MIT team digitizes historic sanctuary of Machu Picchu

For many people, the Inca city of Machu Picchu in the Andes of Peru is one of the most recognizable icons of archaeological and adventure tourism in the world. However, for the Peruvian people and for the international scientific community, Machu Picchu is much more than a tourist destination. In addition to being a United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Site, the historic sanctuary has great cultural and economic importance for Peru and the region of Cusco.

The first references to attempts to document the city of Machu Picchu date back to the late 19th century, when Peruvian and European explorers toured the rugged mountains around the meandering Urubamba River. Some of the explorers did not hesitate to register their visit in the rock. On a wall of the Temple of the Three Windows, Agustin Lizarraga recorded, "July 14, 1902".

But it was Yale University Professor Hiram Bingham who extensively documented the site during his expedition in 1911, and made known to the international community the existence of the lost ruins of the Incas. Over the last 100 years, dozens of archaeological expeditions have contributed to increasing the architectural value and interest in the site, as well as the scientific knowledge of the extraordinary technologies developed by the Incas.

In order to digitally document and develop the foundations for future research, a laboratory team from the MIT Department of Architecture, led by Professor Takehiko Nagakura and PhD student Paloma Gonzales, has been working on the MISTI Global Seed Fund Machu Picchu Design Heritage project since 2016.

The team, the Architecture Representation and Computation Group, has led the first extensive expedition to digitally document Machu Picchu, using the latest generation of instruments and techniques to explore the site’s architectural and urban importance  and develop a 3-D site map using virtual reality and augmented reality. The Architecture Representation and Computation Group has an important record of working with digital capturing technologies on World Heritage Sites in Italy, China, Singapore, and Japan.

"We believe that documentation through computational techniques for the digitalization of architectural monuments is key to the preservation of the cultural heritage of humanity," Nagakura says. “But it is just a simple idea for old practice. From Renaissance time, architects have been going to building sites, and drawing them up to study them. We are just replacing tape measures and Mylar sheets with scanning tools and VR headsets.”

For the project in Peru, the team visited the archaeological complex on two occasions for several weeks in mid-2017 and early 2018. At the site, more than 9,000 images were collected through panoramic cameras, photogrammetric scanning tools, and drones. Gonzales says the working hours were “intense.”

“We had to reach the archaeological monument before the arrival of the tourists and stay after the closure of the monument," she says. “The great commitment and joint work of the MIT team and the San Antonio Abad del Cusco University, supported by the Decentralized Directorate of Culture of Cusco, made the work fruitful and rewarding.”

Based on the photogrammetric data they sampled, the team developed 3-D models and are working on creating virtual reality experiences that would allow people to immerse themselves in Machu Picchu from anywhere on the planet. The same 3-D models are also being deployed to make a new interactive map of Machu Picchu that superimposes the photographic 3-D view of the site through augmented reality.

Last December, the team launched the MIT Design Heritage Platform, where visitors can see and explore part of the work they have done. In addition, they plan to make this platform a tool to collect images from those who can contribute to the data bank through crowdsourcing.

The project has also managed to document the architectural characteristics and construction materials of the city with high-resolution photographic techniques. The images constitute a unique database with rich information on aspects such as landscape and vegetation at the time the photographs were taken. The team will make all of the information collected available to the authorities of the archaeological monument.

At the same time, they expect that other disciplines can use the databases and photogrammetric models they are developing. The documentation has already been used in conservation efforts, including in the reconstruction of Wiñay Wayna, an archeological site located on the Inca Trail leading to Machu Picchu that was destroyed by a recent flood storm.

Fernando Astete, anthropologist and head of the National Archaeological Park of Machu Picchu, says: "We are very excited with the MIT team work. We welcome all efforts to research and preserve Machu Picchu. We have to protect our heritage for the next generations.”

Architect Cesar Medina, responsible for the digitization of the national park, believes that the collaboration with MIT has been enriching.

