Tag Archives: proteins

Encapsulation of proteins in nanoparticles no longer necessary for time release?

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A team of researchers at the University of Toronto (Canada) have developed a technique for the therapeutic use of proteins that doesn’t require ‘nanoencapsulation’ although nanoparticles are still used according to a May 27, 2016 news item on ScienceDaily,

A U of T [University of Toronto] Engineering team has designed a simpler way to keep therapeutic proteins where they are needed for long periods of time. The discovery is a potential game-changer for the treatment of chronic illnesses or injuries that often require multiple injections or daily pills.

For decades, biomedical engineers have been painstakingly encapsulating proteins in nanoparticles to control their release. Now, a research team led by University Professor Molly Shoichet has shown that proteins can be released over several weeks, even months, without ever being encapsulated. In this case the team looked specifically at therapeutic proteins relevant to tissue regeneration after stroke and spinal cord injury.

“It was such a surprising and unexpected discovery,” said co-lead author Dr. Irja Elliott Donaghue, who first found that the therapeutic protein NT3, a factor that promotes the growth of nerve cells, was slowly released when just mixed into a Jello-like substance that also contained nanoparticles. “Our first thought was, ‘What could be happening to cause this?'”

A May 27, 2016 University of Toronto news release (also on EurekAlert) by Marit Mitchell, which originated the news item, provides more in depth explanation,

Proteins hold enormous promise to treat chronic conditions and irreversible injuries — for example, human growth hormone is encapsulated in these tiny polymeric particles, and used to treat children with stunted growth. In order to avoid repeated injections or daily pills, researchers use complicated strategies both to deliver proteins to their site of action, and to ensure they’re released over a long enough period of time to have a beneficial effect.

This has long been a major challenge for protein-based therapies, especially because proteins are large and often fragile molecules. Until now, investigators have been treating proteins the same way as small drug molecules and encapsulating them in polymeric nanoparticles, often made of a material called poly(lactic-co-glycolic acid) or PLGA.

As the nanoparticles break down, the drug molecules escape. The same process is true for proteins; however, the encapsulating process itself often damages or denatures some of the encapsulated proteins, rendering them useless for treatment. Skipping encapsulation altogether means fewer denatured proteins, making for more consistent protein therapeutics that are easier to make and store.

“This is really exciting from a translational perspective,” said PhD candidate Jaclyn Obermeyer. “Having a simpler, more reliable fabrication process leaves less room for complications with scale-up for clinical use.”

The three lead authors, Elliott Donoghue, Obermeyer and Dr. Malgosia Pakulska have shown that to get the desired controlled release, proteins only need to be alongside the PLGA nanoparticles, not inside them. …

“We think that this could speed up the path for protein-based drugs to get to the clinic,” said Elliott Donaghue.

The mechanism for this encapsulation-free controlled release is surprisingly elegant. Shoichet’s group mixes the proteins and nanoparticles in a Jello-like substance called a hydrogel, which keeps them localized when injected at the site of injury. The positively charged proteins and negatively charged nanoparticles naturally stick together. As the nanoparticles break down they make the solution more acidic, weakening the attraction and letting the proteins break free.

“We are particularly excited to show long-term, controlled protein release by simply controlling the electrostatic interactions between proteins and polymeric nanobeads,” said Shoichet. “By manipulating the pH of the solution, the size and number of nanoparticles, we can control release of bioactive proteins. This has already changed and simplified the protein release strategies that we are pursuing in pre-clinical models of disease in the brain and spinal cord.”

“We’ve learned how to control this simple phenomena,” Pakulska said. “Our next question is whether we can do the opposite—design a similar release system for positively charged nanoparticles and negatively charged proteins.”

Here’s a link to and a citation for the paper,

Encapsulation-free controlled release: Electrostatic adsorption eliminates the need for protein encapsulation in PLGA nanoparticles by Malgosia M. Pakulska, Irja Elliott Donaghue, Jaclyn M. Obermeyer, Anup Tuladhar, Christopher K. McLaughlin, Tyler N. Shendruk, and Molly S. Shoichet. Science Advances  27 May 2016: Vol. 2, no. 5, e1600519 DOI: 10.1126/sciadv.1600519

This paper appears to be open access.

Dr. Molly Shoichet was featured here in a May 11, 2015 posting about the launch of her Canada-wide science communication project Research2.Reality.

Biological supercomputers (living, breathing supercomputers) and an international collaboration spearheaded by Canadian scientists

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A living, breathing supercomputer is a bit mind-boggling but scientists at McGill University (Canada) and their international colleagues have created a working model according to a Feb. 26, 2016 McGill University news release on EurekAlert (and received via email), Note: A link has been removed,

The substance that provides energy to all the cells in our bodies, Adenosine triphosphate (ATP), may also be able to power the next generation of supercomputers. That is what an international team of researchers led by Prof. Nicolau, the Chair of the Department of Bioengineering at McGill, believe. They’ve published an article on the subject earlier this week in the Proceedings of the National Academy of Sciences (PNAS), in which they describe a model of a biological computer that they have created that is able to process information very quickly and accurately using parallel networks in the same way that massive electronic super computers do.

Except that the model bio supercomputer they have created is a whole lot smaller than current supercomputers, uses much less energy, and uses proteins present in all living cells to function.

