Collagen structures get the royal reveal

February 15, 2021

HOUSTON - (Feb. 15, 2021) - Collagen is the king of biological proteins, and now it has a SCEPTTr.

That's the handle of an algorithm developed by Rice University scientists who study natural and synthetic versions of collagen, which accounts for about a third of the body's proteins and forms the fibrous glue in skin, bones, muscles, tendons and ligaments.

The program -- full name, Scoring function for Collagen-Emulating-Peptides' Temperature of Transition -- accurately predicts the stability of collagen triple helices, the primary structure that forms fibrils.

The Rice team led by chemist and bioengineer Jeffrey Hartgerink and graduate student Douglas Walker tested SCEPTTr on 431 collagen triple helices from their own experiments and from literature and also used it to guide the design of a novel synthetic collagen helix.

The study in Nature Chemistry could help researchers better understand the critical protein's role in wound healing and cancer and could be used to design synthetic collagens, according to the researchers.

The paper significantly improves upon the lab's 2012 project to predict the stability of synthetic collagen structures. "One of its limitations it that it only understood a very narrow range of amino acids," Hartgerink said.

SCEPTTr expands that to the entire array of natural amino acids. That essentially makes it an Erector set for collagen design, potentially collapsing weeks of trial and error down to seconds on a desktop computer.

"The second major improvement is that while the earlier work couldn't tell you if a species of collagen would be stable at room temperature, Doug's program makes predictions about the melting temperature, the point at which a triple helix falls apart," Hartgerink said. "The great part about that is it's an easily testable value that extends to physiological temperatures as well.

"That's important to us, because if it falls apart when you put it inside a living organism, it's not particularly useful," he said.

SCEPTTr returns more than a single result for a given trio of sequences, detailing all possible combinations of the input peptides and providing a melting temperature for each.

"One of the most important things SCEPTTr does is look at all of the alternative structures that are possible and tells you how stable those are," Walker said. "It helps us understand what these complex mixtures are going to look like before you make them."

Walker brought a unique combination of talents to the project, spending half his time synthesizing collagen peptides and half programming SCEPTTr.

"When I was an undergraduate (studying chemistry at Idaho State University), I kept taking math classes because I really enjoyed it," he explained. "And it got to the point where I thought, 'Well, I'm one class away from a math minor.' And that happened to be a computer science course."

Despite reservations, Walker found he enjoyed programming. "Early on, I said, 'Hey, Doug, do you know anything about computers, because I've got a project for you,'" Hartgerink recalled. "I think the idea was that, if he didn't know about programming, he was going have to figure it out one way or another."

Walker said the program will be freely available online. "We want to make this a more accessible field, and SCEPTTr should make it easier for people to understand collagen," he said.
-end-
Co-authors of the paper are Rice graduate students Sarah Hulgan and Caroline Peterson, undergraduate Kevin Gonzalez and alumnus I-Che Li. Hartgerink is a professor of chemistry and of bioengineering.

The National Science Foundation, the Robert A. Welch Foundation and a Stauffer-Rothrock Fellowship supported the research.

Read the abstract at https://www.nature.com/articles/s41557-020-00626-6.

This news release can be found online at https://news.rice.edu/2021/02/15/collagen-structures-get-the-royal-reveal/.

Follow Rice News and Media Relations via Twitter @RiceUNews.

Related materials:

Rice University lab encodes collagen: http://news.rice.edu/2012/09/25/rice-university-lab-encodes-collagen-2/

'Sticky' ends start synthetic collagen growth: http://news.rice.edu/2014/10/27/sticky-ends-start-synthetic-collagen-growth-2/

Synthetic collagen promotes natural clotting: http://news.rice.edu/2014/04/09/synthetic-collagen-promotes-natural-clotting-2/

Rice unveils new method to grow synthetic collagen: http://news.rice.edu/2011/09/09/rice-unveils-new-method-to-grow-synthetic-collagen/

Hartgerink Research Group: https://hartgerink.rice.edu

Department of Chemistry: https://chemistry.rice.edu

Department of Bioengineering: https://bioengineering.rice.edu

Images for download:

https://news-network.rice.edu/news/files/2021/02/0119_COLLAGEN-1a-WEB.jpg

An algorithm by Rice University scientists predicts the structures and melting temperatures of collagen, the triple helix that accounts for about a third of the body's proteins and forms the fibrous glue in skin, bones, muscles, tendons and ligaments. (Credit: Douglas Walker/Hartgerink Research Group)

https://news-network.rice.edu/news/files/2021/01/0119_COLLAGEN-2-WEB.jpg

CAPTION: Jeffrey Hartgerink. (Credit: Rice University)

https://news-network.rice.edu/news/files/2021/01/0119_COLLAGEN-3-WEB.jpg

CAPTION: Douglas Walker. (Credit: Rice University)

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,978 undergraduates and 3,192 graduate students, Rice's undergraduate student-to-faculty ratio is just under 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for lots of race/class interaction and No. 1 for quality of life by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger's Personal Finance.

Jeff Falk
713-348-6775
jfalk@rice.edu

Mike Williams
713-348-6728
mikewilliams@rice.edu

Rice University

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