Archive by date: October

Consortium members to participate in Biophysical Society 59th Annual Meeting symposia, workshops, and national lecture

MPSDC Awards: Francisco Bezanilla, Past President presenting an award to Robert Nakamoto.
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The Membrane Protein Structural Dynamics Consortium is always very well represented at the annual Biophysical Society meeting, with Consortium members actively involved at the leadership level, including Francisco Bezanilla‘s tenure as president from 2012 to 2014, as well as at the level of participants in a remarkably large number of workshops, symposia, and presentations.

At next year’s meeting in Baltimore, MPSDC members will participate in a number of specialty symposia and workshops organized by the Biophysical society (more information on the nature of these symposia and workshops can be found on the Biophysical Society meeting website here). We would like to highlight the following in particular (though there are and will certainly be more ways in which Consortium members are involved with the meeting):

  • Emad Tajkhorshid (UIUC) will be chairing the Permeation & Transport Subgroup 2015 Symposium. He is also chairing a workshop on Advances in Computing Large Systems.
  • Olga Boudker (Weill Cornell Medical College) is chairing a symposium on Neurotransmitter Transporters.
  • Christopher Ahern (University of Iowa) is participating in a symposium on Probing Ion Channel Structure/Function Using Novel Tools.
  • Jamies Bowie (UCLA) is participating in a workshop on Stabilizing Membrane Proteins.
  • Ivet Bahar (UPittsburgh) is giving a lecture titled “Neurotransmitter Translocation: Insights from Network Models and Multiscale Simulations” at the Biopolymers in Vivo Subgroup 2015 Symposium.
  • José Faraldo Gómez (NIH and MPSDC Associate Member) is giving a lecture titled “Novel Insights into the Structure and Mechanism of Proton and Sodium/Calcium Exchangers” at the Membrane Biophysics Subgroup 2015 Symposium.

Last but not least, MPSDC member and one of our keynote speakers at Frontiers in Membrane Protein Structural Dynamics 2014 Klaus Schulten (UIUC) will give the prestigious National Lecture. The National Lecturer is the highest award given each year by the Biophysical Society. The recipient presents the National Lecture on Monday evening of the Annual Meeting. We would like to congratulate Dr. Schulten on achieving this great honor.

See also: interviews from last year’s Biophysical Society with Francisco Bezanilla, Past President and Robert Nakamoto, Chair of the 2014 BPS Program Committee.

CHARMM-GUI Membrane Builder publication by Im et al. featured as cover image for Journal of Computational Chemistry

Dr. Wonpil Im, University of Kansas

One of the ongoing projects in the laboratory of Wonpil Im (University of Kansas and MPSDC team member) has been to contribute to the development of CHARMM-GUI and CHARMM-GUI modules, such as the Ligand Binder and the Membrane Builder. These tools help users generate a series of CHARMM inputs towards a specific purpose, like calculating a protein/ligand binding free energy or building a protein/membrane complex for molecular dynamics simulations. The Consortium’s Computational Modeling Core has provided partial support for the completion of such modules.

Im and his team recently published a paper about the Membrane Builder module in Journal of Computational Chemistry, titled “CHARMM-GUI Membrane Builder toward realistic biological membrane simulations” (reference below). This publication was featured as the cover image for the issue, which can be viewed below. J Comput Chem attached the following note about the article’s relevance:

On page 1997 (DOI: 10.1002/jcc.23712), Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Dávila‐Contreras, Yifei Qi, Jumin Lee, Viviana Monje‐Galvan, Richard M. Venable, Jeffery B. Klauda, and Wonpil Im report on the CHARMM‐GUI Membrane Builder, a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulation through an automated optimized process. The cover image illustrates the building process of a protein/membrane system by reading the protein structure, generating pore water/bilayer/bulk water/ions, and combining all the components.

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Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem. 2014 Oct 15;35(27):1997-2004. PMID: 25130509. PMCID: PMC4165794 [Available on 2015/10/15].

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