MIT chemists explain why dinosaur collagen may have survived for millions of years

Collagen, a protein found in bones and connective tissue, has been found in dinosaur fossils as old as 195 million years. That far exceeds the normal half-life of the peptide bonds that hold proteins together, which is about 500 years.

A new study from MIT offers an explanation for how collagen can survive for so much longer than expected. The research team found that a special atomic-level interaction defends collagen from attack by water molecules. This barricade prevents water from breaking the peptide bonds through a process called hydrolysis.

“We provide evidence that that interaction prevents water from attacking the peptide bonds and cleaving them. That just flies in the face of what happens with a normal peptide bond, which has a half-life of only 500 years,” says Ron Raines, the Firmenich Professor of Chemistry at MIT.

Raines is the senior author of the new study, which appears today in ACS Central Science. MIT postdoc Jinyi Yang PhD ’24 is the lead author of the paper. MIT postdoc Volga Kojasoy and graduate student Gerard Porter are also authors of the study.

Water-resistant

Collagen is the most abundant protein in animals, and it is found in not only bones but also skin, muscles, and ligaments. It’s made from long strands of protein that intertwine to form a tough triple helix.

“Collagen is the scaffold that holds us together,” Raines says. “What makes the collagen protein so stable, and such a good choice for this scaffold, is that unlike most proteins, it’s fibrous.”

In the past decade, paleobiologists have found evidence of collagen preserved in dinosaur fossils, including an 80-million-year-old Tyrannosaurus rex fossil, and a sauropodomorph fossil that is nearly 200 million years old.

Over the past 25 years, Raines’ lab has been studying collagen and how its structure enables its function. In the new study, they revealed why the peptide bonds that hold collagen together are so resistant to being broken down by water.

Peptide bonds are formed between a carbon atom from one amino acid and a nitrogen atom of the adjacent amino acid. The carbon atom also forms a double bond with an oxygen atom, forming a molecular structure called a carbonyl group. This carbonyl oxygen has a pair of electrons that don’t form bonds with any other atoms. Those electrons, the researchers found, can be shared with the carbonyl group of a neighboring peptide bond.

Because this pair of electrons is being inserted into those peptide bonds, water molecules can’t also get into the structure to disrupt the bond.

To demonstrate this, Raines and his colleagues created two interconverting mimics of collagen — the one that usually forms a triple helix, which is known as trans, and another in which the angles of the peptide bonds are rotated into a different form, known as cis. They found that the trans form of collagen did not allow water to attack and hydrolyze the bond. In the cis form, water got in and the bonds were broken.

“A peptide bond is either cis or trans, and we can change the cis to trans ratio. By doing that, we can mimic the natural state of collagen or create an unprotected peptide bond. And we saw that when it was unprotected, it was not long for the world,” Raines says.

“This work builds on a long-term effort in the Raines Group to classify the role of a long-overlooked fundamental interaction in protein structure,” says Paramjit Arora, a professor of chemistry at New York University, who was not involved in the research. “The paper directly addresses the remarkable finding of intact collagen in the ribs of a 195-million-old dinosaur fossil, and shows that overlap of filled and empty orbitals controls the conformational and hydrolytic stability of collagen.”

“No weak link”

This sharing of electrons has also been seen in protein structures known as alpha helices, which are found in many proteins. These helices may also be protected from water, but the helices are always connected by protein sequences that are more exposed, which are still susceptible to hydrolysis.

“Collagen is all triple helices, from one end to the other,” Raines says. “There’s no weak link, and that’s why I think it has survived.”

Previously, some scientists have suggested other explanations for why collagen might be preserved for millions of years, including the possibility that the bones were so dehydrated that no water could reach the peptide bonds.

“I can’t discount the contributions from other factors, but 200 million years is a long time, and I think you need something at the molecular level, at the atomic level in order to explain it,” Raines says.

The research was funded by the National Institutes of Health and the National Science Foundation.

Study: EV charging stations boost spending at nearby businesses

Charging stations for electric vehicles are essential for cleaning up the transportation sector. A new study by MIT researchers suggests they’re good for business, too.

