Group Research Activities in Molecular Dynamics Simulations

Unfolding/Folding of Small Peptides by Constant Velocity Pulling
Beta hairpin structures are crucial to the secondary structure of proteins that provide function. We are using constant velocity pulling techniques to unfold and refold small beta hairpin peptides. These techniques allow us to probe the folding energetics and atomic level interactions responsible for reversible folding. In-silico mutagenesis is used to perturb the system and observe changes to the folding pathways.

Structure/Function of Proteins and Enzymes Using Umbrella Sampling, Replica Exchange, and Adaptive Biasing Force Simulations
Proteins and enzymes are biomolecules that are responsible for a wide variety of cellular processes from chemotaxis to intermolecular signaling. Many of these processes involve structural rearrangement of the biomolecules. Understanding the structure-function relationships at the atomic level is only possible through a small set of techniques such as NMR, crystallography, and computational methods. We are currently exploring these relationships in casein kinase, an enzyme participating in cellular division and having potential relevance in cancer metastasis. We us computational molecular dynamics simulations to explore putative phosphorylation sites and their effects on structure and function.

Group Members

Faculty - Troy C. Messina

Undergraduate Students - None currently

Computational Methods
All of the molecular simulation techniques we use are implemented through software that is open source and freely available from the University of Illinois, Urbana-Champaign.

Software

NAMD – recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling. (https://www.ks.uiuc.edu/Research/namd/)
VMD - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. (https://www.ks.uiuc.edu/Research/vmd/)
Neither of the software packages are currently installed on the University of Kentucky computing cluster. However, they are freely available as source or pre-compiled binaries.

Collaborators
There are no University of Kentucky collaborators in this research. Dr. Troy Messina is a physics faculty member at Berea College. Berea College is a four-year, undergraduate institution. Dr. Messina periodically has undergraduate students assist in this research. In the past, undergraduate involvement has consisted of training students to use the software and techniques so they can explore potential new directions for the research. This has largely been done using local desktop PC computers.

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