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  • richardmitnick 11:58 am on May 19, 2016 Permalink | Reply
    Tags: , Protein Studies,   

    From U Illinois: “Scientists discover the evolutionary link between protein structure and function” 

    U Illinois bloc

    University of Illinois

    May 18, 2016
    Lauren Quinn

    Heme protein showing loops in orange near the bottom

    Proteins are more than a dietary requirement. This diverse set of molecules powers nearly all of the cellular operations in a living organism. Scientists may know the structure of a protein or its function, but haven’t always been able to link the two.

    “The big problem in biology is the question of how a protein does what it does. We think the answer rests in protein evolution,” says University of Illinois professor and bioinformatician Gustavo Caetano-Anollés.

    Geologists have found remnants of life preserved in rock billions of years old. In some cases, preservation of microbes and tissues has been so good that microscopic cellular structures that were once associated with specific proteins, can be detected. This geological record gives scientists a hidden connection to the evolutionary history of protein structures over incredibly long time periods. But, until now, it hasn’t always been possible to link function with those structures to know how proteins were behaving in cells billions of years ago, compared with today.

    “For the first time, we have traced evolution onto a biological network,” Caetano-Anollés notes.

    Caetano-Anollés and graduate students Fayez Aziz and Kelsey Caetano-Anollés used networks to investigate the linkage between protein structure and molecular function. They built a timeline of protein structures spanning 3.8 billion years across the geological record, but needed a way to connect the structures with their functions. To do that, they looked at the genetic makeup of hundreds of organisms.

    “It turns out that there are little snippets in our genes that are incredibly conserved over time,” Caetano-Anollés says. “And not just in human genomes. When we look at higher organisms, such as plants, fungi and animals, as well as bacteria, archaea, and viruses, the same snippets are always there. We see them over and over again.”

    The research team found that these tiny gene segments tell proteins to produce “loops,” which are the tiniest structural units in a protein. When loops come together, they create active sites, or molecular pockets, which give proteins their function. For example, hemoglobin, the protein that carries oxygen in blood, has two loops which create the active site that binds oxygen. The loops combine to create larger protein structures called domains.

    Remarkably, the new study shows that loops have been repeatedly recruited to perform new functions and that the process has been active and ongoing since the beginning of life.

    “This recruitment is important for understanding biological diversity,” Caetano-Anollés says.

    One important aspect of the study relates to the actual linkage between domain structure and functional loops. The researchers found that this linkage is characterized by an unanticipated property that unfolds in time, an “emergent” property known as hierarchical modularity.

    “Loops are cohesive modules, as are domains, proteins, cells, organs, and bodies.” Caetano-Anollés explains. “We are all made of cohesive modules, including our human bodies. That’s hierarchical modularity: the building of small cohesive parts into larger and increasingly complex wholes.”

    Hierarchical modularity also exists in manmade networks, such as the internet. For example, each router represents a “node” that pushes information to different computers. When millions of computers interact with each other online, larger and more complex entities emerge. Caetano-Anollés suggests that the evolution of manmade networks could be mapped in the same way as the evolution of biological networks.

    “From a computer science point of view, few people have been exploring how to track networks in time. Imagine exploring how the internet grows and changes when new routers are added, are disconnected, or network with each other. It’s a daunting task because there are millions of routers to track and internet communication can be highly dynamic. In our study, we are showcasing how you can do it with a very small network,” Caetano-Anollés explains.

    The methods developed by Caetano-Anollés and his team now have the potential to explain how change is capable of structuring systems as varied as the internet, social networks, or the collective of all proteins in an organism.

    The article, The early history and emergence of molecular functions and modular scale-free network behavior, is published in Scientific Reports. M. Fayez Aziz and Kelsey Caetano-Anollés, also from the University of Illinois, co-authored the report. Full text of the article can be found at: http://www.nature.com/articles/srep25058.

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    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

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  • richardmitnick 4:46 pm on January 25, 2016 Permalink | Reply
    Tags: , Crouching Protein Hidden Enzyme, Protein Studies,   

    From Scripps: “Crouching Protein, Hidden Enzyme” 

    Scripps Research Institute

    January 25, 2016
    Office of Communications
    Tel: 858-784-2666
    Fax: 858-784-8136

    The new research shows the workings of a crucial molecular enzyme. In this image, the green glow in the structure denotes the location of the Rpn11 enzymatic active site in its inhibited conformation at the heart of the isolated lid complex.

    A new study led by scientists at The Scripps Research Institute (TSRI) and the University of California (UC), Berkeley shows how a crucial molecular enzyme starts in a tucked-in somersault position and flips out when it encounters the right target.

    The new findings, published recently in the journal eLife, give scientists a clearer picture of the process through which cells eliminate proteins that promote diseases such as cancer and Alzheimer’s.

    “Having an atomic-resolution structure and a better understanding of this mechanism gives us the ability to someday design therapeutics to combat cancer and neurodegeneration,” said TSRI biologist Gabriel Lander, who was co-senior of author of the study with Andreas Martin of UC Berkeley.

    Keeping Cells Healthy

    The new study sheds light on the proteasome, a molecular machine that serves as a recycling center in cells. Proteasomes break down spent or damaged proteins and can even eliminate harmful misfolded proteins observed in many diseases.

    The new research is the first study in almost 20 years to solve a large component of the proteasome at near-atomic resolution. Lander said the breakthrough was possible with recent advances in cryo-electron microscopy (EM), an imaging technique in which a sample is bombarded with an electron beam, producing hundreds of thousands of protein images that can be consolidated into a high-resolution structure.