Doodling on the back of an envelope

“We’ve managed to create a very complex network in a very small area,” says Dan Nicolau, Sr. with a laugh. He began working on the idea with his son, Dan Jr., more than a decade ago and was then joined by colleagues from Germany, Sweden and The Netherlands, some 7 years ago [there is also one collaborator from the US according the journal’s [PNAS] list of author affiliations, read on for the link to the paper]. “This started as a back of an envelope idea, after too much rum I think, with drawings of what looked like small worms exploring mazes.”

The model bio-supercomputer that the Nicolaus (father and son) and their colleagues have created came about thanks to a combination of geometrical modelling and engineering knowhow (on the nano scale). It is a first step, in showing that this kind of biological supercomputer can actually work.

The circuit the researchers have created looks a bit like a road map of a busy and very organized city as seen from a plane. Just as in a city, cars and trucks of different sizes, powered by motors of different kinds, navigate through channels that have been created for them, consuming the fuel they need to keep moving.

More sustainable computing

But in the case of the biocomputer, the city is a chip measuring about 1.5 cm square in which channels have been etched. Instead of the electrons that are propelled by an electrical charge and move around within a traditional microchip, short strings of proteins (which the researchers call biological agents) travel around the circuit in a controlled way, their movements powered by ATP, the chemical that is, in some ways, the juice of life for everything from plants to politicians.

Because it is run by biological agents, and as a result hardly heats up at all, the model bio-supercomputer that the researchers have developed uses far less energy than standard electronic supercomputers do, making it more sustainable. Traditional supercomputers use so much electricity that they heat up a lot and then need to be cooled down, often requiring their own power plant to function.

Moving from model to reality

Although the model bio supercomputer was able to very efficiently tackle a complex classical mathematical problem by using parallel computing of the kind used by supercomputers, the researchers recognize that there is still a lot of work ahead to move from the model they have created to a full-scale functional computer.

”Now that this model exists as a way of successfully dealing with a single problem, there are going to be many others who will follow up and try to push it further, using different biological agents, for example,” says Nicolau. “It’s hard to say how soon it will be before we see a full scale bio super-computer. One option for dealing with larger and more complex problems may be to combine our device with a conventional computer to form a hybrid device. Right now we’re working on a variety of ways to push the research further.”

What was once the stuff of science fiction, is now just science.

The funding for this project is interesting,

This research was funded by: The European Union Seventh Framework Programme; [US] Defense Advanced Research Projects Agency [DARPA]; NanoLund; The Miller Foundation; The Swedish Research Council; The Carl Trygger Foundation; the German Research Foundation; and by Linnaeus University.

I don’t see a single Canadian funding agency listed.

In any event, here’s a link to and a citation for the paper,

Parallel computation with molecular-motor-propelled agents in nanofabricated networks by Dan V. Nicolau, Jr., Mercy Lard, Till Kortend, Falco C. M. J. M. van Delft, Malin Persson, Elina Bengtsson, Alf Månsson, Stefan Diez, Heiner Linke, and Dan V. Nicolau. Proceedings of the National Academy of Sciences (PNAS): http://www.pnas.org/content/early/2016/02/17/1510825113

This paper appears to be open access.

Finally, the researchers have provided an image illustrating their work,

Caption: Strands of proteins of different lengths move around the chip in the bio computer in directed patterns, a bit like cars and trucks navigating the streets of a city. Credit: Till Korten

Caption: Strands of proteins of different lengths move around the chip in the bio computer in directed patterns, a bit like cars and trucks navigating the streets of a city. Credit: Till Korten

ETA Feb. 29 2016: Technical University Dresden’s Feb. 26, 2016 press release on EurekAlert also announces the bio-computer albeit from a rather different perspective,

The pioneering achievement was developed by researchers from the Technische Universität Dresden and the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden in collaboration with international partners from Canada, England, Sweden, the US, and the Netherlands.

Conventional electronic computers have led to remarkable technological advances in the past decades, but their sequential nature -they process only one computational task at a time- prevents them from solving problems of combinatorial nature such as protein design and folding, and optimal network routing. This is because the number of calculations required to solve such problems grows exponentially with the size of the problem, rendering them intractable with sequential computing. Parallel computing approaches can in principle tackle such problems, but the approaches developed so far have suffered from drawbacks that have made up-scaling and practical implementation very difficult. The recently reported parallel-computing approach aims to address these issues by combining well established nanofabrication technology with molecular motors which are highly energy efficient and inherently work in parallel.

In this approach, which the researchers demonstrate on a benchmark combinatorial problem that is notoriously hard to solve with sequential computers, the problem to be solved is ‘encoded’ into a network of nanoscale channels (Fig. 1a). This is done, on the one hand by mathematically designing a geometrical network that is capable of representing the problem, and on the other hand by fabricating a physical network based on this design using so-called lithography, a standard chip-manufacturing technique.

The network is then explored in parallel by many protein filaments (here actin filaments or microtubules) that are self-propelled by a molecular layer of motor proteins (here myosin or kinesin) covering the bottom of the channels (Fig. 3a). The design of the network using different types of junctions automatically guides the filaments to the correct solutions to the problem (Fig. 1b). This is realized by different types of junctions, causing the filaments to behave in two different ways. As the filaments are rather rigid structures, turning to the left or right is only possible for certain angles of the crossing channels. By defining these options (‘split junctions’ Fig. 2a + 3b and ‘pass junctions’, Fig. 2b + 3c) the scientists achieved an ‘intelligent’ network giving the filaments the opportunity either to cross only straight or to decide between two possible channels with a 50/50 probability.