“We have been working in 3-D documentation since 2013, but the collaboration with the MIT team lead by Professor Nagakura, with the support of our local university, has allowed us to exhaustively document Machu Picchu, making use of the latest technologies and innovative techniques,” Medina says. “Moreover, we have had the opportunity to visit and know the work of his lab; we see with great interest to continue working in the future with MIT.”

The Architecture Representation and Computation Group is already in conversation with institutions of higher education and heritage conservation of Peru to continue advancing the project of digital inheritance. In addition to continuing in Machu Picchu, they may extend the documentation areas to other archaeological sites of Peru. The project has also opened the doors to possible interdisciplinary collaborations with materials science researchers, urban planners, hydrologist, engineers, archaeologists, and historians.

The Machu Picchu Design Heritage project was made possible thanks to the MISTI Global Seed Funds. MISTI is a part of the Center for International Studies within the School of Humanities, Arts, and Social Sciences (SHASS). The project was also sponsored by the Council of Science, Technology and Technological Innovation of Peru, with the support of the National University of Saint Anthony the Abbot in Cuzco and the Decentralized Directorate of Culture of Cusco.

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“At MIT I found my home!”

On a sunny Monday morning on the oval lawn in front of Kresge Auditorium, MIT President L. Rafael Reif and the Institute’s top administrators and selected faculty delivered their annual Convocation to welcome the incoming first-year class of 2022.

Reif recalled some of his fears and concerns when he first arrived at MIT in 1980 as an assistant professor, including whether he would fit in, whether his accent would interfere with communications — and how he would cope with New England’s winters, after arriving from his native Venezuela, where winters were, as he described, “like this,” referring to the summery day with temperatures in the 80s.

“I knew almost no one, I was very far from home, and I was worried,” he said, in a story he described as being typical of many who arrive at MIT. “I was worried about fitting in on a campus more than 2,000 miles from my home.” But he concluded that “I’m here to tell you that all of my concerns, those anxious moments wondering if I had made the right decision, all of them were unfounded.”

Instead, he said, “I discovered a community of students, faculty, researchers, and staff that were a lot like me: They were curious, they asked questions, they were passionate, they liked to tinker. Most of them came from somewhere else. And they cared about helping each other and serving society.”

MIT is still that way, Reif said, in a way that’s deeply ingrained in its culture: “At MIT, I found my home.”

But it won’t always be easy, he told the incoming students. “Your classes will require equal parts of hard work, discipline, and dedication. You will enjoy great moments of success, but you may experience moments of doubt too,” he said. At those moments, he suggested, they should remember three things: “First, you belong here.” The selections overseen by Dean of Admissions Stuart Schmill, he said, show “a remarkable knack for finding the right students” for each year’s classes. In short, he said, “In Stu we trust.”

Second, he said, “all of us experience doubts about ourselves, even the distinguished professors you see on stage.” Those doubts often arise when pushing oneself or trying something new, he said. “If you have doubts about yourself, it’s just a sign that you are learning.”

And finally, he said, “you are surrounded by a community that cares about you. All of us are dedicated to your success, and we believe in you.”

Three faculty members spoke about their own experiences of MIT and of their initial feelings when they arrived here. Yoel Fink, a professor of materials science and engineering and director of the $300 million Advanced Functional Fabrics of America (AFFOA) institute, spoke of his time when he came to MIT as a graduate student, and couldn’t figure out where the Institute was after getting off the subway at Kendall Square. Growing up in Jerusalem, he was accustomed to schools and universities being surrounded by fences and guards, and was surprised to find the campus so open.

He came to realize that such openness was “an important aspect of MIT culture,” he said, and part of what makes it special: “openness, freedom, and with very few imposed boundaries.”

Fink recalled some humbling moments from his early days here, including when he scored a failing grade of 55 on one of his first midterm exams. After interviewing with dozens of professors, he still hadn’t come up with a research project after a year of trying, and his first manuscript was rejected by referees as being neither new nor interesting. And a professor offered him a table in her office because she said he was so shy and socially inept.