The study found that, in California, opening a charging station boosted annual spending at each nearby business by an average of about $1,500 in 2019 and about $400 between January 2021 and June 2023. The spending bump amounts to thousands of extra dollars annually for nearby businesses, with the increase particularly pronounced for businesses in underresourced areas.

The study’s authors hope the research paints a more holistic picture of the benefits of EV charging stations, beyond environmental factors.

“These increases are equal to a significant chunk of the cost of installing an EV charger, and I hope this study sheds light on these economic benefits,” says lead author Yunhan Zheng MCP ’21, SM ’21, PhD ’24, a postdoc at the Singapore-MIT Alliance for Research and Technology (SMART). “The findings could also diversify the income stream for charger providers and site hosts, and lead to more informed business models for EV charging stations.”

Zheng’s co-authors on the paper, which was published today in Nature Communications, are David Keith, a senior lecturer at the MIT Sloan School of Management; Jinhua Zhao, an MIT professor of cities and transportation; and alumni Shenhao Wang MCP ’17, SM ’17, PhD ’20 and Mi Diao MCP ’06, PhD ’10.

Understanding the EV effect

Increasing the number of electric vehicle charging stations is seen as a key prerequisite for the transition to a cleaner, electrified transportation sector. As such, the 2021 U.S. Infrastructure Investment and Jobs Act committed $7.5 billion to build a national network of public electric vehicle chargers across the U.S.

But a large amount of private investment will also be needed to make charging stations ubiquitous.

“The U.S. is investing a lot in EV chargers and really encouraging EV adoption, but many EV charging providers can’t make enough money at this stage, and getting to profitability is a major challenge,” Zheng says.

EV advocates have long argued that the presence of charging stations brings economic benefits to surrounding communities, but Zheng says previous studies on their impact relied on surveys or were small-scale. Her team of collaborators wanted to make advocates’ claims more empirical.

For their study, the researchers collected data from over 4,000 charging stations in California and 140,000 businesses, relying on anonymized credit and debit card transactions to measure changes in consumer spending. The researchers used data from 2019 through June of 2023, skipping the year 2020 to minimize the impact of the pandemic.

To judge whether charging stations caused customer spending increases, the researchers compared data from businesses within 500 meters of new charging stations before and after their installation. They also analyzed transactions from similar businesses in the same time frame that weren’t near charging stations.

Supercharging nearby businesses

The researchers found that installing a charging station boosted annual spending at nearby establishments by an average of 1.4 percent in 2019 and 0.8 percent from January 2021 to June 2023.

While that might sound like a small amount per business, it amounts to thousands of dollars in overall consumer spending increases. Specifically, those percentages translate to almost $23,000 in cumulative spending increases in 2019 and about $3,400 per year from 2021 through June 2023.

Zheng says the decline in spending increases over the two time periods might be due to a saturation of EV chargers, leading to lower utilization, as well as an overall decrease in spending per business after the Covid-19 pandemic and a reduced number of businesses served by each EV charging station in the second period. Despite this decline, the annual impact of a charging station on all its surrounding businesses would still cover approximately 11.2 percent of the average infrastructure and installation cost of a standard charging station.

Through both time frames, the spending increases were highest for businesses within about a football field’s distance from the new stations. They were also significant for businesses in disadvantaged and low-income areas, as designated by California and the Justice40 Initiative.

“The positive impacts of EV charging stations on businesses are not constrained solely to some high-income neighborhoods,” Wang says. “It highlights the importance for policymakers to develop EV charging stations in marginalized areas, because they not only foster a cleaner environment, but also serve as a catalyst for enhancing economic vitality.”

Zheng believes the findings hold a lesson for charging station developers seeking to improve the profitability of their projects.

“The joint gas station and convenience store business model could also be adopted to EV charging stations,” Zheng says. “Traditionally, many gas stations are affiliated with retail store chains, which enables owners to both sell fuel and attract customers to diversify their revenue stream. EV charging providers could consider a similar approach to internalize the positive impact of EV charging stations.”