    Using cryo-EM, scientists investigated part of the proteasome that contains a deubiquitinase enzyme called Rpn11. Rpn11 performs a crucial function called deubiquitination, during which it cleaves molecular tags from proteins scheduled for recycling in the proteasome. This is a key step in proteasomal processing—without Rpn11, the protein tags would clog the proteasome and the cell would die.

    From previous studies, scientists knew Rpn11 and its surrounding proteins latch onto the proteasome to form a sort of lid. “The lid complex wraps around the proteasome like a face-hugger in the movie ‘Alien,’” said Lander.

    The lid complex can also exist separately from the proteasome—which poses a potential problem. If Rpn11 cleaves tags from proteins that haven’t gotten to the proteasome yet, those proteins could skip the recycling stage and cause disease. Scientists had wondered how nature had solved this problem.

    A Guide for Future Therapies

    The study provides an answer, showing the lid complex as it floats freely in cells. In this conformation, Rpn11 is carefully nestled in the crook of surrounding proteins, stabilized and inactive.

    “There’s a sophisticated network of interactions that pin the Rpn11 deubiquitinase against neighboring subunits to keep it inhibited in the isolated proteasome lid,” explained Corey M. Dambacher, a researcher at TSRI at the time of the study and now a senior scientist at Omniome, Inc., who was first author of the study with TSRI Research Associate Mark Herzik Jr. and Evan J. Worden of UC Berkeley.

    “In order for Rpn11 to perform its job, it has to flip out of this inhibited conformation,” said Herzik.

    The new study also shows that, to flip out of the conformation at the proteasome, the proteins surrounding deubiquitinase pivot and rotate—binding to the proteasome and releasing the deubiquitinase active site from its nook.

    Lander called the system “finely tuned,” but said there may be ways to manipulate it. The study collaborators at UC Berkeley made small mutations to the proteins holding Rpn11 in position, and found that any small change will release the deubiquitinase, even when the lid is floating freely.

    Lander said the new understanding of the mechanism that activates Rpn11 could guide future therapies that remove damaged or misfolded proteins.

    “Accumulation of these toxic proteins can lead to diseases such as Parkinson’s and Alzheimer’s, as well as a variety of cancers,” Lander said. “If we can harness the proteasome’s ability to remove specific proteins from the cell, this gives us incredible power over cellular function and improves our ability to target certain cells for destruction.”

    Going forward, the researchers hope to use the same cryo-EM techniques to investigate other components of the proteasome—and figure out exactly how it recognizes and destroys proteins. “There’s still a lot to learn,” said Lander.

    For more information on the study, “Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition,” see http://elifesciences.org/content/early/2016/01/08/eLife.13027

    This research was supported by the Damon Runyon Cancer Research Foundation (grant DFS-#07-13), the Pew Scholars program, the National Institutes of Health (grants DP2 EB020402 and R01-GM094497), the Searle Scholars Program, the National Science Foundation CAREER Program (grant NSF-MCB-1150288), the Howard Hughes Medical Institute and a National Science Foundation Graduate Research Fellowship.

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

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

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

  • richardmitnick 4:49 pm on January 20, 2016 Permalink | Reply
    Tags: , , Protein Studies,   

    From Science Node: “Solving a protein puzzle” 

    Science Node bloc
    Science Node

    20 Jan, 2016
    Greg Moore

    Temp 1
    Stacking up the proteins. After decades of attempts, scientists finally succeeded in unraveling the TIM-barel protein. Here is a graphic depiction of how their simulations fared against the Astral SCOPe 2.04 database. Courtesy Po-Ssu Huang.

    Computational models open up new possibilities for designing proteins for targeted disease treatment. Using the Open Science Grid (OSG), Baker Lab researchers at the University of Washington have simulated a protein that has stymied scientists for the last 25 years, and have opened the way for a new generation of custom-designed enzymes.

    The cylindrical TIM-barrel (triosephosphate isomerase-barrel) protein occurs widely in enzymes and is an attractive goal for research. But ever since it was first targeted in a European Molecular Biology Organization workshop on protein design in 1987, modeling this structure has been an elusive goal. Even the shortest TIM-barrel structure is highly complex.

    Now, thanks to OSG resources, the Baker Lab has generated large numbers of TIM-barrel structures as starting points for enzyme design calculations. Published in Nature Chemical Biology, their results will aid de novo design of custom-made catalysts or binders without the need to negotiate the structural complexity of naturally occurring proteins.

    To scale up simulations for the TIM-barrel computational model, the research team used the OSG, which is supported by the US National Science Foundation and the US Department of Energy’s Office of Science.

    “The massive computing power of the OSG allowed us to quickly get answers,” says Po-Ssu Huang, one of the lead researchers on the paper and a research scientist at the Baker Lab. In the past year, the researchers used an average of 46,000 core OSG hours per week — a total of around 2.4 million core hours.

    “Baker Lab has its own local HTCondor submit host that is connected to the OSG virtual organization HTCondor infrastructure,” says Mats Rynge, a computer scientist at the Information Sciences Institute of the University of Southern California and a member of the OSG User Support team. “Jobs submitted on the host are automatically scheduled onto available resources across the OSG.”

    Temp 2
    Stability comparisons. Strands are sequentially colored from blue to red, and for the orange layer configurations, side chain packing is shown with space-fill spheres. The stabilities of the six different variants correlate strongly with the configurations in the hydrophobic packing layer. Courtesy Po-Ssu Huang.