Then he described an early meeting after he had been given a thick book describing a research project that had just been funded by the U.S. Defense Advanced Research Projects Agency (DARPA). When he read the plan, he found that the solutions being proposed were “beautiful, but highly complex and certainly not very practical.” He thought of a much simpler approach, and was surprised that it wasn’t even mentioned in the report. As a student, he was at first reluctant to say anything about this, since the plan had been drawn up by highly respected, world-leading professors in their field. But at the end of the meeting, he decided to ask about this idea, and his question was greeted with a stunned silence.

In fact, the idea he was suggesting then turned out to form the basis for the discovery of a new type of mirror; then a paper in Nature; an invention that The New York Times described as “the perfect mirror”; his faculty position at MIT; much of his research since then; and the basis for a medical device that helped to cure 300,000 people — many of them with brain tumors. The idea also laid the groundwork for the creation of AFFOA, he said. “I owe my career to that chance moment and to asking that question,” he said. “MIT is the world’s best launchpad for ideas.”

Fink opened his comments by paying tribute to the recently deceased Sen. John McCain, citing his heroism and his long struggle with brain cancer — a struggle that is shared by Fink’s 14-year-old son and by a recent MIT student, he said.

Robotics researcher Cynthia Breazeal, an associate professor of media arts and sciences, described an event she helped to organize when she was a graduate student here. As part of a mini-Olympics during the January Independent Activities Period, she and her classmates decided to put on a tug-of-war, and to make it more interesting they decided to do it with a jello pit — and, being January, it all had to be indoors. She outlined the considerable research and labor needed to bring that about, including finding the supplies and making 500 gallons of non-edible green gelatin, and conducting the event without leaving any residue that would have to be cleaned up by others.

The story, she said, illustrated both MIT’s tolerance for wild and creative forms of play, and for MIT students’ willingness to work long and hard to achieve success in even their most frivolous undertakings. “Go out there and have some hard fun together,” she advised.

Collin Stultz, a professor of electrical engineering and computer science and head of MIT’s Institute for Medical Engineering and Science, said that there is one word that for him “really typifies the MIT experience … and that word is family — the MIT family.”

He said that, like a family, “we comfort each other in difficult times, we help each other when we struggle in the classroom or otherwise, and we collectively celebrate our accomplishments as students and faculty alike. Moreover, the distinction between faculty and students is a bit blurred here, more than in other institutions that I have been at in the past.” (Stultz is a graduate of Harvard University). “We all learn from one another, we grow with one another, and I hope that I have imparted to my students as much as they have imparted to me. … Welcome to the MIT family!”

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New approach makes sprayed droplets hit and stick to their targets

When spraying paint or coatings onto a surface, or fertilizers or pesticides onto crops, the size of the droplets makes a big difference. Bigger drops will drift less in the wind, allowing them to strike their intended targets more accurately, but smaller droplets are more likely to stick when they land instead of bouncing off.

Now, a team of MIT researchers has found a way to balance those properties and get the best of both — sprays that don’t drift too far but provide tiny droplets to stick to the surface. The team accomplished this in a surprisingly simple way, by placing a fine mesh in between the spray and the intended target to break up droplets into ones that are only one-thousandth as big.

The findings are reported today in the journal Physical Review Fluids, in a paper by MIT associate professor of mechanical engineering Kripa Varanasi, former postdoc Dan Soto, graduate student Henri-Louis Girard, and three others at MIT and at CNRS in Paris.

(Courtesy of the Varanasi Lab)

Earlier work by Varanasi and his team had focused on ways to get the droplets to stick more effectively to the surfaces they strike rather than bouncing away. The new study focuses on the other end of the problem — how to get the droplets to reach the surface in the first place. Varanasi explains that typically less that 5 percent of sprayed liquids actually stick to their intended targets; of the 95 percent or more that gets wasted, about half is lost to drift and never even gets there, and the other half bounces away.

Atomizers — devices that can spray liquids in the form of droplets so small that they remain suspended in air rather than settling out — are crucial parts of many industrial processes, including painting and coating, spraying fuel into engines or water into cooling towers, and printing with fine droplets of ink. The new advance developed by this team was to make the initial spray in the form of larger drops, which are much less affected by breezes and more likely to reach their targets, and then to create the much finer droplets just before they reach the surface, by placing a mesh screen in between.

