Archive by category: News and Updates

New Continuum-Molecular Dynamics (CTMD) software made available by Computational Modeling Core

Posted on June 5, 2012 — 13 Comments ↓

The membrane environment is a key determinant of function and/or organization of membrane proteins. It is essential for the activities of the Consortium to have access to quantitative information about the characteristics and energetics of membrane-protein interactions. For multi-segment transmembrane proteins in particular, such characterization is complicated by the different hydrophobic thicknesses of the component transmembrane segments and the radially non-uniform hydrophobic interface created between the membrane and the protein. A hybrid Continuum-Molecular Dynamics (CTMD) approach to compute membrane deformations profiles around multi-segment proteins and corresponding energetics was recently published [Sayan Mondal, George Khelashvili, Jufang Shan, Olaf Andersen, Harel Weinstein (2011), Biophysical J (101): 2092-2101; link]. This stand-alone application implements the CTMD approach.

Protocol for the 3D-CTMD approach, illustrated for rhodopsin in a diC14:1PC lipid bilayer (Mondal et al., BJ 2011). Click to enlarge and learn more.

The CTMDapp software calculates the deformation profiles of the bilayer and the free energy cost of the membrane deformation around multi-segment transmembrane proteins, taking into account the radially non-uniform hydrophobic surface of the protein. As the primary input it requires a molecular dynamics trajectory of a multi-segment, transmembrane protein embedded in a bilayer.

To allow for calculations without a molecular dynamics input, the CTMDapp software also implements a simplified version of the CTMD method that can assess the radial asymmetry of the membrane-protein interface for a particular protein structure at an approximate level.

Methodological details can be found in the original paper (Mondal et al., BJ 2011). In addition, the application is documented with brief usage notes at every step and generates diagnostic intermediate output.

Download the software:

Instructions:
For the Windows version, clicking on the downloadable .exe file will directly launch the Matlab Component Runtime (MCR) installation process and extract the app executable. For the Mac version, the MCR must be installed first by opening MCRinstaller.dmg in the folder. This is a one-time installation, after which CTMDapp can be launched. The Unix version requires an interface like Xwin along with a script setting proper paths.

The software was written by Sayan Mondal (mos2013@med.cornell.edu) in the Harel Weinstein (haw2002@med.cornell.edu) lab at Weill Cornell Medical College, Cornell University. Please feel free to contact us with questions and suggestions about the software.

Frontiers in Membrane Protein Dynamics full schedule announced

Posted on April 3, 2012 — 2 Comments ↓

Click to enlarge poster or download a pdf for 8×11″ printing.

The Membrane Protein Structural Dynamics Consortium (MPSDC) will be holding its first Frontiers in Membrane Protein Dynamics conference on Thursday, May 3rd and Friday, May 4th.

This conference consists of scientific sessions and poster presentations, and will feature both Consortium members and external invitees.

Attendance is open to the public and will take place within the context of our 3rd Annual MPSDC Meeting, where all members, NIH representatives and our External Advisory Committee will participate.

The MPSDC’s Computational Modeling Core will host a NAMD/VMD workshop and a mini-symposium prior to the conference, which will take place on the University of Chicago campus. For more information on either of these events, click here »

We are currently booked over capacity for the conference, and are therefore no longer taking registrations. Please inquire at mpsdc_admin@bsd.uchicago.edu if you have any questions.
Read more »

MPSDC-funded poster author wins Biophysical Society 2012 Student Research Achievement Award

Posted on March 29, 2012 — No Comments ↓

Thomas Chew with the award-winning poster. Click to enlarge.

The MPSDC had a strong showing at the Biophysical Society’s 56th Annual Meeting this year, with members collaborating in a total of 72 posters and presentations taking place in various subgroups, platforms, symposia, mini-symposia, and workshops. Now, we are proud to announce that one of our posters was selected as one of the thirteen 2012 Student Research Achievement Award Winners.

Thomas Chew, the first author of the poster, is an undergraduate student at the University of California, San Diego. He has performed summer research projects in the laboratory of Merritt Maduke at Stanford University.

The winning poster is entitled Structural Investigations of CLC-ec1, A Large Integral Membrane Protein, Using Solution-State NMR and Nanodisc Techology and features Thomas Chew, Sherwin J. Abraham, Shelley M. Elvington, and Merritt Maduke as authors. The poster was selected by the National Institute of General Medical Sciences as the sole NIGMS Poster Winner.

Thomas Chew at the February 27 Awards Ceremony together with the other winners and Steve Block. Click to enlarge.

