Coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. To evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-tRNA synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-tRNA synthetases—Escherichia coli methionyl-tRNA synthetase, Thermus thermophilus leucyl-tRNA synthetase, and Enterococcus faecium prolyl-tRNA synthetase. In the present study, comparison of predicted dynamics based on B-factor and overlap calculations revealed that coarse-grained methods are comparable to the all-atom simulations in depicting the intrinsic global dynamics of the three enzymes. However, the principal component analyses of the motions obtained from the all-atom molecular dynamics simulations provide a superior description of the local fluctuations of these enzymes. In particular, the all-atom model was able to capture the functionally relevant substrate-induced dynamical changes in prolyl-tRNA synthetase. The alteration in the coupled dynamics between the catalytically important proline-binding loop and its neighboring structural elements due to substrate binding has been characterized and reported for the first time. Taken together, the study portrays comparable and contrasting situations in studying the functional dynamics of large multi-domain aminoacyl-tRNA synthetases using coarse-grained and all-atom simulation methods.
Written by Sudeep Bhattacharyay and Sanchita Hati
In This Story
- Alexander Strom
- Samuel Fehling
Departments + Programs
You may also like:
Off to start Ph.D. program
What began as an undergraduate plan aimed at medical school became a series of research experiences that led Jordan Munos to a new goal in the medical field as a biomedical scientist and a doctoral program at the Medical College of Wisconsin.
Impact of COVID-19 on diverse populations
A team of UW-Eau Claire faculty and students who are studying public history, Latin American studies, Spanish and nursing are working together to capture stories about what life has been like during COVID-19 for Spanish-speaking populations in the region.
Twins share commencement stage
Allie and Chloe Knuth, twins from Green Bay, will graduate together this month from UW-Eau Claire, a campus they say is small enough that their lives sometimes overlap as students but big enough that they each could follow their own path.