Though it is a cornerstone of virtually every process that occurs in living organisms, the proper folding and transport of biological proteins is a notoriously difficult and time-consuming process to experimentally study.

In a new paper published in eLife, researchers in the School of Biological Sciences and the School of Computer Science have shown that AF2Complex may be able to lend a hand.

Building on the models of DeepMind’s AlphaFold 2, a machine learning tool able to predict the detailed three-dimensional structures of individual proteins, AF2Complex — short for AlphaFold 2 Complex — is a deep learning tool designed to predict the physical interactions of multiple proteins. With these predictions, AF2Complex is able to calculate which proteins are likely to interact with each other to form functional complexes in unprecedented detail.

“We essentially conduct computational experiments that try to figure out the atomic details of supercomplexes (large interacting groups of proteins) important to biological functions,” explained Jeffrey Skolnick, Regents’ Professor and Mary and Maisie Gibson Chair in the School of Biological Sciences, and one of the corresponding authors of the study. With AF2Complex, which was developed last year by the same research team, it’s “like using a computational microscope powered by deep learning and supercomputing.”

In their latest study, the researchers used this ‘computational microscope’ to examine a complicated protein synthesis and transport pathway, hoping to clarify how proteins in the pathway interact to ultimately transport a newly synthesized protein from the interior to the outer membrane of the bacteria — and identify players that experiments might have missed. Insights into this pathway may identify new targets for antibiotic and therapeutic design while providing a foundation for using AF2Complex to computationally expedite this type of biology research as a whole.

Computing complexes

Created by London-based artificial intelligence lab DeepMind, AlphaFold 2 is a deep learning tool able to generate accurate predictions about the three-dimensional structure of single proteins using just their building blocks, amino acids. Taking things a step further, AF2Complex uses these structures to predict the likelihood that proteins are able to interact to form a functional complex, what aspects of each structure are the likely interaction sites, and even what protein complexes are likely to pair up to create even larger functional groups called supercomplexes.

“The successful development of AF2Complex earlier this year makes us believe that this approach has tremendous potential in identifying and characterizing the set of protein-protein interactions important to life,” shared Mu Gao, a senior research scientist at Georgia Tech. “To further convince the broad molecular biology community, we [had to] demonstrate it with a more convincing, high impact application.”

The researchers chose to apply AF2Complex to a pathway in Escherichia coli (E. coli), a model organism in life sciences research commonly used for experimental DNA manipulation and protein production due to its relative simplicity and fast growth. 

To demonstrate the tool’s power, the team examined the synthesis and transport of proteins that are essential for exchanging nutrients and responding to environmental stressors: outer membrane proteins, or OMPs for short. These proteins reside on the outermost membrane of gram-negative bacteria, a large family of bacteria characterized by the presence of inner and outer membranes, like E. coli. However, the proteins are created inside the cell and must be transported to their final destinations. 

“After more than two decades of experimental studies, researchers have identified some of the protein complexes of key players, but certainly not all of them,” Gao explained. AF2Complex “could enable us to discover some novel and interesting features of the OMP biogenesis pathway that were missed in previous experimental studies.”

New insights

Using the Summit supercomputer at the Oak Ridge National Laboratory, the team, which included computer science undergraduate Davi Nakajima An, put AF2Complex to the test. They compared a few proteins known to be important in the synthesis and transport of OMPs to roughly 1,500 other proteins — all of the known proteins in E. coli’s cell envelope — to see which pairs the tool computed as most likely to interact, and which of those pairs were likely to form supercomplexes. 

To determine if AF2Complex’s predictions were correct, the researchers compared the tool’s predictions to known experimental data. “Encouragingly,” said Skolnick, “among the top hits from computational screening, we found previously known interacting partners.” Even within those protein pairs known to interact, AF2Complex was able to highlight structural details of those interactions that explain data from previous experiments, lending additional confidence to the tool’s accuracy.

In addition to known interactions, AF2Complex predicted several unknown pairs. Digging further into these unexpected partners revealed details on what aspects of the pairs might interact to form larger groups of functional proteins, likely active configurations of complexes that have previously eluded experimentalists, and new potential mechanisms for how OMPs are synthesized and transported. 

“Since the outer membrane pathway is both vital and unique to gram-negative bacteria, the key proteins involved in this pathway could be novel targets for new antibiotics,” said Skolnick. “As such, our work that provides molecular insights about these new drug targets might be valuable to new therapeutic design.”