    The benefit of this setup (submit locally, compute globally) is that a group can maintain their local host – and still manage users, access, and upgrades – but not have to worry about maintaining the entire OSG computing infrastructure.

    “What we do involves computational algorithms, but at the same time everything we design is actually tested here in the lab. We take virtual simulations to practical applications — turning these molecules into new functional molecules for the real world,” says Huang. “The TIM-barrel computational model is an example of taking what we learn to build new proteins for other applications.”

    Applications include disease sensors and drug detectors using proteins as binders for small molecules.

    “The Holy Grail here is to understand enough to build new things,” Huang says. “This breakthrough has implications for neuroscience, industrial applications, biotech, enzymes for drug delivery, vaccines for HIV, and proteins that can inhibit Ebola. It’s just a huge field. This is where computer simulation comes in, and the faster the better. The OSG definitely fits the need.”

    See the full article here .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

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  • richardmitnick 5:22 pm on December 11, 2015 Permalink | Reply
    Tags: , Protein Studies,   

    From Stanford: “Stanford engineers invent process to accelerate protein evolution” 

    Stanford University Name
    Stanford University

    December 7, 2015
    Ramin Skibba

    An overview of the directed evolution process using the new Stanford technique: preparing protein libraries, screening them, extracting desired cells, and then inferring their DNA sequence.
    Cochran Lab

    All living things require proteins, members of a vast family of molecules that nature “makes to order” according to the blueprints in DNA.

    Through the natural process of evolution, DNA mutations generate new or more effective proteins. Humans have found so many alternative uses for these molecules – as foods, industrial enzymes, anti-cancer drugs – that scientists are eager to better understand how to engineer protein variants designed for specific uses.

    Now Stanford engineers have invented a technique to dramatically accelerate protein evolution for this purpose. This technology, described in Nature Chemical Biology, allows researchers to test millions of variants of a given protein, choose the best for some task and determine the DNA sequence that creates this variant.

    “Evolution, the survival of the fittest, takes place over a span of thousands of years, but we can now direct proteins to evolve in hours or days,” said Jennifer Cochran, an associate professor of bioengineering who co-authored the paper with Thomas Baer, executive director of the Stanford Photonics Research Center.

    “This is a practical, versatile system with broad applications that researchers will find easy to use,” Baer said.

    By combining Cochran’s protein engineering know-how with Baer’s expertise in laser-based instrumentation, the team created a tool that can test millions of protein variants in a matter of hours.

    “The demonstrations are impressive and I look forward to seeing this technology more widely adopted,” said Frances Arnold, a professor of chemical engineering at Caltech who was not affiliated with the study.

    Making a million mutants

    The researchers call their tool µSCALE, or Single Cell Analysis and Laser Extraction.

    The “µ” stands for the microcapillary glass slide that holds the protein samples. The slide is roughly the size and thickness of a penny, yet in that space a million capillary tubes are arrayed like straws, open on the top and bottom.

    The microcapillary glass slide, roughly the size and thickness of a penny, holds the protein samples. Courtesy Cochran Lab

    The power of µSCALE is how it enables researchers to build upon current biochemical techniques to run a million protein experiments simultaneously, then extract and further analyze the most promising results.

    The researchers first employ a process termed “mutagenesis” to create random variations in a specific gene. These mutations are inserted into batches of yeast or bacterial cells, which express the altered gene and produce millions of random protein variants.

    A µSCALE user mixes millions of tiny opaque glass beads into a sample containing millions of yeast or bacteria and spreads the mixture on a microcapillary slide. Tiny amounts of fluid trickle into each tube, carrying individual cells. Surface tension traps the liquid and the cell in each capillary.

    The slide bearing these million yeast or bacteria, and the protein variants they produce, is inserted into the µSCALE device. A software-controlled microscope peers into each capillary and takes images of the biochemical reaction occurring therein.

    Once a µSCALE user identifies a capillary of interest, the researcher can direct the laser to extract the contents of that tube without disrupting its neighbors, using an ingenious method devised by Baer.

    “The beads are what enable extraction,” Baer said. “The laser supplies energy to move the beads, which breaks the surface tension and releases the sample from the capillary.”

    Thus µSCALE empties the contents of a single capillary onto a collector plate, where the DNA of the isolated cell can be sequenced and the gene variant responsible for the protein of interest can be identified.

    “One of the unique features of µSCALE is that it allows researchers to rapidly isolate a single desired cell from hundreds of thousands of other cells,” said Bob Chen, a doctoral student in Cochran’s lab who wrote the software to examine and detect signs of interesting protein activity within the test tubes.

    Promising variants can be collected and reprocessed through µSCALE to further evolve and optimize the protein.

    “This is an exciting new tool to answer important questions about proteins,” Cochran said, likening µSCALE to the way that high-throughput tools for gene analysis have allowed researchers to unlock key features of biology underlying human disease.

    Genesis and proofs

    The project began five years ago when Baer and collaborator Ivan Dimov developed the first instrument. They showed how to identify cell types in a microcapillary array and extract a single capillary’s contents using glass beads and a focused laser.

    About three years ago, Cochran and Baer joined forces to develop µSCALE for protein engineering, and the team devised three experiments to showcase µSCALE’s utility and flexibility.

    In one experiment, researchers sifted through a protein library produced in yeast cells to select antibodies that bound most tightly to a cancer target. Antibodies with a high target-binding affinity are known to be effective against cancer.

    In a second example, they engineered a bright orange fluorescent protein biosensor. Using µSCALE, they did this almost 10 times faster than previous methods. Such biosensors are often used as tags in a wide variety of biology experiments.