Though the process could apply to many different spraying applications, “the big motivation is agriculture,” Varanasi says. The runoff of pesticides that miss their target and fall on the ground can be a significant cause of pollution and a waste of the expensive chemicals. What’s more, the impact of finer droplets is less likely to damage or weaken certain plants.

Farmers already cover some kinds of crops with fabric meshes, to protect against birds and insects devouring the plants, so the process is already familiar and widely used. Many kinds of mesh materials would work, the researchers say — what matters is the size of the openings in the mesh and the material’s thickness, parameters the team has precisely quantified through a series of lab experiments and mathematical analysis. For their experiments, the researchers primarily used a commonly available and inexpensive fine stainless steel mesh.

The researchers propose that, after deploying the mesh over the crop, either directly supported by the plant stalks or supported on a framework, a farmer could simply use a conventional sprayer that produces larger drops, which would stay on course even in breezy conditions. Then, as the drops reach the plants, they would be broken up by the mesh into fine droplets, each about a tenth of a millimeter across, which would greatly increase their chances of sticking.

(Courtesy of the Varanasi Lab)

As an extra bonus, the presence of the mesh over the crops could also protect them from damage from rainstorms, by also breaking up the raindrops into smaller droplets that place less stress on the plant when they strike. Crop damage from storms, which can seriously reduce yields in some cases, may be reduced in the process, the researchers say. In addition, bigger drops cause more splashing, which can lead to a spread of pathogens.

Besides being more efficient, the process may also reduce the problem of drift of pesticides, which sometimes blow from one farmer’s field to another, and even from one state to another, Varanasi says, and also sometimes end up in people’s homes. “People want to fix this. They’re looking for solutions.”

The same principle could be applied to other uses, Girard points out, such as the spraying of water into cooling towers such as those used for electric power plants and many industrial or chemical plants. Using a mesh below the spray heads in such towers “can create finer droplets, which evaporate faster and provide better cooling,” he says. Cooling efficiency is related to the drop’s surface area, which is three orders of magnitude greater with the finer droplets, he says.

In recent work, Varanasi and his team found a way to recover much of the water that gets lost to evaporation from such cooling towers, by using a different kind of mesh over the towers’ top. The new finding could be combined with that method, thus improving power plant efficiency on both the input and output sides.

For painting and for applying other kinds of coatings, the finer the droplets are, the better they cover and adhere, Girard says, so the process could improve the quality and durability of the coatings.

While most existing atomization methods rely on high pressure to force liquid through a narrow opening, which requires energy to create the pressure, this method is purely passive and mechanical, Girard says. “Here, we let the mesh do the atomization essentially for free.”

The team included Antoine Le Helloco, and Thomas Binder at MIT and David Quere at CNRS in Paris. The work was supported by the MIT-France program.

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3 Questions: Philip Harris on first observation of long-predicted Higgs boson decay

Today, scientists at CERN, the European Organization for Nuclear Research, have announced that, for the first time, they have observed the Higgs boson transforming into elementary particles known as bottom quarks as it decays. Physicists have predicted this to be the most common way in which most Higgs bosons should decay, but until now, it has been extremely difficult to pick out the decay’s subtle signals. The discovery is a significant step towards understanding how the Higgs boson gives mass to all the fundamental particles in the universe.

The scientists made their discovery using the ATLAS and the CMS detectors, two major experiments designed to analyze the high-energy particle collisions generated by CERN’s Large Hadron Collider (LHC) — the largest, most powerful particle accelerator in the world.

Higgs bosons, which were first discovered in 2012, are an incredible rarity, and are produced in just one out of every billion LHC collisions. Once smashed into existence, the particles vanish almost immediately, decaying into a stream of secondary particles. The Standard Model of physics, which is the most widely accepted theory for describing the interactions of most particles in the universe, predicts that nearly 60 percent of Higgs bosons should decay to bottom quarks, elementary particles that are about four times as massive as a proton.