Zheng also says the findings could support the creation of new funding models for charging stations, such as multiple businesses sharing the costs of construction so they can all benefit from the added spending.

Those changes could accelerate the creation of charging networks, but Zheng cautions that further research is needed to understand how much the study’s findings can be extrapolated to other areas. She encourages other researchers to study the economic effects of charging stations and hopes future research includes states beyond California and even other countries.

“A huge number of studies have focused on retail sales effects from traditional transportation infrastructure, such as rail and subway stations, bus stops, and street configurations,” Zhao says. “This research provides evidence for an important, emerging piece of transportation infrastructure and shows a consistently positive effect on local businesses, paving the way for future research in this area.”

The research was supported, in part, by the Singapore-MIT Alliance for Research and Technology (SMART) and the Singapore National Research Foundation. Diao was partially supported by the Natural Science Foundation of Shanghai and the Fundamental Research Funds for the Central Universities of China.

Spamouflage’s advanced deceptive behavior reinforces need for strong email security

EXECUTIVE SUMMARY:

Ahead of the U.S. elections, adversaries are weaponizing social media to gain political sway. Russian and Iranian efforts have become increasingly aggressive and transparent. However, China appears to have taken a more carefully calculated and nuanced approach.

China’s seeming disinformation efforts have little to do with positioning one political candidate as preferable to another. Rather, the country’s maneuvers may aim to undermine trust in voting systems, elections and America, in general; amplifying criticism and sowing discord.

Spamouflage

In recent months, the Chinese disinformation network, known as Spamouflage, has pursued “advanced deceptive behavior.” It has quietly launched thousands of accounts across more than 50 domains, and used them to target people across the United States.

The group has been active since 2017, but has recently reinforced its efforts.

Fake profiles

The Spamouflage network’s fake online accounts present fake identities, which sometimes change on a whim. The accounts/profiles have been spotted on X, TikTok and elsewhere.

For example:

Harlan claimed to be a New York resident and an Army veteran, age 29. His profile picture showed a well-groomed young man. However, a few months later, his account shifted personas. Suddenly, Harlan appeared to be from Florida and a 31 year-old Republican influencer. 

At least four different accounts were found to mimic Trump supporters – part of a tactic with the moniker “MAGAflage.”

The fake profiles, including the fake photos, may have been generated through artificial intelligence tools, according to analysts.

Accounts have exhibited certain patterns, using hashtags like #American, while presenting themselves as voters or groups that “love America” but feel alienated by political issues that range from women’s healthcare to Ukraine.

In June, one post on X read “Although I am American, I am extremely opposed to NATO and the behavior of the U.S. government in war. I think soldiers should protect their own country’s people and territory…should not initiate wars on their own…” The text was accompanied by an image showing NATO’s expansion across Europe.

Email security implications

Disinformation campaigns that create (and weaponize) fake profiles, as described above, will have a high degree of success when crafting and distributing phishing emails, as the emails will appear to come from credible sources.

This makes it essential for organizations to implement and for employees to adhere to advanced verification methods that can ensure the veracity of communications.

Advanced email security protocols

Within your organization, if you haven’t done so already, consider implementing the following:

  • Multi-factor authentication. Even if credentials are compromised via phishing, MFA can help protect against unauthorized account access.
  • Email authentication protocols. Technologies such as SPF, DKIM and DMARC can assist with verifying the legitimacy of email senders and spoofing prevention.
  • Advanced threat detection. Advanced threat detection solutions that are powered by AI and machine learning can enhance email traffic security.
  • Employee awareness. Remind employees to not only think before they click, but to also think before they link to information – whether in their professional roles or their personal lives.
  • Incident response plans. Most organizations have incident response plans. But are they routinely updated? Can they address disinformation and deepfake threats?

Further thoughts

To effectively counter threats, organizations need to pursue a dynamic, multi-dimensional approach. But it’s tough.

To get expert guidance, please visit our website or contact our experts. We’re here to help!