The time to solve combinatorial problems of size N using this parallel-computing approach scales approximately as N2, which is a dramatic improvement over the exponential (2N) time scales required by conventional, sequential computers. Importantly, the approach is fully scalable with existing technologies and uses orders of magnitude less energy than conventional computers, thus circumventing the heating issues that are currently limiting the performance of conventional computing.

The diagrams mentioned were not included with the press release.

Nature-inspired but not really, a new design rule for nanostructures

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It’s fascinating to observe the news release writer’s attempt to package this research as biomimetic when the new design rule is not found in nature. An Oct. 7, 2015 news item on ScienceDaily provides an introduction to the work from the Lawrence Berkeley National Laboratory,

Scientists aspire to build nanostructures that mimic the complexity and function of nature’s proteins. These microscopic widgets could be customized into incredibly sensitive chemical detectors or long-lasting catalysts. But as with any craft that requires extreme precision, researchers must first learn how to finesse the materials they’ll use to build these structures. A new discovery is a big step in this direction. The scientists discovered a design rule that enables a recently created material to exist.

An Oct. 7, 2015 Lawrence Berekeley National Laboratory (Berkeley Lab) news release (also on EurekAlert), which originated the news item, features more detail about the research and the writer’s gyrations,

The scientists discovered a design rule that enables a recently created material to exist. The material is a peptoid nanosheet. It’s a flat structure only two molecules thick, and it’s composed of peptoids, which are synthetic polymers closely related to protein-forming peptides.

The design rule controls the way in which polymers adjoin to form the backbones that run the length of nanosheets. Surprisingly, these molecules link together in a counter-rotating pattern not seen in nature. [emphasis mine] This pattern allows the backbones to remain linear and untwisted, a trait that makes peptoid nanosheets larger and flatter than any biological structure.

The Berkeley Lab scientists say this never-before-seen design rule could be used to piece together complex nanosheet structures and other peptoid assemblies such as nanotubes and crystalline solids.

What’s more, they discovered it by combining computer simulations with x-ray scattering and imaging methods to determine, for the first time, the atomic-resolution structure of peptoid nanosheets.

“This research suggests new ways to design biomimetic structures, [emphasis mine]” says Steve Whitelam, a co-corresponding author of the Nature paper. “We can begin thinking about using design principles other than those nature offers.”

The news release goes on to note the previous work which this newest research builds on and provides yet more detail about the latest and greatest,

Peptoid nanosheets were discovered by Zuckermann’s group five years ago. They found that under the right conditions, peptoids self assemble into two-dimensional assemblies that can grow hundreds of microns across. This “molecular paper” has become a hot prospect as a protein-mimicking platform for molecular design.

To learn more about this potential building material, the scientists set out to learn its atom-resolution structure. This involved feedback between experiment and theory. Microscopy and scattering data gathered at the Molecular Foundry and the Advanced Light Source, also a DOE Office of Science user facility located at Berkeley Lab, were compared with molecular dynamics simulations conducted at NERSC.

The research revealed several new things about peptoid nanosheets. Their molecular makeup varies throughout their structure, they can be formed only from peptoids of a certain minimum length, they contain water pockets, and they are potentially porous when it comes to water and ions.

These insights are intriguing on their own, but when the scientists examined the structure of the nanosheets’ backbone, they were surprised to see a design rule not found in the field of protein structural biology.

Here’s the difference: In nature, proteins are composed of beta sheets and alpha helices. These fundamental building blocks are themselves composed of backbones, and the polymers that make up these backbones are all joined together using the same rule. Each adjacent polymer rotates incrementally in the same direction, so that a twist runs along the backbone.

This rule doesn’t apply to peptoid nanosheets. Along their backbones, adjacent monomer units rotate in opposite directions. These counter-rotations cancel each other out, resulting in a linear and untwisted backbone. This enables backbones to be tiled in two dimensions and extended into large sheets that are flatter than anything nature can produce.

“It was a big surprise to find the design rule that makes peptoid nanosheets possible has eluded the field of biology until now,” says Mannige [Ranjan Mannige, a postdoctoral researcher at the Molecular Foundry]. “This rule could perhaps be used to build many more unrealized structures.”

Adds Zuckermann [Peptoid nanosheets were discovered by Zuckermann’s group five years ago. They found that under the right conditions, peptoids self assemble into two-dimensional assemblies that can grow hundreds of microns across. This “molecular paper” has become a hot prospect as a protein-mimicking platform for molecular design.

To learn more about this potential building material, the scientists set out to learn its atom-resolution structure. This involved feedback between experiment and theory. Microscopy and scattering data gathered at the Molecular Foundry and the Advanced Light Source, also a DOE Office of Science user facility located at Berkeley Lab, were compared with molecular dynamics simulations conducted at NERSC.

The research revealed several new things about peptoid nanosheets. Their molecular makeup varies throughout their structure, they can be formed only from peptoids of a certain minimum length, they contain water pockets, and they are potentially porous when it comes to water and ions.

These insights are intriguing on their own, but when the scientists examined the structure of the nanosheets’ backbone, they were surprised to see a design rule not found in the field of protein structural biology.

Here’s the difference: In nature, proteins are composed of beta sheets and alpha helices. These fundamental building blocks are themselves composed of backbones, and the polymers that make up these backbones are all joined together using the same rule. Each adjacent polymer rotates incrementally in the same direction, so that a twist runs along the backbone.

