Volume 1  |  Issue 3  |  2019

Welcome!

We invite you to explore the third issue of the CBSD Quarterly Courier! Through this issue, we provide a sneak peek at the 8th Annual CBSD CoBRE Research Symposium, report marks of achievements and share recent publications citing the use of CoBRE resources. Each quarter, we will continue to highlight a different CBSD core facility and research project, and introduce you to one of the many talented students mentored by CBSD faculty. Stay tuned for the October 2019 issue – we plan to dedicate a significant portion to demonstrate the success our researchers have experienced in garnering extramural grant support over the last year. If you have suggestions for content, simply reply to this email or connect with any one of the CBSD team members. We look forward to connecting!

Sneak Peek: 8th Annual CBSD CoBRE Research Symposium

Featured Core Facility: Molecular Computation Core Facility (MCCF)

Dr. Oliver Serang Awarded NSF CAREER Grant
Student Highlight: Michael Campbell

Recent Publications

Sneak Peek: 8th Annual CBSD CoBRE Research Symposium

The time has come to register for the 8th Annual CBSD CoBRE Research Symposium. Perhaps you are wondering what we have in store for you this year. In the spirit of brevity, we plan to kick the Symposium off at 2 p.m. on Friday, Sept. 13 in UC 330-331. Friday afternoon will consist of opening remarks by Steve Sprang followed by poster preview talks, poster session, and networking dinner at Rumour (1855 Stephens Ave) for participants. Saturday, Sept. 14 will include presentations by our pilot project PIs, Start-Up Funded Faculty, and Junior Investigators. 

Undergraduate and graduate students that are interested in participating in the poster session are encouraged to indicate as such on their registration form. Students indicating interest in being considered to preview their poster will be notified of their selection to present no later than Friday, August 16.

Reserve your space today by visiting the following URL: cbsd-2019.eventbrite.com! Registration closes on Monday, August 12 at 5 p.m. Any questions about the Symposium can be directed to CBSD Program Coordinator, Sara Jestrab (sara.jestrab@umontana.edu or 406-243-6003).

Featured Core Facility: Molecular Computation Core Facility (MCCF)

It is our pleasure to highlight the work arising from the CBSD’s Molecular Computational Core Facility (MCCF) in this July issue. During the last year, MCCF has been busy:
  • Using computational methods to determine structural interactions within the NMDA receptor ligand binding domain (LBD);
  • Collaborating on a project incorporating quantum calculations for ruthenium and hydride ions into the Generalized Amber Force Field for MD simulations;
  • And performing various docking studies to evaluate structure-activity relationships (SARs), to name just a few activities!
Over the past several years, MCCF expanded their capabilities, focusing on user-Computational techniques such as small molecule docking and molecular dynamics will be used in Kendal Ryter's lab (Dept. of Chem) to probe structure and function of Toll-like receptors (TLR) to aid in antagonist design. TLR models were obtained from Ilpo Vattulainen's lab at the Tampere University of Technology.friendly software such as YASARA and powerful GPU-accelerated hardware. Software available through the MCCF includes modeling and simulation tools such as Amber 18, Gaussian 09, NAMD, SYBYL X, PyMol, and ChemDraw. Dr. Holley will deliver a seminar covering computational techniques on Oct. 4, 2019, in Skaggs 169 at 11 a.m.

Like other CBSD Facilities, the NIH-CoBRE primarily supports the MCCF with additional funding provided by UM’s Vice President of Research and Creative Scholarship (VPRCS). To enhance the sustainability of the Core, it has operated as a recharge facility with an established fee structure. UM faculty members who are unable to provide funding for their use of core facilities or need to acquire preliminary data leading to publications or grant applications are encouraged to consider applying for voucher funding. Staff and students from individual research laboratories are invited to consult with Dr. David Holley about how the MCCF resources can advance their research programs.

Dr. Oliver Serang Awarded NSF CAREER Grant

Dr. Oliver Serang was recently awarded a five-year NSF CAREER grant to address three unmet computer science needs in analyzing mass spectrometry data. Image of Dr. Oliver SerangSpecifically, the first unmet need Dr. Serang’s team will be tackling is to statistically identify proteins in a biological sample (this is important for understanding what makes cells different, e.g., what makes a skin cell different from a blood cell). The second is the identification of chemical species in a biological sample; this is crucial in applications such as, for example, enabling accurate and automated disease diagnosis. The third is finding the "alphabet" of basic molecular ingredients in a sample. This approach can be used to learn about chemical structures without any prior knowledge. 

All of these problems are united by fundamental “combinatoric” challenges (i.e., coming up with ways to efficiently count things). For example, how many different orders can you place at Big Dipper ice cream that would add up to exactly $100? These counting problems are challenging but can be solved efficiently due to mathematical algorithms invented by Dr. Serang and his team.

These combinatoric approaches will also be used to create a new season of the Exploring Scientific Wilderness podcast and to create a K-12 combinatorics curriculum. These fun exercises will not only be taught in Montana schools, but instruction plans will also be posted online for free use by teachers and parents around the world. 

You are encouraged to follow the progress of the project by visiting: https://alg.cs.umt.edu/nsf-career.html

NSF CAREER grants are highly prestigious awards aimed at providing foundational support to early-career faculty who have the potential to serve as role models in research and education. Such awards enable a lifetime of leadership for integrating education with research.

Student Highlight: Michael Campbell

During Michael Campbell’s time as the Molecular Computational Core Facility (MCCF) core fellow, he has collaborated on several projects. In theImage of MCCF Core Fellow, Michael Campbell process, Mr. Campbell has learned a variety of computational techniques that are used to investigate small molecules, macromolecules, and model the interactions between them. One such collaboration with Dr. Richard Bridges focused on the cystine/glutamate antiporter. Since a crystal structure of the human cystine/glutamate antiporter does not exist, a homology model was needed to enable docking studies with small molecules. As a result, four homology models representing different stages in the dynamic movement of the antiporter’s transport mechanism were made. These were created using the sequence of the human antiporter, the crystal structures of several bacterial homologues, and their respective alignments found in the literature. A group of small molecules including endogenous ligands and known inhibitors (both competitive and non-competitive) were docked in each of the homology models and visualized to develop a better understanding of the structure-activity relationship shown in Dr. Bridges research. Most recently, Mr. Campbell is collaborating with Dr. Philippe Diaz and docking a series of compounds into homology models of the metabolic enzyme Cyp26A1 and Cyp26B1. 

Mr. Campbell has plans to complete his degree in Medicinal Chemistry in the next couple of years. In his free time, you can find him outdoors playing soccer, camping, and rafting.

Recent Publications Supported by the CBSD

View all publications citing CBSD CoBRE. If you are working on a manuscript that has used CBSD CoBRE resources please remember to cite P20GM103546.
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We want to extend a special thank you to our newsletter contributors this month: Michael Campbell, David Holley, Sara Jestrab, and Oliver Serang. CBSD would also like to thank it's newsletter content reviewers: Bruce Bowler, Sara Jestrab and Stephen Sprang.
Copyright © 2019 Center for Biomolecular Structure and Dynamics, All rights reserved.


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