Name | Region | Skills | Interests |
---|---|---|---|
Adrian Del Maestro | Northeast | ||
Aaron Jezghani | Campus Champions | ||
Michael Blackmon | Campus Champions, ACCESS CSSN | ||
Kevin Bryan | Campus Champions | ||
Craig Gross | Campus Champions, CCMNet | ||
Christopher Bl… | Campus Champions | ||
Cody Stevens | Campus Champions, CCMNet | ||
Bala Desinghu | ACCESS CSSN, Campus Champions, CAREERS, Northeast | ||
Deborah Penchoff | Campus Champions | ||
Daniel Howard | ACCESS CSSN, Campus Champions, CCMNet, RMACC | ||
Dung Vu | ACCESS CSSN, Campus Champions | ||
Elie Alhajjar | ACCESS CSSN, CCMNet | ||
Edwin Posada | Campus Champions | ||
Eden Furtak-Cole | Campus Champions | ||
Gaurav Khanna | Campus Champions, CAREERS, Northeast, CCMNet | ||
Yu-Chieh Chi | Campus Champions | ||
Jacob Fosso Tande | ACCESS CSSN, Campus Champions, CCMNet | ||
Juan Jose Garc… | ACCESS CSSN | ||
Juanjo Garcia Mesa | Campus Champions, CCMNet, ACCESS CSSN | ||
Jordan Hayes | Campus Champions | ||
Jonathan Komperda | Campus Champions | ||
Jason Yalim | Campus Champions | ||
Katia Bulekova | ACCESS CSSN, Campus Champions, CAREERS, CCMNet, Northeast | ||
Od Odbadrakh | ACCESS CSSN | ||
Kenneth Bundy | CAREERS | ||
Lonnie Crosby | Campus Champions, ACCESS CSSN | ||
Martin Cuma | RMACC, Campus Champions | ||
James Hutcheson | Campus Champions, ACCESS CSSN | ||
Michael Puerrer | Campus Champions, Northeast | ||
Justin Oelgoetz | Campus Champions, CCMNet | ||
Paul Rulis | Campus Champions | ||
Rebecca Belshe | Campus Champions, CCMNet | ||
David Reddy | Campus Champions | ||
Ron Rahaman | Campus Champions | ||
Grant Scott | Great Plains | ||
Shane Sanders | Campus Champions | ||
Xiaoqin Huang | ACCESS CSSN | ||
Swabir Silayi | ACCESS CSSN, CCMNet, Campus Champions | ||
Soham Pal | ACCESS CSSN, Campus Champions, CCMNet | ||
Sumit Saluja | Campus Champions | ||
William Sanders | Campus Champions | ||
Sathish Srinivasan | ACCESS CSSN | ||
Tyler Burkett | Kentucky | ||
Thomas Pranzatelli | |||
Xiaoge Wang | Campus Champions | ||
Wirawan Purwanto | Campus Champions, Northeast, ACCESS CSSN | ||
William Lai | ACCESS CSSN |
Yersinia pestis, the bacterium that causes the bubonic plague, uses a type III secretion system (T3SS) to inject toxins into host cells. The structure of the Y. pestis T3SS needle has not been modeled using AI or cryo-EM. T3SS in homologous bacteria have been solved using cryo-EM. Previously, we created possible hexamers of the Y. pestis T3SS needle protein, YscF, using CollabFold and AlphaFold2 Colab on Google Colab in an effort to understand more about the needle structure and calcium regulation of secretion. Hexamers and mutated hexamers were designed using data from a wet lab experiment by Torruellas et. al (2005). T3SS structures in homologous organisms show a 22 or 23mer structure where the rings of hexamers interlocked in layers. When folding was attempted with more than six monomers, we observed larger single rings of monomers. This revealed the inaccuracies of these online systems. To create a more accurate complete needle structure, a different computer software capable of creating a helical polymerized needle is required. The number of atoms in the predicted final needle is very high and more than our computational infrastructure can handle. For that reason, we need the computational resources of a supercomputer. We have hypothesized two ways to direct the folding that have the potential to result in a more accurate needle structure. The first option involves fusing the current hexamer structure into one protein chain, so that the software recognizes the hexamer as one protein. This will make it easier to connect multiple hexamers together. Alternatively, or additionally the cryo-EM structures of the T3SS of Shigella flexneri and Salmonella enterica Typhimurium can be used as models to guide the construction of the Y. pestis T3SS needle. The full AlphaFold library or a program like RoseTTAFold could help us predict protein-protein interactions more accurately for large structures. Based on our needs we have identified the TAMU ACES, Rockfish and Stampede-2 as promising resources for this project. The generated model of the Y. pestis T3SS YscF needle will provide insight into a possible structure of the needle.
Baylor University
Campus Champions, ACCESS CSSN
research computing facilitator, cssn
University of California, San Diego
ACCESS CSSN
mentor, research software engineer
University of Tennessee, Knoxville
ACCESS CSSN
researcher/educator, research computing facilitator