This rule doesn’t apply to peptoid nanosheets. Along their backbones, adjacent monomer units rotate in opposite directions. These counter-rotations cancel each other out, resulting in a linear and untwisted backbone. This enables backbones to be tiled in two dimensions and extended into large sheets that are flatter than anything nature can produce.

“It was a big surprise to find the design rule that makes peptoid nanosheets possible has eluded the field of biology until now,” says Mannige. “This rule could perhaps be used to build many more unrealized structures.”

Adds Zuckermann, [Ron Zuckermann directs the Molecular Foundry’s Biological Nanostructures Facility.] “We also expect there are other design principles waiting to be discovered, which could lead to even more biomimetic nanostructures.”

They might have been better off describing the work as “bioinspired” but it is a tricky thing to describe and there doesn’t seem to be an easy way out of describing this discovery which is based on observations from nature but follows no rule found in nature.

Here’s a link to and a citation for the paper,

Peptoid nanosheets exhibit a new secondary-structure motif by Ranjan V. Mannige, Thomas K. Haxton, Caroline Proulx, Ellen J. Robertson, Alessia Battigelli, Glenn L. Butterfoss, Ronald N. Zuckermann, & Stephen Whitelam. Nature (2015) doi:10.1038/nature15363 Published online 07 October 2015

This paper is behind a paywall.

Northwestern University’s (US) International Institute for Nanotechnology (IIN) rakes in some cash

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Within less than a month Northwestern University’s International Institute for Nanotechnology (IIN) has been granted awarded two grants by the US Department of Defense.

4D printing

The first grant, for 4D printing, was announced in a June 11, 2015 Northwestern news release by Megan Fellman (Note: A link has been removed),

Northwestern University’s International Institute for Nanotechnology (IIN) has received a five-year, $8.5 million grant from the U.S. Department of Defense’s competitive Multidisciplinary University Research Initiative (MURI) program to develop a “4-dimensional printer” — the next generation of printing technology for the scientific world.

Once developed, the 4-D printer, operating on the nanoscale, will be used to construct new devices for research in chemistry, materials sciences and U.S. defense-related areas that could lead to new chemical and biological sensors, catalysts, microchip designs and materials designed to respond to specific materials or signals.

“This research promises to bring transformative advancement to the development of biosensors, adaptive optics, artificially engineered tissues and more by utilizing nanotechnology,” said IIN director and chemist Chad A. Mirkin, who is leading the multi-institution project. Mirkin is the George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences.

The award, issued by the Air Force Office of Scientific Research, supports a team of experts from Northwestern, the University of Miami, the University of California, San Diego, and the University of Maryland.

In science, “printing” encodes information at specific locations on a material’s surface, similar to how we print words on paper with ink. The 4-dimensional printer will consist of millions of tiny elastomeric “pens” that can be used individually and independently to create nanometer-size features composed of hard or soft materials.

The information encoded can be in the form of materials with a defined set of chemical and physical properties. The printing speed and resolution determine the amount and complexity of the information that can be encoded.

Progress in fields ranging from biology to chemical sensing to computing currently are limited by the lack of low-cost equipment that can perform high-resolution printing and 3-dimensional patterning on hard materials (e.g., metals and semiconductors) and soft materials (e.g., organic and biological materials) at nanometer resolution (approximately 1,000 times smaller than the width of a human hair).

“Ultimately, the 4-D printer will provide a foundation for a new generation of tools to develop novel architectures, wherein the hard materials that form the functional components of electronics can be merged with biological or soft materials,” said Milan Mrksich, a co-principal investigator on the grant.

Mrksich is the Henry Wade Rogers Professor of Biomedical Engineering, Chemistry and Cell and Molecular Biology, with appointments in the McCormick School of Engineering and Applied Science, Weinberg and Northwestern University Feinberg School of Medicine.

A July 10, 2015 article about the ‘4D printer’ grant  by Madeline Fox for the Daily Northwestern features a description of 4D printing from Milan Mrksich, a co-principal investigator on the grant,

Milan Mrksich, one of the project’s five senior participants, said that while most people are familiar with the three dimensions of length, width and depth, there are often misconceptions about the fourth property of a four-dimensional object. Mrksich used Legos as an analogy to describe 4D printing technology.

“If you take Lego blocks, you can basically build any structure you want by controlling which Lego is connected to which Lego and controlling all their dimensions in space,” Mrksich said. “Within an object made up of nanoparticles, we’re controlling the placement — as we use a printer to control the placement of every particle, our fourth dimension lets us choose which nanoparticle with which property would be at each position.”

Thank you Dr. Mrksich and Ms. Fox for that helpful analogy.

Designing advanced bioprogrammable nanomaterials

The second grant, announced in a July 6, 2015 Northwestern news release by Megan Fellman, is apparently the only one of its kind in the US (Note: A link has been removed),

Northwestern University’s International Institute for Nanotechnology (IIN) has been awarded a U.S. Air Force Center of Excellence grant to design advanced bioprogrammable nanomaterials for solutions to challenging problems in the areas of energy, the environment, security and defense, as well as for developing ways to monitor and mitigate human stress.

The five-year, $9.8 million grant establishes the Center of Excellence for Advanced Bioprogrammable Nanomaterials (C-ABN), the only one of its kind in the country. After the initial five years, the grant potentially could be renewed for an additional five years.

“Northwestern University was chosen to lead this Center of Excellence because of its investment in infrastructure development, including new facilities and instrumentation; its recruitment of high-caliber faculty members and students; and its track record in bio-nanotechnology and cognitive sciences,” said Timothy Bunning, chief scientist at the U.S. Air Force Research Laboratory (AFRL) Materials and Manufacturing Directorate.