Both the ATLAS and CMS teams spent several years refining techniques and incorporating more data in their hunt for this most common Higgs boson decay. Both experiments ultimately confirmed that, for the first time, they saw evidence of a Higgs boson decaying to a bottom quark, with a statistically high degree of confidence.

MIT physicists in the Laboratory for Nuclear Science have been involved in analyzing and interpreting data for this new discovery, including Philip Harris, assistant professor of physics. MIT News spoke with Harris, who is also a member of the CMS experiment, about the mind-bending search for a vanishing transformation, and how the new Higgs discovery may help physicists to understand why the universe has mass.

Q: Put this discovery in context for us a bit. How significant is it that your team has observed the Higgs boson decaying to bottom quarks?

A: The Higgs boson has two distinct mechanisms: It gives mass to the force particles involved in electroweak interactions, the force responsible for nuclear beta decay; and it gives mass to the fundamental particles inside the atom, the quarks and the leptons (such as electrons and muons). Despite the fact that it is responsible for both mechanisms, the Higgs discovery and the subsequent Higgs property measurements have largely been performed with the electroweak force particles. We have only recently directly observed Higgs interactions with matter. This measurement, the Higgs boson decaying to a bottom quark, is the first time we have directly observed Higgs-to-quark interactions. This confirms that quarks do indeed get mass from the Higgs mechanism. 

Q: How tricky was this detection to make, and how was it finally observed?

A: Roughly 60 percent of all Higgs decays are to bottom quarks. This is the largest single decay channel of the Higgs boson. However, it is also the channel that has the largest background [noise from surrounding particles]. Depending on how you count it, it’s about a million times larger than the channels we used to discover the Higgs boson.

People like to compare Higgs measurements with finding a needle in a haystack. Here, I think that a more apt analogy is a magic-eye stereogram. You are looking for a broad distortion in the data that is very difficult to see. The trick of trying to see this distortion is like a magic eye: You have to figure out how to focus right.

To calibrate our “focus,” we looked at the electroweak force particle, the Z boson, and its decay to bottom quarks. Once we were able to see the Z boson going into bottom quarks, we set our target to the Higgs boson, and there it was. I should stress that to see this distortion clearly we had to rely on technology that was at its infancy at the time of the Higgs boson discovery, including some of the most recent advancements in machine learning. In fact, only a few years ago it was taught in your standard particle physics class that it was impossible to observe the Higgs decays in some of these channels. 

Q: The original discovery of the Higgs boson has been touted as a landmark discovery that will ultimately reveal the mystery to why atoms have mass. How will this new discovery of the Higgs decay help to solve this mystery?

A: Following the Higgs boson discovery, we have learned a lot about how the Higgs mechanism gives mass to different particles. However, many would argue that after the Higgs boson discovery, high energy physics has gotten even more interesting because it is starting to look like our conventional view of particle physics doesn’t fit just right.

One of the best ways to test our view is by measuring the properties of the Higgs boson. The Higgs-to-bottom-quark decay is essential to this understanding because it allows us to directly probe the properties of Higgs and quark matter interactions and because of its large decay rate, which means we can measure the Higgs boson in all sorts of scenarios that are not possible with other decay modes.

This observation gives us a new and powerful tool to probe the Higgs boson. In fact, as part of this measurement, we were able to measure Higgs bosons with energies over twice the energy of the highest Higgs bosons previously observed. 

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Exploring cancer metabolism

Nearly 100 years ago, the German chemist Otto Warburg discovered that cancer cells metabolize nutrients differently than most normal cells. His discovery launched the field of cancer metabolism research, but interest in this area waned; by the 1970s most cancer scientists had shifted their focus to the genetic mutations that drive cancer development.

In the past decade or so, interest in cancer metabolism has resurged, and the first drugs that target cancer cells’ abnormal metabolism were approved to treat leukemia in 2017.

“Cancer metabolism is a very sophisticated field at this point,” says Matthew Vander Heiden, an associate professor of biology at MIT. “We have a lot better understanding of what nutrients cancer cells use and what determines how those nutrients are used. This has led to different ways to think about drugs.”

