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    Full Steam Ahead: Revolutionizing Protein Design for Warfighters

    Triosephosphate Isomerase Barrel Blueprint

    Courtesy Photo | Triosephosphate isomerase barrel blueprint: The eight-fold symmetric TIM-barrel...... read more read more



    Courtesy Story

    Defense Threat Reduction Agency's Chemical and Biological Technologies Department

    Fort Belvoir, Va. - Similar to the steam engine revolutionizing the speed of manufacturing during the industrial revolution, new breakthroughs in computational protein design are revolutionizing warfighter countermeasures against chemical and biological threats. Proteins, composed of linear chains of amino acids, are miniature machines responsible for most critical functions in living organisms. The sequence of amino acids determines the shape of the protein, which is essential to carrying out its biological function.

    Of the possible patterns in protein molecules, only a fraction occur naturally, leaving room for scientists to fill functional gaps. This includes the production of an entire new class of materials patterned with atomic level accuracy that hold promise for support of warfighter needs.

    In a project managed by Dr. Ilya Elashvili from the Defense Threat Reduction Agency’s Joint Science and Technology Office, researchers in Dr. David Baker’s lab at the University of Washington have reported several major advances in the computational design and construction of new proteins from scratch that possess desired characteristics.

    Just as the manufacturing industry was revolutionized by creating interchangeable parts designed to precise specifications, modular proteins have the possibility to revolutionize the future of biotechnology. In a Nature article titled “Exploring the Repeat Protein Universe Through Computational Protein Design,” Dr. Baker’s team reported building a series of novel repeat proteins with a broad range of geometries that are comparable to structural beams in manufacturing. The team designed and built robust structures with sequences unrelated to known repeat proteins with atomic level accuracy that were highly stable both chemically and thermally.

    For example, in contrast to almost all native proteins, more than half (53 out of 83) of the designs were found to be monomeric proteins that were stable up to 95°C and four of the six designs tested did not denature at guanidine hydrochloride concentrations up to 7.5 mol/L. The ability to design computationally, highly stable proteins to precise specification is an enabling technology for rapid response to emergent military threat agents.

    Repeat proteins can form very large binding surfaces using only a short amino acid sequence that is repeated in tandem. The computer designed repeat sequence enables designers to make proteins that take on shapes which are straight, or twist with defined pitch, and even bend back on themselves to form nano-rings. Dr. Baker’s team, in collaboration with Dr. Philip Bradley’s group at the Fred Hutchinson Cancer Research Center, reported this in a Nature article titled “Rational Design of α-Helical Tandem Repeat Proteins with Closed Architectures.” These proteins open a wide variety of new possibilities for biomolecular engineering such as the ability to create new enzymes, organized catalytic complexes, protein materials and biosensors.

    In another article in eLIFE titled “Precise Assembly of Complex Beta Sheet Topologies from De Novo Designed Building Blocks,” the Baker researchers demonstrated successful design of larger beta sheet domains by recombining smaller independently folded beta sheet proteins. They demonstrated that protein topologies with six- and seven-stranded beta sheets can be designed by inserting a de novo, designed from scratch, beta sheet containing protein into another, so the two beta sheets are merged to form a single extended sheet.

    In addition to their robust design methods in made-to-specification repeat proteins and enlarging beta sheet domains, the Baker group also expanded their fundamental understanding of scaffolds used in biocatalysts. Baker lab postdoctoral fellow Po-Ssu Huang, together with Dr. Birte Höcker at the Max Planck Institute for Developmental Biology (Tübingen, Germany) turned their attention to the (beta/alpha)8 topology — commonly known as the triosephosphate isomerase barrel, or TIM-barrel fold, which is one of the most widely used enzyme folds in biology.

    Enzymes that adopt this fold are responsible for five of the six enzyme class reaction types. It has been considered one of the most important folds for designing novel catalysts. For nearly three decades, multiple attempts have been made to design the barrel fold, but none demonstrated success. The researchers were the first to achieve this goal, reported in the Nature Chemical Biology article titled “De Novo Design of a Four-Fold Symmetric TIM-Barrel Protein with Atomic-Level Accuracy.” The success of understanding TIM-barrel fold enables technologies for designing catalysts that can inactivate chemical agents which threaten warfighters in the battlefield. Particularly, many native TIM-barrel enzymes interact with phosphate-containing compounds, and this feature alone has significant implications in designing new proteins that can sense and breakdown organophosphate agents, such as the nerve agents sarin and VX.

    With this success, researchers now understand down to the residue level the roles of every amino acid in this designed scaffold; this designed protein is among one of the most well behaved TIM-barrels. This represents a new platform for designing future catalysts and biosensors for various small molecule chemical agents. Researchers anticipate extending this science to interact with proteinaceous agents through the various loops built on the barrel. This would essentially mimic antibodies, but with a larger footprint, having a significant impact in protecting warfighters from chemical and biological agents.

    The options for engineering brand new protein materials through modular construction with atomic level precision have been thrown open. In addition to repeat proteins and TIM-barrels, the Baker group has also reported the precision sculpting of smaller de novo designed folds made to order, never before seen in nature. This progress was reported in Proceedings of the National Academy of Sciences in a paper titled “Control Over Overall Shape and Size in De Novo Designed Proteins.”

    This paper further explains methods for systematically varying protein architecture inspired by nature controlling structural variation within the same fold. Finesse in protein design is needed to optimize designed proteins to take on exact shapes to perform specified functions. Baker graduate student Yu-Ru Lin, in collaboration with Dr. Nobuyasu Koga from the Institute for Molecular Science in Japan, led this research.

    Future applications of atomic level accurate protein de novo design strategies with control over fold shape, size, twist, length, surface features, loop locations and several other architectural features will enable the simultaneous design of robust protein sequences for form and function. These advances in biotechnology could revolutionize computationally designed high-affinity binding proteins, enzymes and protein-based nanomaterials that meet specific needs for the warfighter in chemical and biological defense.



    Date Taken: 03.30.2016
    Date Posted: 03.30.2016 15:17
    Story ID: 193902
    Location: FORT BELVOIR , VA, US 

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