Led by IIN director Chad A. Mirkin, C-ABN will support collaborative, discovery-based research projects aimed at developing bioprogrammable nanomaterials that will meet both military and civilian needs and facilitate the efficient transition of these new technologies from the laboratory to marketplace.

Bioprogrammable nanomaterials are structures that typically contain a biomolecular component, such as nucleic acids or proteins, which give the materials a variety of novel capabilities. [emphasis mine] Nanomaterials can be designed to assemble into large 3-D structures, to interface with biological structures inside cells or tissues, or to interface with existing macroscale devices, for example. These new bioprogrammable nanomaterials and the fundamental knowledge gained through their development will ultimately lead to the creation of wearable, portable and/or human-interactive devices with extraordinary capabilities that will significantly impact both civilian and Air Force needs.

In one research area, scientists will work to understand the molecular underpinnings of vulnerability and resilience to stress. They will use bioprogrammable nanomaterials to develop ultrasensitive sensors capable of detecting and quantifying biomarkers for human stress in biological fluids (e.g., saliva, perspiration or blood), providing means to easily monitor the soldier during times of extreme stress. Ultimately, these bioprogrammable materials may lead to methods to increase human cellular resilience to the effects of stress and/or to correct genetic mutations that decrease cellular resilience of susceptible individuals.

Other research projects, encompassing a wide variety of nanotechnology-enabled goals, include:

Developing hybrid wearable energy-storage devices;
Developing devices to identify chemical and biological targets in a field environment;
Developing flexible bio-electronic circuits;
Designing a new class of flat optics; and
Advancing understanding of design rules between 2-D and 3-D architectures.

The analysis of these nanostructures also will extend fundamental knowledge in the fields of materials science and engineering, human performance, chemistry, biology and physics.

The center will be housed under the IIN, providing researchers with access to IIN’s strong entrepreneurial community and its close ties with Northwestern’s renowned Kellogg School of Management.

This second news release provides an interesting contrast to a recent news release from Sweden’s Karolinska Intitute where the writer was careful to note that the enzymes and organic electronic ion pumps were not living as noted in my June 26, 2015 posting. It seems nucleic acids (as in RNA and DNA) can be mentioned without a proviso in the US. as there seems to be little worry about anti-GMO (genetically modified organisms) and similar backlashes affecting biotechnology research.

Animation: art and science

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Being in the process of developing an art/science piece involving poetry and visual metaphors as realized through video, I was quite fascinated to read about someone else’s process and issues in Stephen Curry’s and Drew Berry’s June 9, 2015 joint post on the Guardian science blogs (Note: Links have been removed),

Yesterday [June 8, 2015] I [Stephen Curry] was trying to figure out why it seems to be so difficult to connect to the biological molecules that we are made of – proteins, DNA and such like. My piece might have ended on a frustrated note but I have no wish to be negative, especially since the problem has only arisen because animators like Drew Berry are now able to use the results of structural biology to make quite exquisite movies of the molecules of life at work inside the cells of our bodies. As I was working though my difficulties, I wrote to ask Berry how he approached the task of representing molecular complexity in ways that would make sense to people. This is his considered and insightful reply:

“The goal of my [Drew Berry] work is to show non-experts – the general public aged 4 to 99, students of biology, journalists and politicians, and so on – what is being discovered in biology, in a format that is accessible, meaningful, and engaging. I hope that my work provides some sense of what biologists and medical researchers are discovering and thinking about, to provide the public with a framework of understanding to discuss these important new discoveries and the impact it will have on us as a society as we head into the future.

These passages, in particular, caught my attention as they are descriptive of the art and the science inherent in Berry’s work,

… I should avoid overstating how accurately I have depicted the reality of the molecular world. It is vastly messier, random and crowded, and it’s physical nature is unimaginably alien to our normal perception of the world around us. That said, my work is not intended to be a lab-bench-calculated model for research use, it is an impressionistic, artist-generated crude sketch of phenomena and structures science is measuring and discovering at the molecular scale.

… I would then assert that the animations are firmly founded on real data and are as accurate as I can possibly make them, while making them watchable and interpretable to a human audience. By far the largest portion of my time is spent conducting broad ranging literature reviews of the topic I am working on, gathering the fragments of data scattered throughout the journals, and holistically reconstructing what currently we know and do not know. Wherever data and models are available, I incorporate them directly into the construction of the animation, including molecular structures, dynamics simulations, speed measurements, and so on. My work is most akin to a ‘review’ paper in the literature, presented in visual form.

Here is one of the problems Berry and other animators struggle with,

… I am friends with the dozen or so people who are at the top of the game at creating biomedical animations (most have a PhD scientific background) and we all struggle with the problem of having a molecule arrive at a particular location from the thick molecular soup of the cytoplasm and not look directed. I can make the molecule wander around in a Brownian type manner, but for story telling and visual explanations, I need it to get to a certain point and do it’s thing at a certain time to move the story along. This can make it look determined and directed.

Berry also discusses the unexpected,

An unexpected outcome I stumbled across more than a decade ago is that the public loves it when ‘real time’ speeds are displayed and the structures and reactions are derived from research data. This takes a lot of time to build, but then the animations have a remarkable longevity of use and strongly resonate with the audience.