Vander Heiden, who is also a member of MIT’s Koch Institute for Integrative Cancer Research, is one of the people responsible for the recent surge in cancer metabolism research. As a graduate student and postdoc, he published some of the first studies of how cancer cells alter their metabolism, and now his lab at MIT is devoted to the topic.

“All of the time that I was in grad school and working as a postdoc, I was never working in a lab that was dedicated to studying metabolism. So my vision, if someone gave me a job, was to set up a lab that could really be built in a way that would allow us to ask questions about metabolism,” he says.

Metabolism and cancer

Vander Heiden grew up in a small town in Wisconsin, and unlike most of his high school classmates, he headed out of state for college, to the University of Chicago. He was interested in science, so decided on a pre-med track. A work-study job in a plant biology lab led him to discover that he also enjoyed doing research.

“At that point I already had this idea I was going to go to medical school, but then the idea of MD/PhD came up, and I ended up going down that path,” Vander Heiden says.

While in the MD/PhD program at the University of Chicago Medical School, he worked in the lab of Craig Thompson, now president of Memorial Sloan Kettering Cancer Center. At that time, Thompson was studying the biochemical regulation of apoptosis, the programmed cell death pathway. For his PhD thesis, Vander Heiden investigated the function of a protein called Bcl-x, which is a regulator of apoptosis found in the membranes of mitochondria — cell organelles responsible for generating energy.

“That project really got me thinking about how the mitochondria work and how metabolism works,” Vander Heiden recalls. “At the time, I came to the realization that we don’t understand cell metabolism anywhere near as well as we thought we did, and someone should really study this.”

After finishing his degrees, he spent five years doing clinical training, then decided to pursue research in cancer metabolism.

“Altered metabolism has been known about in cancer for 100 years, but few people were studying it,” Vander Heiden says. “The challenge was finding a lab that would allow me to study metabolism and cancer, which in 2004-2005 was not such an obvious thing to do.”

He ended up going to Harvard Medical School to work with Lewis Cantley, who studies signaling pathways in cells and was receptive to the idea of exploring cancer metabolism. There, Vander Heiden began studying an enzyme called pyruvate kinase M2 (PKM2), which is involved in regulation of glycolysis, a biochemical process that cells use to break down sugar for energy.

In 2008, Vander Heiden, Cantley, and others at Harvard Medical School reported that when cells shift between normal and Warburg (cancer-associated) metabolism, they start using PKM2 instead of PKM1, the enzyme that adult cells normally use for glycolysis. Cantley and Craig Thompson have since founded a company, Agios Pharmaceuticals, that is developing potential drugs that target PKM2, as well as other molecules involved in cancer metabolism.

While at Harvard, Vander Heiden also worked on a paper that contributed to the eventual development of drugs that target cancer cells with a mutation in the IDH gene. These drugs, the first modern FDA-approved cancer drugs that target metabolism, shut off an alternative pathway used by cancer cells with the IDH mutation.

New drug targets

In 2010, Vander Heiden became one of the first new faculty members hired after the creation of MIT’s Koch Institute, where he set up a lab focused on metabolism, particularly cancer metabolism.

His research has yielded many insights into the abnormal metabolism of cancer cells. In one study, together with other MIT researchers, he found that tumor cells turn on an alternative pathway that allows them to build lipids from the amino acid glutamine instead of the glucose that healthy cells normally use. He also found that altering the behavior of PKM2 to make it act more like PKM1 could stop tumor cell growth.

Studies such as these can offer insights that may help researchers to develop drugs that starve tumor cells of the nutrients they need, offering a new way to fight cancer, Vander Heiden says.

“If one wants to develop drugs that target metabolism, one really needs to focus on the context in which it’s happening, which is the environment of the cell plus the genetics of the cell,” he says. “That is what defines the sensitivity to drugs.”