    A third experiment, carried out with Stanford biochemistry Professor Daniel Herschlag, used µSCALE to improve upon a model enzyme.

    “This system will allow us to explore the evolutionary and functional relationships between enzymes, guiding the engineering of new enzymes that can carry out novel beneficial reactions,” Herschlag said.

    The Stanford team included graduate students Sungwon Lim and Arvind Kannan, postdoctoral scholar Spencer Alford and researcher Fanny Sunden.

    Support for this work included a Wallace H. Coulter Translational Partnership Award, which made this pioneering interdisciplinary research possible.
    Media Contact

    Tom Abate, Stanford Engineering: (650) 736-2245, tabate@stanford.edu

    Bjorn Carey, Stanford News Service: (650) 725-1944, bccarey@stanford.edu

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  • richardmitnick 10:29 am on November 26, 2015 Permalink | Reply
    Tags: , Protein Studies,   

    From TUM: “The “dark matter” in the protein universe” 

    Techniche Universitat Munchen

    Techniche Universitat Munchen

    Dr. Andrea Schafferhans
    Technical University of Munich
    Chair of Bioinformatics, Prof. Burkhard Rost
    Tel.: +49 289 17833

    Scientists try to reveal the structures of the dark proteome. (Picture: Schafferhans / Aquaria)

    Whether in the form of antibodies, enzymes or carriers: proteins play a crucial role in biology. While researchers have been able to at least partially determine the three-dimensional structure of many proteins, the structures of many other protein building blocks and even entire protein molecules remain as yet unknown. These “dark proteins” could be the key to understanding diseases. Using bioinformatics methods, an international team of scientists including researchers from the Technical University of Munich (TUM) has come one step closer to unveiling the mystery that surrounds the dark proteome. Protein research and biomedicine are two of TUM’s core research areas.

    Fifteen percent of the mass of an average human: that is the overall amount of all proteins, also known as the proteome. The protein molecules perform essential functions in the body and cells. They initiate metabolic processes, help the organism ward off diseases and ensure that vital biological substances are transported.

    The function of these proteins is significantly determined by their three-dimensional structure. Yet there are also proteins that either completely or at least partially differ from the structure that has so far been elucidated by scientific experiments. As a result, their structure cannot be modeled. Researchers refer to these proteins and protein building blocks as “dark proteins” and collectively as the “dark proteome”, in analogy to the dark matter found in outer space. Up until now, scientists still did not know how many of these proteins form part of the dark proteome.

    Half of the proteome is dark

    Together with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Sydney and the University of Lisbon, Dr. Andrea Schafferhans from the Chair of Bioinformatics at TUM studied the properties of the dark proteome. They did so by filtering out pieces of information from various databases, linking them with each other and evaluating the data.

    The “Aquaria” database, a joint project organized by CSIRO and TUM, played an important role in this process. The website went live in early 2015 and allows all researchers to have the 3D structure of protein sequences computed. The database does this by referring to existing structures and using that information to create a probable model for the new structure. This website helps researchers determine which protein structures are in fact “dark”.

    The result: Half of the proteome of all living beings whose cells have a nucleus – and that includes humans – is part of the dark proteome. “And again half of that has structures that remain completely unidentified,” says Schafferhans.

    Few relatives, hardly any interactions with other proteins

    Furthermore, the researchers were able to identify the following properties of dark proteins: Most dark proteins are short, rarely interact with other proteins, are frequently excreted and only have a small number of evolutionary relatives.

    The scientists also found out that some of the assumptions previously held about dark proteins are in fact wrong. The majority of them are not disordered proteins, for example. The latter only adopt their actual structure once they perform a function. The remainer of the time they aopt varying shapes. Moreover, the majority of dark proteins are not transmembrane proteins, i.e. proteins located inside a membrane that separates cell components or entire cells from each other. Up until now, these two assumptions were believed to explain why the structure of dark proteins is so hard to identify.

    With their findings, which were published in the specialist journal Proceedings of the National Academy of Sciences, the researchers have laid important groundwork that will help scientists better analyze these mysterious protein molecules in the future.

    The researchers also hope to draw more attention to the dark proteome, because it could contain proteins that play a key role in human health.

    Medical protein research at TUM

    Biomedicine is a key research area at TUM, which consequently combines basic and applied research. As part of this concept, the following new research facilities were set up: the TUM Center for Functional Protein Assemblies (CPA), the Bavarian Nuclear Magnetic Resonance Center, the Central Institute for Translational Cancer Research of the Tech­nical University of Munich (TranslaTUM) and the Klaus Tschira Foundation’s Research Center for Multiple Sclerosis. As an integrative research center, TUM’s MUNICH SCHOOL OF BIOENGINEERING forms a joint learning and research platform for all pertinent activities carried out in medically relevant fields of engineering in the various faculties, including imaging technologies. TUM is also a major stakeholder in the Center for Integrated Protein Science Munich (CIPSM) cluster of excellence.

    Nelson Perdigãoa et al.: Unexpected features of the dark proteome. Proceedings of the National Academy of Sciences (2015). DOI: 10.1073/pnas.1508380112

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    Techniche Universitat Munchin Campus

    Technische Universität München (TUM) is one of Europe’s top universities. It is committed to excellence in research and teaching, interdisciplinary education and the active promotion of promising young scientists. The university also forges strong links with companies and scientific institutions across the world. TUM was one of the first universities in Germany to be named a University of Excellence. Moreover, TUM regularly ranks among the best European universities in international rankings.