Engineering proteins to treat cancer

Like many children of first-generation immigrants, Oscar Molina grew up feeling like he had two career choices: doctor or lawyer. He seemed destined for the former as he excelled in high school and planned to major in biochemistry at the University of California at Los Angeles, but as an undergraduate, he fell in love with research.

“I was fascinated by discovery. As I did it more in college, I realized I didn’t want to be a doctor,” he says. “Once I saw that I could make an impact and be at the forefront of therapy with biotech, I knew I wanted to do that.”

If the next couple of years go as planned, his parents will indeed see their son become a doctor — just not exactly the way they might have guessed. He’s entering the fifth year of his PhD program in biology at MIT and is currently working in the lab of Professor Ronald Raines, researching the potential of proteins to kill cancer cells.

Molina, who is the first in his family to attend college, also works to support his fellow students through outreach and community-building efforts. In various roles, including as a Graduate Community Fellow in MIT’s Office of Graduate Education, he sought to connect and encourage students from underrepresented backgrounds as they pursued their own graduate studies.

“I had a lot of opportunities presented to me that made me ask, ‘Why me?’” he says. “I recognize that they were super valuable, and that’s why I should deliver that back to other people.”

Unlocking protein construction chemically

The spirit of giving back isn’t just limited to Molina’s work outside of the lab. He chose chemical biology and the pursuit of new cancer therapies as his research focus partly because his grandfather has been dealing with the disease for the last 10 years. The ultimate goal guiding his research is to make all protein-based cancer therapies more effective.

He and other collaborators in the Raines Lab published a paper in June that takes an important step in that direction, suggesting a way to make fusion proteins with greater customization and improved performance. They discovered that a chemical called 3-bromo-5-methylene pyrrolone can be used to combine three proteins efficiently and with high levels of control and modularity, a significant advance given most of the techniques for protein conjugation are only able to combine two at a time in a single spot.

“Now, we can have chemical control of where we include different things, where we can kind of plug-and-play,” he says.

Researchers can now adjust multiple characteristics at the same time — for example, increasing the protein’s half-life or improving its ability to target cancer cells — while still achieving a homogenous end product. They’re also relevant to immune cell redirection therapies, which require multimeric protein chimeras to activate immune clearance of cancer cells.

“That’s the most interesting thing to me,” he says. “How do we give a biologic therapy the best opportunity to be active and efficacious?”

His upcoming thesis will center around that question as it relates to chemotherapies based on ribonuclease 1, an enzyme that is best-known for cleaving RNA.

Paying it back and paying it forward

While that thesis will likely demand more of Molina than any other project he’s worked on in the past, he’s no stranger to hard work. After his mother and father left their respective homes of Guatemala and El Salvador in the 1990s, they dedicated their lives to giving their children futures that they themselves didn’t have access to.

Witnessing their efforts impressed two beliefs into Molina’s worldview: the value of education and the importance of support. Among his family, he is the first to graduate from a U.S. high school, the first to attend a four-year college, and the first to attend graduate school. These “firsts” can weigh heavily, and as he began his studies at MIT, he knew how difficult it can be to carry that burden alone.

“I saw the need and wanted to help other people be the first in their family to do things like go to college,” he says. “I also wanted to help people with similar backgrounds to mine, like being an underrepresented minority or a first-generation college student.”

That desire led Molina to join MIT’s Office of Graduate Education as a Graduate Community Fellow in January 2022, where he worked on supporting various affinity groups across the Institute. This included helping groups out with logistics, funding applications, community outreach and cross-group collaborations. He also spent part of last summer as a pod leader for the MIT Summer Research Program, which works to prepare underrepresented students for graduate education and research.

He’s also leveraged his personal interests to volunteer with various community organizations in Cambridge and Boston. Despite his numerous commitments, he’s an avid marathon runner, and ran the 2022 Boston Marathon while raising nearly $8000 for Boston Scores, a program that provides educational and athletic opportunities for students in the Boston Public Schools system.