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Scientists alter membrane proteins to make them easier to study

About 30 percent of the proteins encoded by the human genome are membrane proteins — proteins that span the cell membrane so they can facilitate communication between cells and their environment. These molecules are critical for learning, seeing, and sensing odors, among many other functions.

Despite the prevalence of these proteins, scientists have had difficulty studying their structures and functions because the membrane-bound portions are very hydrophobic, so they cannot be dissolved in water. This makes it much harder to do structural analyses, such as X-ray crystallography.

In an advance that could make it easier to perform this type of structural study, MIT researchers have developed a way to make these proteins water-soluble by swapping some of their hydrophobic amino acids for hydrophilic ones. The technique is based on a code that is much simpler than previously developed methods for making these proteins soluble, which rely on computer algorithms that have to be adapted to each protein on a case-by-case basis.

“If there is no rule to follow, it’s difficult for people to understand how to do it,” says Shuguang Zhang, a principal research scientist in the MIT Media Lab’s Center for Bits and Atoms. “The tool has to be simple, something that anyone can use, not a sophisticated computer simulation that only a few people know how to use.”

Zhang is the senior author of the study, which appears in the Proceedings of the National Academy of Sciences the week of Aug. 27. Other MIT authors are former visiting professor Fei Tao, postdoc Rui Qing, former visiting professor Hongzhi Tang, graduate student Michael Skuhersky, former undergraduate Karolina Corin ’03, SM ’05, PhD ’11, former postdoc Lotta Tegler, graduate student Asmamaw Wassie, and former undergraduate Brook Wassie ’14.

A simple code

Of the approximately 8,000 known membrane proteins found in human cells, scientists have discovered structures for about 50. They are widely viewed as very difficult to work with because once they are extracted from the cell membrane, they only maintain their structure if they are suspended in a detergent, which mimics the hydrophobic environment of the cell membrane. These detergents are expensive, and there is no universal detergent that works for all membrane proteins.

Zhang started working on a new way to tackle this problem in 2010, inspired by the late Alexander Rich, an MIT professor of biology. Rich posed the question of whether protein structures called alpha helices, which make up the bulk of the membrane-embedded portion of proteins, could be switched from hydrophobic to hydrophilic. Zhang immediately began working out possible solutions, but the problem proved difficult. Over the past eight years, he has had several students and visiting researchers help work on his idea, most recently Qing, who achieved success.

The key idea that allowed Zhang to develop the code is the fact that a handful of hydrophobic amino acids have very similar structures to some hydrophilic amino acids. This similarities allowed Zhang to come up with a code in which leucine is converted to glutamine, isoleucine and valine are converted to threonine, and phenylalanine is converted to tyrosine.

Another important factor is that none of these amino acids are charged, so swapping them appears to have a minimal effect on the overall protein structure. In fact, isoleucine and threonine are so similar that ribosomes, the cell structures that assemble proteins, occasionally insert the wrong one — about once in every 200 to 400 occurrences.

The researchers call their code the QTY code, after the three letters that represent glutamine, threonine, and tyrosine, respectively.

In their earliest efforts to implement this code, the researchers substituted only a small fraction of the hydrophobic amino acids embedded in the membrane, but the resulting proteins still needed some detergent to dissolve. They increased the replacement rate to about 50 percent, but the proteins were still not fully water-soluble, so they replaced all instances of glutamine, isoleucine, valine, and phenylalanine embedded in the membranes. This time, they achieved success.

“It’s only when we replace all the hydrophobic residues in the transmembrane regions that we’re able to get proteins that are stable and completely free of detergent in an aqueous system,” Qing says.

Structural similarities

In this study, the researchers demonstrated their technique on four proteins that belong to a class of proteins known as G protein-coupled receptors. These proteins help cells to recognize molecules such as hormones or immune molecules called chemokines and trigger an appropriate response within the cell.

Joel Sussman, a professor of structural biology at the Weizmann Institute of Science, described the new method as “incredibly simple and elegant.”

“Although a number of scientists have been trying to find a way to ‘solubilize’ G protein-coupled receptors and other integral membrane proteins, until now their methods have not been of general use and often involved very complex computational methods that would not be widely applicable,” says Sussman, who was not involved in the research.