  • richardmitnick 4:07 pm on November 24, 2015 Permalink | Reply
    Tags: , , Protein Studies   

    From ORNL: “New supercomputer simulations enhance understanding of protein motion and function” 


    Oak Ridge National Laboratory

    November 23, 2015
    Morgan McCorkle, Communications
    mccorkleml@ornl.gov, 865.574.7308

    Miki Nolin

    Illustration of the structure of a phosphoglycerate kinase protein that was subjected to molecular dynamics simulations. The relative motions of the red and blue domains of the proteins are highly complex, and can be described in terms of motion of a configurational point on a rough energy landscape (illustrated). The transitions of the structure between energy minima on the landscape can be described in terms of a network (illustrated), which is found to be fractal (self-similar) on every timescale. Image credit: Thomas Splettstoesser; http://www.scistyle.com

    Supercomputing simulations at the Department of Energy’s Oak Ridge National Laboratory could change how researchers understand the internal motions of proteins that play functional, structural and regulatory roles in all living organisms. The team’s results are featured in Nature Physics.

    “Proteins have never been seen this way before,” said coauthor Jeremy Smith, director of ORNL’s Center for Molecular Biophysics and a Governor’s Chair at the University of Tennessee (UT). “We used considerable computer power to provide a unified conceptual picture of the motions in proteins over a huge range of timescales, from the very shortest lengths of time at which atoms move (picoseconds) right up to the lifetimes of proteins in cells (roughly 1000 seconds). It changes what we think a protein fundamentally is.”

    Studying proteins—their structure and function—is essential to advancing understanding of biological systems relevant to different energy and medical sciences, from bioenergy research and subsurface biogeochemistry to drug design.

    Results obtained by Smith’s UT graduate student, Xiaohu Hu, revealed that the dynamics of single protein molecules are “self-similar” and out of equilibrium over an enormous range of timescales.

    With the help of Titan— the fastest supercomputer in the U.S., located at the DOE Office of Science’s Oak Ridge Leadership Computing Facility—Smith’s team developed a complete picture of protein dynamics, revealing that the structural fluctuations within any two identical protein molecules, even if coded from the same gene, turn out to be different.


    “A gene is a code for a protein, producing different copies of the protein that should be the same, but the internal fluctuations of these individual protein molecules may never reach equilibrium, or converge,” Smith said. “This is because the fluctuations themselves are continually aging and don’t have enough time to settle down before the protein molecules are eaten up in the cell and replaced.”

    Understanding the out-of-equilibrium phenomenon has biological implications because the function of a protein depends on its motions. Two individual protein molecules, even though they come from the same gene, will not function precisely the same way within the cell.

    “You may have, for example, two identical enzyme molecules that catalyze the same reaction,” said Smith. “But due to the absence of equilibrium, the rate at which the catalysis happens will be slightly different for the two proteins. This affects the biological function of the protein.”

    The team also discovered that the dynamics of single protein molecules are self-similar, or fractal over the whole range of timescales. In other words, the motions in a single protein molecule look the same however long you look at them for, from picoseconds to hundreds of seconds.

    “The motions in a protein, how the bits of the protein wiggle and jiggle relative to each other, resemble one another on all these timescales,” Smith said. “We represent the shape of a protein as a point. If it changes its shape due to motions, it goes to a different point, and so on. We joined these points, drawing pictures, and we found that these pictures are the same when you look at them on whatever timescale, whether it’s nanoseconds, microseconds, or milliseconds.”

    By building a more complete picture of protein dynamics, the team’s research reveals that motions of a single protein molecule on very fast timescales resemble those that govern the protein’s function.

    To complete all of the simulations, the team combined the power of Titan with two other supercomputers—Anton, a specialty parallel computer built by D.E. Shaw Research, and Hopper, the National Energy Research Scientific Computing Center’s Cray XE6 supercomputer located at Lawrence Berkeley National Laboratory.



    “Titan was especially useful for us to get accurate statistics,” Smith said. “It allowed us to do a lot of simulations in order to reduce the errors and get more confident results.”

    The title of the Nature Physics paper is The Dynamics of Single Protein Molecules is Non-Equilibrium and Self-Similar Over Thirteen Decades in Timehttp://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys3553.html

    This research was supported by the DOE Office of Science through an Advanced Scientific Computing Research (ASCR) Leadership Computing Challenge (ALCC) allocation and funded in part by a DOE Experimental Program to Stimulate Competitive Research (EPSCoR) award. The Oak Ridge Leadership Computing Facility and National Energy Research Scientific Computing Center are DOE Office of Science User Facilities.

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    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.


  • richardmitnick 8:57 am on October 16, 2015 Permalink | Reply
    Tags: , , Protein Studies,   

    From U Illinois: “COMPASS method points researchers to protein structures” 

    U Illinois bloc

    University of Illinois

    Oct 9, 2015
    Liz Ahlberg

    Graduate student Joseph Courtney and chemistry professor Chad Rienstra developed a method to quickly and reliably determine a protein’s intricately folded structure. Photo by L. Brian Stauffer

    Searching for the precise, complexly folded three-dimensional structure of a protein can be like hacking through a jungle without a map: a long, intensive process with uncertain direction. University of Illinois researchers developed a new approach, dubbed COMPASS, that points directly to a protein’s likely structure using a combination of advanced molecular spectroscopy techniques, predictive protein-folding algorithms and image recognition software.

    Led by U. of I. chemistry professor Chad Rienstra, the team published its results in the journal Structure.

