Coarse-grained Molecular Dynamics Simulations Depicted on BiophysJ Cover

bpj_104_1_coverAuthors Qiang Cui and Jejoong Yoo describe the latest Biophysical Journal cover, which depicts the latest results in their coarse-grained molecular dynamics simulations, introduced in the paper the image is based on, Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association. The image was rendered using VMD.

There is now mounting experimental and theoretical evidence supporting the idea that lipid molecules can mediate interactions between membrane proteins, although the underlying mechanism remains somewhat unclear. Our simulation results demonstrate that those interactions can indeed be substantially attractive, especially in the presence of significant hydrophobic mismatches, leading to the formation of clusters that consist of multiple Gramicidin A dimers packed into certain shapes. In the cover image, we illustrate the distribution of lipids between clusters using a transparent surface representation in order to emphasize the role of lipids in the cluster formation.

Representing complex environments such as water and lipids clearly is not trivial in rendering scientific images. Showing atomistic details can lead to overcrowded figures; on the other hand, ignoring the environment also leads to misinterpretation of the results. In our case, using a surface representation for the water and lipids turns out to be very effective. Tachyon ray tracing program implemented in VMD does a really good job for the rendering of surfaces.

This is the first cover image for Dr. Yoo as a first author (two papers in which he was a co-author were also featured as cover art in BJ). We are very excited and motivated to submit other cover images to the Biophysical Journal in the future. Showing our key finding as a cover art in the Biophysical Journal is one of the best ways to present our new results to the community, and presenting our scientific results using artistic images or movies can enhance the effectiveness in communicating our results.

Readers can view additional research online:
http://www.chem.wisc.edu/~cui/gallery_2.html
http://bionano.physics.illinois.edu/People/jejoong.html

– Qiang Cui and Jejoong Yoo

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s