Bonneau Laboratory


    At both the WCG and BOINC web sites you will find many other really exciting projects in which you may participate. All WCG projects run on the BOINC software, along with the many independent projects at the BOINC web site.

    Once you have installed the BOINC software and attached to your chosen projects, you can be as active or passive in this process as you wish. You can pretty much simply let the stuff happen in the background and pay it scant attention. However, each project has its own forum covering many topics, including the science involved and the operation of the software. You can also check to see how your are doing by signing on at BOINCstats.com

    There are currently 286,105 “users” (people) on 515,015 “hosts” (computers) in all of BOINC. Currently we are doing 5,337 TeraFLOPS of work in a 24 hour period. That’s over half a PetafLOP, which would put us somewhere around 14th or 15th on the TOP500 list of supercomputers in the world. Except, in that world, we don’t count. WCG currently has 94,007 users on 211,163 hosts. We are currently at 278 TeraFLOPS.

    BOINC software will run on Windows, Mac and Linux based computers. So, whatever your flavor, why don’t you visit BOINC and WCG, give us a look, and try us out? The BOINC process never interferes with anything else that you are doing on the computer. If on occasion you require huge amounts of resources, such as “storming the castle”, BOINC will instantaneously give up its resources and pause until your battle is finished. I hope to run into you in a forum.

    Mr. Patterson work is an example of why I started this blog.

  • richardmitnick 5:29 pm on November 25, 2011 Permalink | Reply
    Tags: , , , , , The Baker Lab, ,   

    From WCG Project Human Proteome Folding (HPF2) Exciting Updates 

    Human Proteome Folding (HPF2)., a WCG project in The Bonneau Lab at New York University has posted some very exciting news. The report is copyright protected, so I will not trespass on that.

    Depictions of proteins

    HPF2 utilizes software developed by BOINC project Rosetta@home, in the The Baker Lab at University of Washington.

    You can see the report here.

    But WCG crunchers can be proud of the fact that we have contributed – this from the WCG web site – 96,695 years, 223 days, 09 hours,26 minutes, 30 seconds to this effort. This is the power of Public Distributed Computing via the BOINC software on which our projects are run.

    I cannot begin to contemplate how this work would have gotten to this point without us, except at the expensive cost of processing time on some supercomputer.


    You, too, dear reader, can be a part of this incredible process. Visit either WCG or BOINC, download and install the software, and attach to this and other worthy projects at the WCG web site and also at the BOINC website. You financial cost is about the same as a 100-150 watt light bulb. Your personal satisfaction at being a part of this is immeasurable.

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