News


Papers on Inhibitors of Snake Venom Toxins

Viperid snakebites are a major public health in some areas of Colombia. Lina María Preciado, a PhD student from the Universidad de Antioquia in Medellín, Colombia, brought her interest in discovering new treatments for tissue damage caused by these snakebites to the Comer Research Group, spending five months at Kansas State University. During her relatively short stay, Ms. Preciado learned to perform molecular simulation and free-energy calculations, which she applied to study interactions between candidate drugs and snake venom enzymes (metalloproteinases) that damage human tissue. This work has resulted in two recently published papers considering a set of triterpene compounds ( DOI: 10.3390/toxins10100397 ) and the flavonoid myricetin ( DOI: 10.3390/molecules23102662 ).

Although both betulinic acid and β-boswellic acid bind strongly to the snake venom metalloproteinase BaP1, they bind in different orientations, leading to very different biological activities.

Although both betulinic acid and β-boswellic acid bind strongly to the snake venom metalloproteinase BaP1, they bind in different orientations, leading to very different biological activities.

Posted: 24 Oct 2018



Study of Heat Conduction in Gold Nanoparticles Engineered for Cancer Treatment

In a technique known as hyperthermal therapy, raising tumors to high temperatures can help to eradicate cancer from the body. The Comer Research Group is collaborating with chemist Dr. Santosh Aryal and his group to develop gold nanoparticles that can target the tumor site that heat up when exposed to infrared light. These nanoparticles are coated with polymers to make them more compatible with living tissue and stay in the bloodstream longer. Dr. Comer used molecular simulation to reveal the structure of this coating and to calculate how coatings of different thicknesses conduct heat. The results of this study were recently published in the journal Nanoscale ( DOI: 10.1039/C8NR03026J ).

(Top) Simulation of a gold surface coated with polyethylene glycol. (Bottom) Temperature profile of polyethylene glycol coating when gold is heated.

(Top) Simulation of a gold surface coated with polyethylene glycol. (Bottom) Temperature profile of polyethylene glycol coating when gold is heated.

Posted: 31 May 2018



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