    “We’ve taken a process that would take months and brought it down to hours,” said Joseph Courtney, an Illinois graduate student and first author of the paper. “We expect this to not only accelerate the rate at which we can study proteins, but also increase its repeatability and the reliability of the results.”

    Proteins carry out functions within the cell, and those functions are determined by the proteins’ precise structures – the way they fold and twist into an intricate three-dimensional shape.

    “Many diseases are caused by a protein that’s not acting correctly, or there is too much of it. If you can understand what the proteins look like, you can study how they work, and you can help design drugs and treatments for those diseases,” Courtney said. “A major benefit is that if you can design a drug to perfectly fit a single protein, that cuts down on side effects, because it won’t interact with other molecules.”

    One key method for determining a protein’s share is a technique called X-ray crystallography. However, many medically interesting proteins – for example, the fibrils that characterize Parkinson’s disease – do not form crystals, so researchers have turned to more advanced spectroscopic techniques. Those techniques require months to years of intensive data collection and analysis, taking numerous readings and measurements of the protein’s spectrum.

    The Illinois team saw an opportunity to take advantage of recent advances in structure prediction algorithms, computational models that generate numerous possible ways a protein could fold based on its sequence.

    “The major shortcoming of those modeling approaches is that they never know if they’re right,” Rienstra said. “It’s great to have models, but it still leaves thousands of possibilities. We need some type of experimental data to determine which is the right one.”

    For COMPASS, the researchers rely on a single spectrum measurement using a spectroscopic technique called nuclear magnetic resonance, which gives a molecular “fingerprint” – no two protein structures have the same spectrum.

    The COMPASS platform looks at the possible structures generated by the predictive models, projects a spectrum for each one, and uses advanced image-recognition software to compare each projected spectrum with the spectrum collected from the experimental sample.

    “We call it COMPASS because we’re using a magnetic field to hopefully point us in the right direction of which protein structure is the right one out of all these options,“ Rienstra said.

    The researchers compared COMPASS results of 15 proteins to the structure information determined from traditional methods, and found that COMPASS was successful in correctly determining the proteins’ structures.

    The researchers hope that other chemists will adopt the COMPASS method. One advantage, Rienstra said, is that a chemist does not have to be an expert to use COMPASS, as the results from the algorithms are automatic, objective and repeatable.

    Rienstra’s group plans to use COMPASS in biomedical applications, hoping to study proteins that have thus far eluded researchers because of structural complexity and scarcity of samples.

    “We already have collaborators sending us samples to compare,” Rienstra said. “We’re working to compare the samples of a protein from Parkinson’s disease patients with the sample we study in the lab, to see if it’s the same in their brains as it is when we make it in the lab. That’s a very important question to address. The samples are very small and the signals are weak, but we can get one spectrum and see if the structures match. This would be impossible with traditional approaches because we would need brain samples a hundred times larger, and you just can’t do that with human patients.”

    “The normal bottleneck of collecting and analyzing the data is now completely gone,” Courtney said. “What would be an entire thesis project for a graduate student can now be reduced to a day. And as the prediction algorithms get better, COMPASS will be able to take advantage of those advances to help find even more difficult protein structures.”

    The National Institutes of Health supported this work.

    See the full article here .

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    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 1:48 pm on October 15, 2015 Permalink | Reply
    Tags: , , Protein Studies,   

    From TUM: “New field of application for versatile helper” 

    Techniche Universitat Munchen

    Techniche Universitat Munchen

    Prof. Dr. Bernd Reif
    Technical University of Munich
    Solid State NMR Spektroscopy
    Lichtenbergstr 4, 85747 Garching, Germany
    Tel.: +49 89 289 13667

    Space-filling model of alphaB crystallin. The hexameric subunit is indicated in color – Image: Andi Mainz / TUM

    Small heat shock protein as model for Alzheimer medication

    In Alzheimer’s disease proteins clump together to long fibrils causing the death of nerve cells. Small heat shock proteins can counteract this effect. Scientists, therefore, hope to deploy them as agents in the treatment of neurodegenerative diseases. Using the example of a small heat shock protein, researchers at the Technical University of Munich (TUM) and the Helmholtz Zentrum München have now uncovered how the protein interacts with other proteins.

    Small heat shock proteins are the “catastrophe aid workers” of the cell. When exposed to strong heat or radiation, vital cell proteins lose their structure and clot up to entangled clumps. Once these clumps have formed there is no return – the proteins become useless and the cells begin to die. Small heat shock proteins, however, attach to the deformed proteins before they clump together and preserve them in a soluble state – helping to restore their proper form.

    Promising candidate for new forms of therapy

    The helper proteins are true multi-talents. They can bind large numbers of badly folded proteins and keep them from clumping together. This also includes the potentially disease-causing proteins that collect in the cells of patients with neurodegenerative disorders – for example, beta amyloids that agglomerate to form long fibrils in the nerve cells of Alzheimer’s patients. Heat shock proteins are also associated with other nervous system disorders like Parkinson’s disease and multiple sclerosis.

    Although it is still unclear what role these catastrophe aid workers play in the various ailments, they are already being considered as models for agents in new medications. If the precise mechanisms by which these heat shock proteins hook up to their disease-causing counterparts were known, scientists could deploy this knowledge to develop agents utilizing these mechanisms to fight disease.

    Two ways out of the chaos

    A group of researchers led by Bernd Reif, professor at the Department of Chemistry of the Technical University of Munich (TUM) and group leader at the Helmholtz Zentrum München, have now succeeded in uncovering precisely this mechanism. Using a refined procedure of solid-state nuclear magnetic resonance spectroscopy (solid-state NMR), they managed, for the first time ever, to identify the sites in the alpha-B-crystallin that attach to the beta-amyloid.