Beyond this pathway, the researchers are hopeful that AF2Complex could mean big things for biology research. 

“Unlike predicting structures of a single protein sequence, predicting the structural model of a supercomplex can be very complicated, especially when the components or stoichiometry of the complex is unknown,” Gao noted. “In this regard, AF2Complex could be a new computational tool for biologists to conduct trial experiments of different combinations of proteins,” potentially expediting and increasing the efficiency of this type of biology research as a whole.

AF2Complex is an open-source tool available to the public and can be downloaded here.

This work was supported in part by the DOE Office of Science, Office of Biological and Environmental Research (DOE DE-SC0021303) and the Division of General Medical Sciences of the National Institute Health (NIH R35GM118039). DOI: https://doi.org/10.7554

By Frida Carrera

On Wednesday, April 13th 2022, the Undergraduate Research Opportunities Program (UROP) hosted the 16th annual Spring Undergraduate Research Symposium. UROP’s annual symposium is Georgia Tech’s largest undergraduate research colloquium and allows students to present their research and gain valuable skills and presentation experience. Each year the symposium also presents awards to the top poster and oral presentation from each college and honors the Outstanding Undergraduate Researcher (OUR) from each college. And with over 40 oral presentations and nearly 90 poster presentations, this year’s symposium proved to be another success for UROP and Georgia Tech.  

This year the symposium was held in Exhibition Hall and opened with an introduction and keynote address to students, faculty, and other non-presenters. Shortly after, the event moved into the poster presentations segment where undergraduate students displayed their research to judges, faculty, and other attendees. The oral presentations followed soon after and gave student researchers the opportunity to go more in-depth with their research and findings and answer any questions the judges and attendees had. To end the event, sponsoring colleges and departments recognized Outstanding Undergraduate Researchers from their respective colleges. Additionally, the symposium judges were tasked with selecting the top student researchers having exceptional poster and oral presentations. 

Any Georgia Tech undergraduate student interested in presenting their research is encouraged to apply for future symposiums and to build on research presentation skills, connect with other undergraduate researchers and faculty, and the chance to be recognized with awards by members of the Georgia Tech research community. UROP also hosts other research-related events and workshops throughout the school year to assist undergraduate students interested in research and build on their passions! 

To view the list of awardees and pictures from the event visit: https://symposium.urop.gatech.edu/awards/ 

To learn more about undergraduate research at Georgia Tech visit: https://urop.gatech.edu/

By Frida Carrera

During the summer of 2021, computer science student Neil Sanghavi and computer science recent grad Ahan Shah, both from Fairfax, VA, reconnected to catch up with one another and discuss the projects they were working on. In doing so they discovered a mutual resolve to create something using innovative technology and solve a problem relating to intellectual property, specifically patents. Both Neil and Ahan had just started to get into crypto trading and realized that NFT technology had more to offer than its collectible aspect. Here the idea of PatentX was created: to use NFT technology to provide utility in an antiquated space that lacked efficiency.

“It is estimated that we have $1 trillion in unused IP in the United States currently. Additionally, it is reported that there is $25.6 billion worth of patent monetization available today. This is why we created PatentX, a blockchain-backed marketplace to facilitate intellectual property transactions. We built this to make sure the little man innovators and entrepreneurs have an outlet to monetize and connect their patents with the world. Not only that, we are creating tools for large businesses, law firms, venture capitals to manage all of their IP on the blockchain that can handle transactions in seconds.”

Neil and Ahan describe their product launch process as a great learning experience and are firm believers that there can never be too much help. They are currently supported by DXPartners and have received help from various mentors and blockchain professionals. They have been able to traverse obstacles and learn about the marketing, finance, and business aspects behind building a startup despite coming from a technical background. 

Their vision for PatentX is to disrupt the traditional way intellectual property is being transacted and to become the World’s Next Web3 Patent Office. PatentX will be releasing an NFT collection of the most historic patent innovations this early March and encourage interested individuals to stay tuned for their launch. 