After graduation, Molina plans on joining a startup in Boston’s biotech scene while learning more about the venture capital firms that fund their research. Wherever he ends up, he plans on continuing to apply the core truths that brought him where he is now.

“I want to be at the forefront of creating therapies. I really like science. I really like helping others. I really like the ability to create things that are impactful,” he says. “Now it’s time to take that and find my way to what’s next.”

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MIT team wins grand prize at NASA’s First Nations Launch High-Power Rocket Competition

The members of the MIT First Nations Launch team had never built a drone before when they faced the 2024 NASA First Nations Launch High-Power Rocket Competition. This year’s challenge invited teams to design, build, and launch a high-power rocket carrying a scientific payload that deploys mid-air and safely returns to the ground, integrating Indigenous methodologies.

The eight-student team of all Indigenous students earned the compatition’s grand prize, as well as first place in the written portion.

Deploying a drone from a rocket

Building even the simplest drone demands precise calculations of weight, power, and functionality. But this drone had extra layers of complexity. It needed to fold inside the 7.5-inch diameter rocket and deploy to a full 16 x 16-inch configuration. Team captain and rising junior Hailey Polson explains: “The arms of the drone, which hold the propellers, need to lock in place. Once it unfolds, you don’t want it to re-fold while you’re trying to fly it around. Therefore, you need to have some kind of locking mechanism, as well as a mechanism to ensure it extends and unfolds properly.”

Deploying the drone from the rocket presented a significant challenge. The competition required that the drone’s separation from the rocket could not rely on gravity. To ensure successful deployment, the students planned to use a black powder charge to push the drone from an interior rail, but they had no prior experience testing explosives to see if it would work as intended. So, the team enlisted the expertise of their friends from the MIT Rocket Team, who helped conduct black powder testing in the MIT blast chamber.

Despite all these difficulties, the team decided to rise to the challenges of the competition yet again by designing their own parachute release mechanism, while many teams opted for commercial ones. They used an Arduino controller, a servo, and a special snap shackle. “We tested around 15 different ones because it’s pretty difficult to find something that a servo motor can easily pull and actually release in the correct way,” Polson says.

Once the parachute is released, the drone must be piloted to a safe landing. Nicole McGaa ’24 and second-year student Alex Zhindon-Romero took the FAA Part 107 drone pilot exam so they could legally pilot the drone.

The advantages of an all-indigenous team

According to a 2021 report from the U.S. National Science Foundation, Native Americans formed only 0.6 percent of the STEM workforce.

Polson grew up on the Cherokee Nation Reservation of Claremore, Oklahoma, where she enjoyed being surrounded by other people in her tribe and celebrating her rich culture. “I want to set an example for other people from my background that they can attend MIT, be a rocket scientist, and do basically anything they want and still feel connected to their community.”

Polson planned to join an Edgerton Center build team when she came to MIT, “but I never imagined there would be enough interest for an all-Indigenous build team,” she says. “It’s special because any build team forms a unique bond between the members and fosters a great sense of community. However, having that extra layer of shared values, aspirations, and backgrounds has really gone a long way in driving us towards the same goals. We are not only committed to excellence in engineering and achieving the tasks they ask of us, but also to helping each other and finding excellence within ourselves as engineers.”

The MIT First Nations Launch team was formed in 2022 to participate in the annual NASA Artemis student challenge. The team uses Indigenous methodologies and structures to learn and understand how engineers can shape the world through aerospace and beyond. Polson describes their Indigenous approach as “prioritizing both the human aspect, focusing on the interactions between our teammates, and making sure that they are getting everything they need out of this, as well as on the impacts beyond that, with outreach, education, and the environment.”

Professor J. Kim Vandiver, director of the Edgerton Center, says, “We non-Native American engineers have a lot to learn from these students. I am particularly drawn to their more holistic view of life and the interconnectedness of everything we do and the world in which we live.”