Thomas was recognized and received a monetary award at the Awards Ceremony on February 27, preceding the 2012 National Lecture delivered by Steve Block. He was also selected to attend the NIGMS/NIH’s 50th anniversary symposium in October 2012.

Congratulations, Thomas and Merritt!

Read the Biophysical Society’s press release »

Five new publications by Emad Tajkhorshid added

Posted on March 5, 2012 — 1 Comment ↓

To date, the Membrane Protein Structural Dynamics Consortium (MPSDC) has produced 22 publications which can be found in the popular PubMed database of references and abstracts on life sciences and biomedical topics and were assigned PMID identifiers. These collaborative publications were buttressed by funding provided by the NIH/NIGMS Glue Grant which supports the MPSDC, and the findings produced by these publications are consonant with the Consortium’s overall mission.

Dr. Emad Tajkhorshid

So far in 2012, six publications have been added to the website, five of which were co-authored by Emad Tajkhorshid. Tajkhorshid is Associate Professor of Pharmacology, Biochemistry and Biophysics at the University of Illinois, Urbana-Champaign, and an active participant in its Theoretical and Computational Physics Group together with fellow Consortium member Klaus Schulten. His research focuses on structure function relationships in membrane proteins and understanding the mechanism of their function using simulation and computational methodologies. Examples of his research include the mechanism of permeation of water, ions, and other substrates through membrane channels; simulation of photoactivation in rhodopsin and other visual receptors; and, quantum mechanical calculations of the chromophore in bacteriorhodopsin.

Within the MPSDC, Tajkhorshid is a frequent collaborator of the Computational Modeling Core (link). Additionally, Tajkhorshid also oversees the computational components of the Structural Dynamics of ABC Transporter bridge project (link) and the Conformational Dynamics in the CLC Channel/Transporter Family pilot project (link).

We would like to thank Emad for his collaborative endeavors, and congratulate him on his prolific output!

Emad Tajkhorshid’s publications in 2012 to date:

	Structural basis for iron piracy by pathogenic Neisseria Noinaj N, Easley NC, Oke M, Mizuno N, Gumbart J, Boura E, Steere AN, Zak O, Aisen P, Tajkhorshid E, Evans RW, Gorringe AR, Mason AB, Steven AC, Buchanan SK. Nature 483(7387): 53-58 (2012). PMID: 22327295. Learn more »
	A gate-free pathway for substrate release from the inward-facing state of the Na(+)-galactose transporter Li J, Tajkhorshid E. Biochimica et Biophysica Acta (BBA) – Biomembranes 1818(2): 263-271 (2012). PMID: 21978597. PMCID: PMC3253917. Learn more »
	Tracing cytoplasmic Ca²⁺ ion and water access points in the Ca²⁺-ATPase Musgaard M, Thøgersen L, Schiøtt B, Tajkhorshid E. Biophysical Journal 102(2): 268-277 (2012). Learn more »
	Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains Khalili-Araghi F, Tajkhorshid E, Roux B, Schulten K. Biophysical Journal 102(2): 258-267 (2012). Learn more »
	Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter Barnard T, Gumbart J, Peterson J, Noinaj N, Easley N, Dautin D, Kuszak A, Tajkhorshid E, Bernstein H, Buchanan S. Journal of Biological Chemistry 415(1): 128-42 (2012). PMID: 22094314. PMCID: PMC3230255. Learn more »

MPSDC at the 56th Annual Biophysical Society Meeting

Posted on February 17, 2012 — No Comments ↓

The 56th Annual Biophysical Society Meeting is fast approaching, and this year members of the Membrane Protein Structural Dynamics Consortium (MPSDC) have collaborated on no less than 72 presentations and posters taking place in various subgroups, platforms, symposia, mini-symposia, and workshops.

Additionally, Klaus Schulten will be honored at the Meeting’s Awards Ceremony as a 2012 Society Fellow during the Biophysical Society’s on Monday February 27, 2012 for his groundbreaking effort to develop computational molecular biology as an important tool to solve problems in biophysics. Francisco Bezanilla was voted President-Elect during the 2011 Society meetings and will begin officially holding this office at the Meeting. His term as President will begin at the 2013 Annual Meeting in Philadelphia, Pennsylvania. Finally, Merritt Maduke will begin her three-year term as a Councilor of the Biophysical Society as well.

The table after the jump provides a complete itinerary of all Consortium-affiliated presentations and posters. We would like to feature especially those 12 in which two or more Consortium members or associate members have collaborated (highlighted in light blue). The table is ordered by date and time.

Download a pdf of this itinerary including abstracts »