To learn more about PatentX visit their social media: 

Twitter: @PatentXNFT

Instagram: @PatentX.io

To learn more about student innovation at Georgia Tech visit: https://innovation.cae.gatech.edu/

By Frida Carrera

On April 2, 2022, Team carSEAL will represent Georgia Tech in the 6^th annual ACC InVenture Prize Competition hosted this year by Florida State University. Team members Shovan Bhatia, Joshua Cruz, Nicholas Lima, Derek Prusener, and Giancarlo Riccobono will compete against other teams in the ACC Conference for a chance to win up to $30,000 in prizes. 

carSEAL began with five biomedical engineering students collaborating on a capstone project. After being accepted into the highly sought-after Mayo Clinic Capstone Project, they received mentorship from Dr. Rabih Tawk, a world-renowned neurosurgeon. With his guidance, they learned that surgeons currently lack the tools to close the carotid artery after endovascular procedures. Through a pragmatic approach, the team developed 100+ conceptual designs and iterations. After numerous discussions with attending surgeons across the nation and preliminary testing, they developed carSEAL – a vascular closure device for the carotid artery. 

So far, the team has found the InVenture Prize process to be exhilarating.

“Through each round of this process, we have seen incredible teams working on impactful projects and it is exciting to be surrounded by such brilliant minds from numerous backgrounds. It has been especially rewarding working with so many supportive advisors from Georgia Tech, who have been through the startup process and have freely offered their expertise. Along each step of this process, we have learned something new to refine our pitch and ensure we are presenting our most competitive self at the ACC.”

Currently, aside from preparing for the ACC InVenture Prize, the carSEAL team is performing benchtop lab testing to evaluate its efficacy in animal models. Soon after, the team will be moving to pre-clinical studies on their path to obtaining FDA clearance before carSEAL is commercialized. Winning the ACC InVenture Prize would help them gain more traction and gather sufficient funds to help them with this process.

“I am extremely proud of our team’s achievements in the short 6 months that we have worked together. carSEAL has gained a lot of traction already and we are excited to see how far we can take this, hopefully bringing carSEAL to clinical practice within a few years,” Bhatia stated.

The Georgia Tech community can support carSEAL in the competition by voting for them for the People’s Choice Awards by visiting: https://accinventureprize.com/peoples-choice-voting. Online voting begins March 28.

To learn more about the ACC InVenture Prize visit https://accinventureprize.com.

By Frida Carrera

After almost a year of preparation, practice, and refinement, Georgia Tech’s annual InVenture Prize is down to six finalists competing in the final round on March 16^th. In this televised round, the final teams will pitch their inventions to a panel of judges and compete for the top prize of $20,000, assistance in patent-filing, and a spot in CREATE-X’s Startup Launch program.

In its 14^th year, the InVenture Prize competition features different innovations created by Georgia Tech students from all disciplines and backgrounds. For months prior to the final round, the finalists received coaching and assistance from mentors and coaches on building their prototypes, developing business models, and rehearsing their pitches to investors. The final six teams were chosen from previous preliminary and semifinal rounds that included a broad range of competitors. 

The finals of the InVenture Prize will air live from Georgia Tech’s Ferst Center for the Arts at 7:30 p.m. on March 16^th on Georgia Public Broadcasting. 

The 2022 finalist teams are:

The Foambuster: The Foambuster is a unique handheld tool that allows construction contractors to drastically cut down on the mess, hassle, and money spent that comes with installing exterior insulation.

Edward Diller, Mechanical Engineering, Los Angeles, CA

Davis Waln, Mechanical Engineering, Atlanta, GA

Christophe Senghor, Mechanical Engineering, Peachtree City, GA

Katelyn Sand, Mechanical Engineering, Westlake Village, CA

Jaime Paris Meseguer, Mechanical Engineering, Spain

Magic Crop: An application that uses the power of Artificial Intelligence and the rule of thirds to format any number of inputted pictures into the perfect headshot within seconds and without ever sending any images to the cloud or to a third-party server.

Megan Dass, Computer Science, Woodbridge, VA

Reflex: Emergency Medical Drone Response System to deliver life-saving medical equipment.

Nevin Gilbert, Computer Science, Boulder, CO

Usman Jamal, Computer Science, Tucker, GA

Sola: Sola provides a data-driven supplemental insurance plan which covers immediate out-of-pocket expenses for US homeowners following losses from tornadoes.

Brayden Drury, Mechanical Engineering, Park City, Utah

Wesley Pergament, Mechanical Engineering, Old Westbury, NY

StrideLink: Accessible gait analysis wearable for remote monitoring of walking asymmetry.