For the last excerpt from this essay, I include Berry’s description of one of his most challenging projects and the video he produced,

The most heavily researched and technically challenging animation I have ever built is the kinetochore which can be seen in the video below . The kinetochore is a gigantic structure that assembles on chromosomes just after they have been duplicated and helps them to be pulled apart during cell division (mitosis). It has about 200 proteins of which I depicted about 50. I gathered data from more than 180 scientific papers with everything built as accurately as possible with hundreds of little scientific details built into the structure and dynamics.”

There are more illustrations and one more video embedded along with more from Berry in the essay, which includes these biographical details (Note: Links have been removed),

Drew Berry is the Biomedical Animations Manager at the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia. @Stephen_Curry is a professor of structural biology at Imperial College [London, UK].

SWEET, sweet transporters

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A Sept. 4, 2014 news item on Azonano is all about sugar,

Sugars are an essential source of energy for microrganisms, animals and humans. They are produced by plants, which convert energy from sunlight into chemical energy in the form of sugars through photosynthesis.

These sugars are taken up into cells, no matter whether these are bacteria, yeast, human cells or plant cells, by proteins that create sugar-specific pores in the membrane that surrounds a cell. These transport proteins are thus essential in all organisms. It is not surprising that the transporters of humans and plants are very similar since they evolved from their bacterial ancestors.

Sugar transporters can also be a source of vulnerability for plants and animals alike. In plants they can be susceptible to takeover by pathogens, hijacking the source of the plant’s food and energy. In animals, mutations in sugar transporters can lead to diseases, such as diabetes.

New work from a team led by the Stanford University School of Medicine’s Liang Feng and including Carnegie’s [Carnegie Institution for Science] Wolf Frommer has for the first time elucidated the atomic structures of the prototype of the sugar transporters (termed “SWEET” transporters) in plants and humans. These are bacterial sugar transporters, called SemiSWEETs (because they are just half the size of the human and plant ones). …

A Sept. 3, 2014 Carnegie Institution for Science news release, which originated the news item, describes the importance of understanding these transporters,

Until now, there was very limited information about the unique structures of these important transport proteins, which it turns out are different from all other known sugar transporters.

Discovering the structure of these proteins is important, as it is the key to unlocking the mechanism by which they work. And understanding their mechanism is crucial for figuring out what happens when these functions fail to work properly, because that knowledge can help in addressing the resulting diseases or growth problems in both plants and animals.

The research team performed a combination of structural and functional analyses of SemiSWEETs and SWEETs and was able to crystallize two examples in different states, demonstrating not only the protein’s structure, but much about its functionality as well.

They found that the SemiSWEETs do not act as a sugar channel, or tunnel, which allow sugars to pass across the membrane. Rather they act like an airlock, moving the sugars in multiple stages, two of which can be observed in the crystal structures. The SemiSWEETs, among the smallest known transport proteins, assemble in pairs, thereby creating a structure that looks like their bigger plant and human SWEET homologs. This marks the SWEET family of proteins as drastically different from other sugar transport proteins.

“One of the most-exciting parts of this discovery is the speed with which we were able to move from discovering these novel sugar transporters, to determining their actual structure, to showing how they work,” Frommer said. “Fantastic progress made possible by a collaboration with a structural biologist from Stanford University. Our findings highlight the potential practical applications of this information in improving crop yields as well as in addressing human diseases.”

Here’s a link to and a citation for the paper,

Structures of bacterial homologues of SWEET transporters in two distinct conformations by Yan Xu, Yuyong Tao, Lily S. Cheung, Chao Fan, Li-Qing Chen, Sophia Xu, Kay Perry, Wolf B. Frommer, & Liang Feng. Nature (2014) doi:10.1038/nature13670 Published online 03 September 2014

This paper is behind a paywall.

2013 Nobel Prize in Physiology/Medicine and nanotechnology

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I missed it when the 2013 Nobel Prize for Medicine/Physiology was announced but T.C. writing for The Economist in an Oct. 7, 2013 piece points out that the winning team’s work could be described as nanotechnological (although ‘I’m more comfortable with the phrase ‘processes occurring at the nanoscale’),

NANOTECHNOLOGY is a hot topic in science. Not a day goes by without news of some clever device forged using components measuring billionths of a metre. But as is often the case, Mother Nature got there long before humans did. Living cells are nanotechnological factories of stunning complexity, containing the assembly lines, power stations, conveyor belts and control rooms necessary to keep life going.

This year’s Nobel prize in physiology or medicine has gone to three researchers who explained how one of these nanotechnological systems works. James Rothman, Randy Schekman and Thomas Südhof explained how cellular bodies called vesicles—little bubbles encased in fat—are used to ship hormones, enzymes and various other manufactured goods around a cell, and to export them to the outside world.

The Oct.7, 2013 nobelprize.org press release provides details about the prize-winning work,

The 2013 Nobel Prize honours three scientists who have solved the mystery of how the cell organizes its transport system. Each cell is a factory that produces and exports molecules. For instance, insulin is manufactured and released into the blood and signaling molecules called neurotransmitters are sent from one nerve cell to another. These molecules are transported around the cell in small packages called vesicles. The three Nobel Laureates have discovered the molecular principles that govern how this cargo is delivered to the right place at the right time in the cell.

Randy Schekman discovered a set of genes that were required for vesicle traffic. James Rothman  unravelled protein machinery that allows vesicles to fuse with their targets to permit transfer of cargo. Thomas Südhof revealed how signals instruct vesicles to release their cargo with precision.