    It is the first direct structure analysis of a complete heat shock protein during interaction with a bonding partner, because the catastrophe aid workers do not make the observer’s job easy. “Alpha-B-crystallin exists in various different forms comprising 24, 28 or 32 subunits that are permanently being swapped,” explains Reif. “In addition, it has a large molecular weight. These factors make structure analysis very difficult.”

    In close collaboration with his TUM colleagues Johannes Buchner, professor of biotechnology and Sevil Weinkauf, professor of electron microscopy, Reif determined that the small heat shock protein uses a specific non-polar beta-sheet structure pile in its center for interactions with the beta-amyloid, allowing it to access the aggregation process in two locations at once: For one it attaches to individual dissolved beta-amyloids, preventing them from forming fibrils. In addition, it “seals” existing fibrils, so that further amyloids can no longer accumulate.

    Template for artificial protein construction

    Precise knowledge about the way in which alpha-B-crystallin attaches to the Alzheimer’s protein is particularly interesting for researchers using so-called protein engineering to develop new agents that bind specifically to beta-amyloid and similar proteins. If the newly discovered beta-sheet structure idea could be integrated as building blocks into such artificially designed proteins, it would improve their ability to attach to the disease-causing fibrils – a first step in the development of new agents against Alzheimer’s and other neurodegenerative diseases.

    In future work, the scientists want to take a closer look at the N-terminal region of the alpha-B-crystallin. As Reif and his colleagues have discovered, it binds protein types that, unlike the beta-amyloid, clump together in an unordered manner. The researchers will be supported by the new NMR Center that is currently under construction at the Garching campus of the Technical University of Munich and slated to open in 2017. A further 5 million euro facility geared specifically to solid-state NMR is currently under construction at the Helmholtz Zentrum in Neuherberg.

    The research was funded by the Helmholtz Zentrum München and the German Research Foundation (DFG) (SFB-1035 and the Excellence Cluster “Center for Integrated Protein Science Munich” (CIPSM)).


    Andi Mainz, Jirka Peschek, Maria Stavropoulou, Katrin C. Back, Benjamin Bardiaux, Sam Asami, Elke Prade, Carsten Peters, Sevil Weinkauf, Johannes Buchner, Bernd Reif: The Chaperone alpha B-Crystallin Deploys Different Interfaces to Capture an Amorphous and an Amyloid Client,
    Nature Structural Molecular Biology, Oct. 12, 2015; DOI: 10.1038/nsmb.3108

    See the full article here .

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    Techniche Universitat Munchin Campus

    Technische Universität München (TUM) is one of Europe’s top universities. It is committed to excellence in research and teaching, interdisciplinary education and the active promotion of promising young scientists. The university also forges strong links with companies and scientific institutions across the world. TUM was one of the first universities in Germany to be named a University of Excellence. Moreover, TUM regularly ranks among the best European universities in international rankings.

  • richardmitnick 2:08 pm on April 7, 2015 Permalink | Reply
    Tags: , , , Protein Studies   

    From MedicalXpresss: “Food for thought: Master protein enhances learning and memory” 

    Medicalxpress bloc


    April 7, 2015
    No Writer Credit

    Salk researchers and collaborators discovered that physical and mentalactivities rely on a single metabolic protein, ERRγ, that controls theflow of blood and nutrients throughout the body. In this image, ERRγ isshown (stained red) in the hippocampus, the area of the brain largely responsible for memory. The new work could point to a way to enhance learning. Credit: Salk Institute

    Just as some people seem built to run marathons and have an easier time going for miles without tiring, others are born with a knack for memorizing things, from times tables to trivia facts. These two skills ― running and memorizing ― are not so different as it turns out.

    Salk scientists and collaborators have discovered that physical and mental activities rely on a single metabolic protein that controls the flow of blood and nutrients throughout the body, as reported in the journal Cell Metabolism. The new study could point to potential treatments in regenerative and developmental medicine as well as ways to address defects in learning and memory.

    “This is all about getting energy where it’s needed to ‘the power plants’ in the body,” says Ronald Evans, director of Salk’s Gene Expression Laboratory and senior author of the new paper, published April 7, 2015.”The heart and muscles need a surge of energy to carry out exercise and neurons need a surge of energy to form new memories.”

    Energy for muscles and brains, the scientists discovered, is controlled by a single protein called estrogen-related receptor gamma (ERRγ). Evans’research group has previously studied the role of ERRγ in the heart and skeletal muscles. In 2011, they discovered that promoting ERRγ activity int he muscle of sedentary mice increased blood supply to their muscles and doubled their running capacity. ERRγ, they went on to show, turns on a whole host of muscle genes that convert fat to energy.

    Thus, ERRγ became known as a master metabolic switch that energized muscle to enhance performance. Although studies had also shown that ERRγ was active in the brain, researchers didn’t understand why ― the brain burns sugar and ERRγ was previously shown to only burn fat. So the team decided to look more closely at what the protein was doing in brain cells.

    By first looking at isolated neurons, Liming Pei, lead and co-corresponding author of the paper, found that, as in muscle, ERRγactivates dozens of metabolic genes in brain cells. Unexpectedly, this activation related to sugar instead of fat. Neurons that lacked ERRγ could not ramp up energy production and thus had a compromised performance.