Marzeah (Zea) Khorramabadi, Computer Engineering, Birmingham, AL

Cassandra (Cassie) McIltrot, Biomedical Engineering, Sykesville, MD

Neel Narvekar, Computer Engineering, Arcadia, CA

Tony Wineman, Electrical Engineering, Woodstock, GA

Tabnam: AI-powered shopping assistant that leverages the knowledge of user experience data.

SooHoon Choi, Computer Science, South Korea

Daksh Gupta, Computer Science, Noida, India

Robert (Davis) Liddell, Computer Science, Lutherville, MD

Ethan Perry, Computer Science, Wellesley, MA

To request tickets for the event visit: https://inventureprize.gatech.edu/form/inventure-prize-ticket-request-f

To learn more about InVenture Prize visit: https://inventureprize.gatech.edu/

By Frida Carrera

On December 3, 2021, Startup Exchange presented the Fall 2021 Fellowship Pitch Competition sponsored by the Georgia Tech Student Innovation Program, Office of Undergraduate Education. The event took place at ATL Social Club in Tech Square, a major startup hub situated on Georgia Tech’s campus and perfect for those eager for innovation at GT. The event also welcomed partner companies and recruiters such as NCR and Stord. 

At this pitch-style event, six founder teams presented their innovative pitches and competed for first, second, and third place, each with a cash prize to aid in the advancement of their ideas. The first and second place winners of the competition were determined by three guest judges: Kathryn Petralia, co-founder of Kabbage and Drum; Thomas Suarez, co-founder of Teleport and Thiel Fellow; and Evan Jarecki, serial entrepreneur and BM at Startup Atlanta. The event commenced with a brief introduction by Startup Exchange executive board members, followed by presentations from the 6 teams including Fino, InSite, Jargon, and Tokenstack. After hearing each team’s pitch, the judges had time to deliberate and select the top two winners while the audience voted for the People’s Choice winner. Meanwhile, attendees were also able to hear from the partner companies and network while enjoying free perks such as food and beverages. 

“There are students everywhere across campus really starting on their start-ups and pursuing their dreams. Atlanta is a growing city and Georgia Tech is the perfect hub for that. These teams, we’re introducing them to entrepreneurship and giving those resources and intro-connections. By doing so, we’re inspiring them in a way. It’s just a great learning experience for them,” explained Startup Exchange’s Director of Fellowship Revanth Tiruveedhi.

Following the intermission, the judges presented the first-place award of $750 to Jargon, a browser extension that points out red flags in user contract agreements, as pitched by team members Kaleb Rasmussen and Devansh Khunteta. Second place of $500 was awarded to Eartheal by team members Colin Burnett, Philip Colt, Neal Austensen, and Brandon Sherrard. People's Choice of $250 was awarded to Tokenstack by team members Nitin Paul, Samrat Sahoo, Yatharth Bhargava, and Mohit Sahoo. The event then closed with remarks by Startup Exchange’s board members and photos with the participants.

To learn more about student innovation at Georgia Tech visit https://innovation.gatech.edu/  

By Frida Carrera

After almost a year since the completion of the 2021 InVenture Prize Competition, we caught up with Matt McMullen and Emma Bivings who competed as finalists on the SPOT Harness team, a harness that uses sensors and vibrators to help blind dogs navigate. Their experience in the competition exposed them to multiple experiences, environments, and demands necessary for startups for the first time. As a result, they were able to distinguish their areas of growth, gain valuable insights, and make potential changes in the direction of their product.

Today, Matt is currently a graduate student seeking a master’s in music technology and Emma is a full-time operations management trainee at McMaster-Carr. The team is still developing the SPOT Harness and has even grown its team to five members. Through funding and participating in Georgia Tech’s CREATE-X Startup Launch program, they have been able to launch their company Saving Grace Pet Solutions LLC. They plan to launch SPOT Harness under this company as well as develop other future products.

To future InVenture participants, Matt advises, “Don’t give up on your idea! The most important part of making it the distance is having a team with a passion for your product.”

The SPOT Harness team will be launching a kick-starter soon for preorders ahead of the official market launch of the SPOT Harness for blind dogs. They also advise anyone who has or knows someone who has a dog suffering from vision loss to visit their website to sign up for their newly refined prototype!

Visit their website here: www.savinggrace.tech

To learn more about the upcoming InVenture Prize Competition visit https://inventureprize.gatech.edu/ . Registration closes on Jan. 19.