Through their discoveries, Rothman, Schekman and Südhof have revealed the exquisitely precise control system for the transport and delivery of cellular cargo. Disturbances in this system have deleterious effects and contribute to conditions such as neurological diseases, diabetes, and immunological disorders.
How cargo is transported in the cell

In a large and busy port, systems are required to ensure that the correct cargo is shipped to the correct destination at the right time. The cell, with its different compartments called organelles, faces a similar problem: cells produce molecules such as hormones, neurotransmitters, cytokines and enzymes that have to be delivered to other places inside the cell, or exported out of the cell, at exactly the right moment. Timing and location are everything. Miniature bubble-like vesicles, surrounded by membranes, shuttle the cargo between organelles or fuse with the outer membrane of the cell and release their cargo to the outside. This is of major importance, as it triggers nerve activation in the case of transmitter substances, or controls metabolism in the case of hormones. How do these vesicles know where and when to deliver their cargo?
Traffic congestion reveals genetic controllers

Randy Schekman was fascinated by how the cell organizes its transport system and in the 1970s decided to study its genetic basis by using yeast as a model system. In a genetic screen, he identified yeast cells with defective transport machinery, giving rise to a situation resembling a poorly planned public transport system. Vesicles piled up in certain parts of the cell. He found that the cause of this congestion was genetic and went on to identify the mutated genes. Schekman identified three classes of genes that control different facets of the cell´s transport system, thereby providing new insights into the tightly regulated machinery that mediates vesicle transport in the cell.
Docking with precision

James Rothman was also intrigued by the nature of the cell´s transport system. When studying vesicle transport in mammalian cells in the 1980s and 1990s, Rothman discovered that a protein complex enables vesicles to dock and fuse with their target membranes. In the fusion process, proteins on the vesicles and target membranes bind to each other like the two sides of a zipper. The fact that there are many such proteins and that they bind only in specific combinations ensures that cargo is delivered to a precise location. The same principle operates inside the cell and when a vesicle binds to the cell´s outer membrane to release its contents.

It turned out that some of the genes Schekman had discovered in yeast coded for proteins corresponding to those Rothman identified in mammals, revealing an ancient evolutionary origin of the transport system. Collectively, they mapped critical components of the cell´s transport machinery.
Timing is everything

Thomas Südhof was interested in how nerve cells communicate with one another in the brain. The signalling molecules, neurotransmitters, are released from vesicles that fuse with the outer membrane of nerve cells by using the machinery discovered by Rothman and Schekman. But these vesicles are only allowed to release their contents when the nerve cell signals to its neighbours. How is this release controlled in such a precise manner? Calcium ions were known to be involved in this process and in the 1990s, Südhof searched for calcium sensitive proteins in nerve cells. He identified molecular machinery that responds to an influx of calcium ions and directs neighbour proteins rapidly to bind vesicles to the outer membrane of the nerve cell. The zipper opens up and signal substances are released. Südhof´s discovery explained how temporal precision is achieved and how vesicles´ contents can be released on command.
Vesicle transport gives insight into disease processes

The three Nobel Laureates have discovered a fundamental process in cell physiology. These discoveries have had a major impact on our understanding of how cargo is delivered with timing and precision within and outside the cell.  Vesicle transport and fusion operate, with the same general principles, in organisms as different as yeast and man. The system is critical for a variety of physiological processes in which vesicle fusion must be controlled, ranging from signalling in the brain to release of hormones and immune cytokines. Defective vesicle transport occurs in a variety of diseases including a number of neurological and immunological disorders, as well as in diabetes. Without this wonderfully precise organization, the cell would lapse into chaos.

You can find out more about the recipients here (scroll down).

Blood-, milk-, and mucus-powered electronics

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Researchers at Tel Aviv University ([TAU] Israel) have already begun to develop biodegradable display screens in their quest to create electronic devices powered by blood, milk, and mucus proteins found in our bodies. From the March 7, 2012 news item on Nanowerk,

… a team including Ph.D. students Elad Mentovich and Netta Hendler of TAU’s Department of Chemistry and The Center for Nanoscience and Nanotechnology, with supervisor Dr. Shachar Richter and in collaboration with Prof. Michael Gozin and his Ph.D. student Bogdan Belgorodsky, has brought together cutting-edge techniques from multiple fields of science to create protein-based transistors — semi-conductors used to power electronic devices — from organic materials found in the human body. They could become the basis of a new generation of nano-sized technologies that are both flexible and biodegradable.

The March 7, 2012 news release on the American Friend of TAU website notes some of the issues with silicon-based electronics,

One of the challenges of using silicon as a semi-conductor is that a transistor must be created with a “top down” approach. Manufacturers start with a sheet of silicon and carve it into the shape that is needed, like carving a sculpture out of a rock. This method limits the capabilities of transistors when it comes to factors such as size and flexibility.

The TAU researchers turned to biology and chemistry for a different approach to building the ideal transistor. When they applied various combinations of blood, milk, and mucus proteins to any base material, the molecules self-assembled to create a semi-conducting film on a nano-scale. In the case of blood protein, for example, the film is approximately four nanometers high. The current technology in use now is 18 nanometers, says Mentovich.

Together, the three different kinds of proteins create a complete circuit with electronic and optical capabilities, each bringing something unique to the table. Blood protein has the ability to absorb oxygen, Mentovich says, which permits the “doping” of semi-conductors with specific chemicals in order to create specific technological properties. Milk proteins, known for their strength in difficult environments, form the fibers which are the building blocks of the transistors, while the mucosal proteins have the ability to keep red, green and, blue fluorescent dyes separate, together creating the white light emission that is necessary for advanced optics.