The researchers are still working towards obtaining the precise structures of these proteins using X-ray crystallography or nuclear magnetic resonance (NMR), but they performed some experiments that suggest the structures are similar. In one, they showed that the water-soluble proteins denature at nearly the same temperature as the original versions of the proteins. They also showed that the modified proteins bind to the same target molecules that the original proteins bind to, although not as strongly.

Being able to synthesize water-soluble versions of these proteins could enable new applications such as sensors that can detect environmental pollutants, the researchers say.

Another possibility is designing water-soluble versions of the proteins that bind to molecules normally expressed by cancer cells, which could be used to diagnose tumors or identify metastatic cancer cells in blood samples, Zhang says. Researchers could also create water-soluble molecules in which a membrane-bound receptor that viruses normally bind to is attached to part of an antibody. If these “decoy therapies” were injected into the body, viruses would bind to the receptors and then be cleared by the immune system, which would be activated by the antibody portion.

The research was funded by OH2 Laboratories and the MIT Center for Bits and Atoms Consortium, which includes the Bay Valley Innovation Center.

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Sun-powered car shines in American Solar Challenge

MIT’s Solar Electric Vehicle Team (SEVT) completed their first race in three years, the 2018 American Solar Challenge (ASC), last month. The team was awarded 5th place overall in the single-occupant vehicle class.

The event was a series of competitions during which the team proved their exceptional talent and problem-solving abilities. In order to qualify for the American Solar Challenge, teams have to successfully complete various tests and races that fall under one of two categories: Scrutineering and the Formula Sun Grand Prix (FSGP).

Scrutineering is a four-day process during which race officials test each car to confirm they are in line with challenge regulations. Included are electrical, dynamic, and mechanical tests. The team performed exceptionally well in electrical scrutineering. Mechanical scrutineering, however, brought bsome bumps in the road, mainly issues arising from the vehicle’s suspension system. The group did not let this setback bring them down, however.

“The team was able to locate and debug each issue efficiently, collaboratively, and successfully,” noted MIT SEVT captain and junior Caroline Jordan.

The group successfully passed all mechanical and dynamic tests on the fourth and final day of Scrutineering. Jordan recalled that — although it was a stressful time for the team — “we gained a lot of knowledge and grew as engineers and people.”

Qualifying continued with the FSGP, a three-day track race held at the Motorsport Park Hastings in Hastings, Nebraska. Teams who successfully completed the race would be granted entrance to the American Solar Challenge.

At the start of FSGP, an issue surfaced for the MIT SEVT: The tires on their vehicle were burning through. Instead of feeling discouraged, the team came together and inspected the car to find a solution. The following day, they were back in the game. The team drove 107 laps and received fourth place for single-occupant vehicles.

“At this point, the car was doing amazingly and we qualified for ASC that day,” Jordan said.

The ASC itself lasted nine days. This year's challenge was a 1762.7 mile race that followed the Oregon Trail from Omaha, Nebraska to Bend, Oregon.

“Because of all of the fixes we had already identified, the car was very reliable going into the road race,” Jordan explains. The group performed well in spite of some small issues due to weather and race operations. MIT SEVT’s vehicle completed the race within their time limit using only solar power. The team received fifth place in the single-occupant vehicle class.

Team member and sophomore Cece Chu notes that in spite of some technical difficulties, her team members kept her motivated throughout the competition.

“The amount of planning, time, and effort that was put into the car during and leading up to the race was extraordinary, and the team had to display a lot of determination and sheer grit to get us through the qualifications,” she said. “My teammates are honestly the most hardworking and dedicated people I know, and seeing these qualities brought out firsthand during the race was incredibly motivating for me.”

Jordan noted that the upcoming school year is set to be a big one for the MIT SEVT.

“We will be entering a design year, during which we can pull from the vast amount of knowledge we gained during this race to use in the design process of our next car,” she explained. “It will be a very exciting time for the team.”

de MIT News https://ift.tt/2wkbZ2n