By Frida Carrera 

Several months after the completion of the 2021 InVenture Prize Competition, we caught up with John Wooten to see what he’s been up to! In 2021’s competition, John’s innovation Block Transfer, a decentralized stock transfer agent protocol for global financial markets, placed as a finalist.  

Today, John Wooten has been actively working to grow Block Transfer by securing final SEC approval, acquiring funding by US Bank, and submitting utility patents. He believes that by combining blockchain tech with traditional financial markets, we can fundamentally change the world. John describes his experience as a finalist in the competition as being invaluable and advises, “We didn't know we could partake given prior admission to CX. Biggest advice is to just TRY!” 

You can learn more about Block Transfer here: https://www.blocktransfer.io/consult 

To learn more about the upcoming InVenture Prize Competition visit https://inventureprize.gatech.edu/  . Registration closes on Jan. 19. 

By Frida Carrera

After almost a year since the completion of the 2021 InVenture Prize Competition, we caught up with finalist Sammie Hasen to see what she’s been up to over the past couple of months! For 2021’s competition, Sammie’s invention, BCase, placed as a finalist for its accessible, discreet, and secure birth control storage that attaches directly to the back of your phone. 

Today, Sammie successfully launched BCase in New York City on World Contraception Day as one of five brands featured by Medsur Inc, the consumer goods company founded by Sammie. On September 26th, Medsur was even invited by The Pill Club, a leading contraceptive company, to participate in the launch of their uterus-shaped vending machines in New York. Medsur now continues to garner the attention from many leading health companies in the birth control space and this is just the beginning for Sammie. 

“I plan to keep growing Medsur and follow our vision of creating a suite of innovative products for uterus owners. I am slowly growing the team, and I have now added the incredible Alexa Graham as COO. She is a rockstar, and she will help me grow Medsur to be all that we envision it to be!”, she explained. 

Sammie adds that Medsur is always looking for new ambassadors to join the team and encourages anyone passionate about the femtech space and building innovative products to consider signing up!

You can learn more about Medsur and BCase on their website here: https://www.medsurinc.com/

To learn more about the upcoming InVenture Prize Competition visit https://inventureprize.gatech.edu/ . Registration closes on Jan. 19.

By Jessica Barber

On April 21, 2021, biomedical engineering student Michael Pullen will serve as Georgia Tech’s representative in the fifth annual ACC InVenture Prize. Here he will compete with teams from twelve other universities for the chance to take home $30,000 in prizes.

Pullen’s invention first took root when he experienced the struggle of getting turf burn while playing football. While most players seek protection through regular compression sleeves, this often leads to decreased grip, more fumbles, and difficulty in maneuvering plays.

While working in sports medicine with the Atlanta Falcons, Pullen found a way to directly avoid this problem. LZRD Sleeve is a compressive sleeve that integrates gripping and moisture-wicking technology to deliver protection and control without sacrificing mobility nor comfort. 

Since then, LZRD Sleeve has secured its place in non-athletic arenas. A year ago, the world of sports halted due to COVID-19 shutdowns. It was then that Pullen sought other applications for his innovative sleeve — LZRD Sleeve has expanded its market to delivery drivers, gardeners, and maintenance workers seeking better performance and protection from harm. 

LZRD Sleeve is now being used by the largest U.S. courier service, and it has also been featured in Neil DeGrasse Tyson’s podcast StarTalk. On the same hand, Pullen has been in contact with a whopping five Fortune 500 companies. He ultimately hopes that InVenture Prize will show that with hard work, nothing is impossible.

 “Never in a million years would I have thought I would be representing Georgia Tech in the ACC InVenture Prize. Getting out of your comfort zone and trying new things is important, and by winning, I hope to set an example so that others might do the same,” Pullen stated.

Overall, winning the ACC InVenture Prize would allow LZRD Sleeve to expand even further through capital investments, uptakes in production, and coverage of associated legal fees.

The Georgia Tech community is encouraged to show Pullen its support through voting for the People’s Choice Award of $5,000. Voting is open from 8 a.m. on Monday, April 5 until midnight on Tuesday, April 6.

To vote, please text GATech to win the ACC InVenture Prize People’s Choice Award to 415-965-7445.

Winners will be announced on Wednesday, April 21 at 7 p.m. on PBS stations throughout the ACC region. 

More information about LZRD Sleeve can be found at lzrdtech.com.