    “We assumed that ERRγ did the same thing throughout the body,” says Evans.”But we learned that it’s different in the brain.” ERRγ, they now conclude, turns on fat-burning pathways in muscles and sugar-burning pathways in the brain.

    Evans and his collaborators noticed that ERRγ in live mice was most active in the hippocampus ― an area of the brain that is active in producing new brain cells, is involved in learning and memory and is known to require lots of energy. They wondered whether ERRγ had a direct role in learning and memory. By studying mice lacking ERRγ in the brain, they found a link.

    While mice without the protein had normal vision, movement and balance,they were slower at learning how to swim through a water maze ― and poor at remembering the maze on subsequent trials ― compared to mice with normal levels of ERRγ.

    “What we found is that mice that missing ERRγ are basically very slow learners,” says Pei. Varying levels of ERRγ could also be at the root of differences between how individual humans learn, he hypothesizes.”Everyone can learn, but some people learn and memorize more efficiently than others, and we now think this could be linked to changes in brain metabolism.”

    A better understanding of the metabolism of neurons could help point the way to improved treatments for learning and attention disorders. And possibly, revving up levels of ERRγ could even enhance learning, just as it enhances muscle function.

    “What we’ve shown is that memories are really built on a metabolic scaffold,” says Evans. “And we think that if you want to understand learning and memory, you need to understand the circuits that underlie and power this process.”

    See the full article here.

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    Medical Xpress is a web-based medical and health news service that is part of the renowned Science X network. Medical Xpress features the most comprehensive coverage in medical research and health news in the fields of neuroscience, cardiology, cancer, HIV/AIDS, psychology, psychiatry, dentistry, genetics, diseases and conditions, medications and more.

  • richardmitnick 5:57 am on March 10, 2015 Permalink | Reply
    Tags: , , , Protein Studies,   

    From Scripps: “TSRI Scientists Reveal Structural Secrets of Nature’s Little Locomotive” 


    Scripps Research Institute

    March 9, 2015
    No Writer Credit

    Findings Could Help Shed Light on Alzheimer’s, Parkinson’s, ALS and Other Diseases

    A team led by scientists at The Scripps Research Institute (TSRI) has determined the basic structural organization of a molecular motor that hauls cargoes and performs other critical functions within cells.

    The new research provides the first picture of a molecular motor called the “dynein-dynactin complex,” which is critical for cell division and cargo transport. (Image courtesy of the Lander lab, The Scripps Research Institute.)

    Biologists have long wanted to know how this molecular motor—called the “dynein-dynactin complex”—works. But the complex’s large size, myriad subunits and high flexibility have until now restricted structural studies to small pieces of the whole.

    In the new research, however, TSRI biologist Gabriel C. Lander and his laboratory, in collaboration with Trina A. Schroer and her group at Johns Hopkins University, created a picture of the whole dynein-dynactin structure.

    “This work gives us critical insights into the regulation of the dynein motor and establishes a structural framework for understanding why defects in this system have been linked to diseases such as Huntington’s, Parkinson’s, and Alzheimer’s,” said Lander.

    The findings are reported in a Nature Structural & Molecular Biology advance online publication on March 9, 2015.

    Unprecedented Detail

    The proteins dynein and dynactin normally work together on microtubules for cellular activities such as cell division and intracellular transport of critical cargo such as mitochondria and mRNA. The complex also plays a key role in neuronal development and repair, and problems with the dynein-dynactin motor system have been found in brain diseases including Alzheimer’s, Parkinson’s and Huntington’s diseases, and amyotrophic lateral sclerosis (ALS). In addition, some viruses (including herpes, rabies and HIV) appear to hijack the dynein-dynactin transport system to get deep inside cells.

    “Understanding how dynein and dynactin interact and work, and how they actually look, is definitely going to have medical relevance,” said Research Associate Saikat Chowdhury, a member of the Lander lab who was first author of the study.

    To study the dynein-dynactin complex, Schroer’s laboratory first produced individual dynein and dynactin proteins, which are themselves complicated, with multiple subunits, but have been so highly conserved by evolution that they are found in almost identical form in organisms from yeast to mammals.

    Chowdhury and Lander then used electron microscopy (EM) and cutting-edge image-processing techniques to develop two-dimensional “snapshots” of dynein’s and dynactin’s basic structures. These structural data contained unprecedented detail and revealed subunits never observed before.

    Chowdhury and Lander next developed a novel strategy to purify and image dynein and dynactin in complex together on a microtubule—a railway-like structure, ubiquitous in cells, along which dynein-dynactin moves its cargoes.

    “This is the first snapshot of how the whole dynein-dynactin complex looks and how it is oriented on the microtubule,” Chowdhury said.

    Pushing the Limits

    The structural data clarify how dynein and dynactin fit together on a microtubule, how they recruit cargoes and how they manage to move those cargoes consistently in a single direction.

    Lander and Chowdhury now hope to build on the findings by producing a higher-resolution, three-dimensional image of the dynein-dynactin-microtubule complex, using an EM-related technique called electron tomography.

    “The EM facility at TSRI is the best place in the world to push the limits of imaging complicated molecular machines like these,” said Lander.

    The other co-author of the paper, Structural organization of the dynein–dynactin complex bound to microtubules, (doi:10.1038/nsmb.2996) was Stephanie A. Ketcham of the Schroer laboratory.

    The research was supported by the Damon Runyon Cancer Research Foundation (DFS-#07-13), the Pew Scholars program, the Searle Scholars program and the National Institutes of Health (DP2 EB020402-01, GM44589).

    See the full article here.

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

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

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

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