New Paper on Peptide–Graphene Interaction

In a paper just published in Journal of Physical Chemistry B as part of the Klaus Schulten Memorial issue, we have determined the effect of the graphene–water interface on protein backbone structure ( DOI: 10.1021/acs.jpcb.7b01130 ). This work was done by postdoc Dr Horacio Poblete and Dr Jeffrey Comer with additional calculations performed by visiting student Ingrid Miranda-Carvajal. We appreciate Ingrid's contribution to our work during her 6-month stay at in the Comer Lab at Kansas State University.

The amide groups of alanine dipeptide lies flat against the graphene surface.

Posted: 20 Mar 2017

Input Examples Available for DiffusionFusion

The Comer Group's code for calculating position-dependent diffusivity from molecular dynamics trajectories, available on our GitHub page, now includes example inputs. The approach implemented by DiffusionFusion has been described in several publications, including DOI: 10.1021/ct300867e and 10.1038/srep35913.

Posted: 20 Dec 2016

Paper Published on Anomalous Diffusion in Drug Permeation through Membranes

In a paper just published in Scientific Reports ( DOI: 10.1038/srep35913 ), Dr Comer and collaborator Dr Christophe Chipot demonstrated that diffusion of methanol within a pure lipid bilyaer membrane exhibits subdiffusion.

subdiffusion of methanol in a POPC lipid bilayer

Posted: 02 Nov 2016

Amercican Chemical Society 51st Regional Meeting

At this meeting in Manhattan, Kansas, group members Dr Jeffrey Comer and Dr Horacio Poblete gave talks entitled “Unpacking the thermodynamics of small solute adsorption on carbon nanomaterials” and “New insights into conformational equilibria of proteins absorbed to graphene and graphene oxide.”

ACS Midwest Regional Meeting

Posted: 28 Oct 2016

60th Biophysical Society Meeting

Group members Dr Horacio Poblete and Dr Ariela Vergara-Jaque presented posters at the Biophysical Society Meeting in Los Angeles.

  • Is the sodium monocarboxylate transporter (SMCT1) a protein involved in the apical iodide transport? Ariela Vergara-Jaque, Peying Fong, Jeffrey Comer
  • New Insight into Peptide-Silver Nanoparticle Interaction: Deciphering the Role of Cysteine and Lysine in the Peptide Sequence. Horacio Poblete, Anirudh Agarwal, Suma S. Thomas, Cornelia Bohne, Ranjihkumar Ravichandran, Jaywant Phospase, Jeffrey Comer, Emilio I. Alarcon

Group members were coauthors on a third poster with our collaborator Dr Delany Torres

  • Insights into the anion channel gating mechanism in Excitatory Amino Acid Transporters. Delany Torres-Salazar, Horacio Poblete, Aneysis Gonzalez, Ariela Vergara-Jaque, Susan G Amara and Jeffrey Comer
Horacio Poblete at the 2016 BPS Meeting

Posted: 28 Feb 2016

First International Conference in Bioinformatics, Simulation and Modeling in Talca, Chile

Group members Dr Jeffrey Comer, Dr Horacio Poblete, and Dr Ariela Vergara-Jaque gave talks at the First International Conference in Bioinformatics, Simulation and Modeling which took place in Talca, Chile.

  • Predicting transport mechanisms in membrane proteins through the repeat-swap homology modeling technique. Dr Ariela Vergara-Jaque
  • Molecular Dynamics as a Tool for Nanomaterial Design: Adsorption Affinities of Small Molecules on Carbon Nanotubes and Silver Nanoparticles. Dr Jeffrey Comer
  • Membrane Remodeling in the Inward- and Outward- Facing Conformations of Amino Acid Transporters: From Coarse-Grained to Large-Scale Molecular Dynamics Simulations. Dr Horacio Poblete

Our group furthermore presented two workshops:

  • Fast Free Energy Calculations of Binding to Surfaces. Dr Jeffrey Comer and Dr. Horacio Poblete
  • Molecular Modeling of Membrane Proteins. Dr Ariela Vergara-Jaque
  • The materials used in these workshops will soon be available on our Tutorials page.

Ariela Vergara-Jaque at the First International Conference in Bioinformatics, Simulation and Modeling in Talca, Chile

Posted: 06 Nov 2015