Nurturing success

The start and finish of a degree program are pivotal moments in the lives of MIT’s graduate students. In her first three years in MIT’s Department of Political Science, professor Mariya Grinberg’s mentorship has helped numerous students start their graduate journeys with confidence and direction. Nuh Gedik, who joined the Department of Physics in 2008, looks to the finish line: he finds joy in seeing his students reach personal and professional success at the end of their PhDs. Both were recently honored as “Committed to Caring” for their support of graduate students. 

Mariya Grinberg: Commitment to intellectual growth

When Mariya Grinberg joined the MIT Security Studies Program as a faculty member in 2021, the department was in a state of flux. The Covid-19 pandemic was in full swing, several core faculty members were nearing retirement, and the program had welcomed the largest cohort of PhD students in its history. As Grinberg entered the community, she embraced these challenges, meeting and exceeding her expected duties as an advisor.

In her role as assistant professor of political science, Grinberg’s research interests center on the question of how time and uncertainty shape the strategic decisions of states, focusing on economic statecraft, military planning, and questions of state sovereignty.

As a junior faculty member, Grinberg shoulders one of the largest advising loads in the department. Despite this, multiple nominators praised Grinberg for her prompt and discerning feedback. Students note her efforts in reading through and commenting on many rounds of paper drafts, supplemented by hour-long brainstorming sessions at her whiteboard. “It’s rare that someone can become both your most incisive critic and staunchest advocate,” a nominator noted. “I never took it for granted.”

Throughout these sessions, Grinberg delivers her advice with both confidence and empathy. One nominator shared how meetings put them at ease: “Normally, I am quite anxious about meeting with faculty, but I never felt that way during my meetings with Mariya.”

Grinberg believes that failure is an integral part of the learning process and encourages her students to embrace and learn from setbacks. She acknowledges that the pressure to accomplish tasks within time constraints often leaves little room for failure, which can lead to decision paralysis. Grinberg reassures her students that investing time in a dissertation idea, even if it turns out to be non-viable, is not time wasted.

When asked about her philosophy on mentorship, Grinberg emphasizes that the advice of mentors is just that — advice. It represents their best effort to steer students in what they perceive to be a fruitful direction, but it does not mean the advice is invariably correct. Grinberg encourages students to critically evaluate any feedback and make their own judgments that may not align with their advisor’s thoughts.

Grinberg shares a concept she first learned from a creative writing professor: “When someone tells you there is something wrong with your work, 90 percent of the time they are right. When someone tells you how to fix it, 90 percent of the time they are wrong.”

Nuh Gedik: Mentoring the next generation of scientists

Gedik is the Donner Professor of Physics at MIT. His group investigates quantum materials by using advanced optical and electron-based spectroscopies. Gedik employs these techniques to study topological insulators, high-temperature superconductors, and atomically layered materials.

When asked about what keeps him motivated, Gedik says that he is driven by the professional development of his students. Gedik prioritizes the growth of his students above all else, and believes that academic output follows naturally with personal and professional growth. One nominator shared one of Gedik’s favorite sayings: “Finding a job for you is my job.”

As a result of this mindset, the alumni of Gedik’s group have achieved spectacular professional success, including members who are now faculty at top universities such as Stanford, Harvard, and Columbia universities. Several group members are also in leadership roles at companies like Intel, Meta, or ASML.

Alongside his academic pursuits, Gedik is deeply committed to promoting diversity, equity, and inclusion within his research group and the broader academic community. He dedicates regular portions of the weekly group meetings to discussing literature and practices related to these topics. Not only do these discussions educate the group on important issues, but they also help lab members integrate inclusive practices into their day-to-day endeavors.

By integrating inclusive principles into his teaching and mentoring, Gedik creates a culture where students are supported personally and academically. In fact, a nominator shared that many of these practices stem from the professional development courses that Gedik voluntarily attends. His proactive approach not only benefits his current students, but also sets a standard that influences others as well.

In addition to his efforts within the lab, Gedik is proactive in scientific outreach and mentorship within the broader community. He attends annual science fairs in educationally under-resourced communities, aiming to inspire the younger generation to pursue careers in STEM. One nominator praises these fairs for “igniting interest in science and technology among diverse audiences,” with a particular focus on inspiring the younger generation.