Overall, the natural abilities of each protein give the researchers “unique control” over the resulting organic transistor, allowing adjustments for conductivity, memory storage, and fluorescence among other characteristics.

I have previously featured work on vampire (blood-powered) fuel cells and batteries  in my July 18, 2012 posting and my April 3, 2009 posting so the notion of using blood (and presumably other bodily fluids) as a source for electrical power is generating (pun intended, weak though it is) interest in many research labs.

While the researchers don’t speculate about integrating these new carbon-based devices, which are smaller and more flexible than current devices, in bodies (from the American Friends of TAU news release),

Technology is now shifting from a silicon era to a carbon era, notes Mentovich, and this new type of transistor could play a big role. Transistors built from these proteins will be ideal for smaller, flexible devices that are made out of plastic rather than silicon, which exists in wafer form that would shatter like glass if bent. The breakthrough could lead to a new range of flexible technologies, such as screens, cell phones and tablets, biosensors, and microprocessor chips.

Just as significant, because the researchers are using natural proteins to build their transistor, the products they create will be biodegradable. It’s a far more environmentally friendly technology that addresses the growing problem of electronic waste, which is overflowing landfills worldwide.

The biodegradability of these proposed devices may be a problem if they are integrated into our bodies but it is certain that this will be attempted as we continue to explore machine/flesh possibilities.

Memristors and proteins

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The memristor, a two-terminal circuit element joining the resistor, capacitor, and inductor, has until now been demonstrated using nonbiological materials such as metal oxides, carbon, etc. Researchers in Singapore have reported in a paper (in the Sept. 5, 2011 online edition of Small, Protein-Based Memristive Nanodevice)  that a memristive nanodevice can be based on a protein. From the Sept. 15, 2011 Spotlight article by Michael Berger on Nanowerk,

Memristors – the fourth fundamental two-terminal circuit element following the resistor, the capacitor, and the inductor – have attracted intensive attention owing to their potential applications for instance in nanoelectronic memories, computer logic, or neuromorphic computer architectures.

…

“Previous work on memristors were based on man-made inorganic/organic materials, so we asked the question whether it is possible to demonstrate memristors based on natural materials,” Xiaodong Chen, an assistant professor in the School of Materials Science & Engineering at Nanyang University, tells Nanowerk. “Many activities in life exhibit memory behavior and substantial research has focused on biomolecules serving as computing elements, hence, natural biomaterials may have potential to be exploited as electronic memristors.”

…

This work provides a direct proof that natural biomaterials, especially redox proteins, could be used to fabricate solid state devices with transport junctions, which have potential applications in functional nanocircuits.

My last posting about memristors was April 13, 2011, Blood, memristors, cyborgs plus brain-controlled computers, prosthetics, and art.

ETA Sept. 21, 2011: Dexter Johnson at Nanoclast (on the Institute of Electrical and Electronics Engineers website) offers another take on memristors in his Sept. 20,2011 posting, Memristors Go Biological. I particularly liked this bit,

It’s been just three years since the memristor was identified so if statistical norms of commercialization are in place we can expect another four years of waiting before we see this material in our smart phones. In fact, this timeline is pretty close to HP’s expectations of 2014 as a target date for its incorporation into electronic devices.

During this time researchers have not been and will not be sitting on their hands while engineers work out scalability and yields.

Biomimicry, proteins, muscles, and the University of British Columbia’s Dr. Hongbin Li

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This morning, I was excited to receive a news release about Dr. Hongbin Li’s recent work which has been published in Nature magazine. A Canada Research Chair in Molecular Nanoscience  and Protein Engineering at the University of British Columbia (Canada), Dr. Li’s work has been featured here before. (Part 1 and Part 2 of the interviews where he patiently answered my uninformed questions about his 2008 work on proteins where he had them behave like shock absorbers.) This latest work builds on his 2008 discoveries and extends them as he considers muscle elasticity.

From the news release,

University of British Columbia researchers have cast artificial proteins into a new solid biomaterial that very closely mimics the elasticity of muscle.

The approach, detailed in the current issue of the journal Nature, opens new avenues to creating solid biomaterials from smaller engineered proteins, and has potential applications in material sciences and tissue engineering.

“There are obvious long-term implications for tissue engineers,” says Hongbin Li, associate professor in the Dept. of Chemistry. “But at a fundamental level, we’ve learned that the mechanical properties we engineer into the individual proteins that make up this biomaterial can be translated into useful mechanical properties at the larger scale.”

The work will be published tomorrow “Designed biomaterials to mimic the mechanical properties of muscles” by Shanshan Lv, Daniel M. Dudek, Yi Cao, M. M. Balamurali, John Gosline, Hongbin Li in Nature 465, 69-73 (6 May 2010) doi:10.1038/nature09024 Letter.

Again from the news release,

The mechanical properties of these biomaterials can be fine-tuned, providing the opportunity to develop biomaterials that exhibit a wide range of useful properties – including mimicking different types of muscles. The material is also fully hydrated and biodegradable.

I wonder where are these ‘muscles’ going to appear? On robots?

Congratulations to Dr. Hongbin Li and your colleagues, Shanshan Lv, Daniel M. Dudek, Yi Cao, M. M. Balamurali, and John Gosline.