2012 | Membrane Protein Structural Dynamics Gateway

Benoît Roux and the Computational Modeling Core

Posted on March 12, 2012 — No Comments ↓

We are delighted to introduce the latest feature on the Membrane Protein Structural Dynamics Consortium (MPSDC) website: Behind the Scenes. Within this section, we will be exploring the inner workings of the Consortium with a camera in hand, dedicating to showing you what takes place within the laboratory setting and outside of it.

For our inaugural piece, we present the following video feature of Benoît Roux, the PI of the Consortium’s Computational Modeling Core (CMC). We sat down with Benoît and asked him about computational modeling, the CMC’s collaborations and function within the MPSDC, and where he sees the Consortium in five years. Let us know what you think in the comments!

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 »

MPSDC Symposium to take place on May 3rd and 4th, 2012

Posted on February 1, 2012 — No Comments ↓

Click to enlarge flyer

The Membrane Protein Structural Dynamics Consortium (MPSDC) will be holding its first Membrane Protein Structural Dynamics Symposium on Thursday, May 3rd and Friday, May 4th. This Symposium will feature both scientific sessions and workshops, and we expect the sessions to include not only Consortium members but also additional 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.

This year the meeting will be held in downtown Chicago at the University of Chicago’s Gleacher Center located at 450 North Cityfront Plaza Drive, Chicago IL 60611.

margin-top: online casino australia 0; padding-bottom: 5px;”> The Gleacher Center is the downtown home of the University of Chicago

The Gleacher Center

This is a wonderful and centrally located venue that we think will enhance our interactions and allow for easy transportation to and from the meeting.

Overall, we envision the event to consist of two sections. First, the Symposium will occupy all of Thursday, May 3 and the morning of Friday, May 4. Our Consortium meeting will then follow Friday afternoon and is intended only for Consortium members, our NIH liaison and the External Advisory Committee.

Schulten and Tajkhorshid to host workshop on Computational Biophysics

Posted on January 9, 2012 — No Comments ↓

The Fenna-Matthews-Olson Trimer

This “hands on” workshop on computational physics, which has Consortium Members Klaus Schulten and Emad Tajkhorshid as co-hosts, will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations.

The workshop forms part of the NIH-sponsored Workshops on Theoretical and Computational Biophysics and will take place on February 11 – 15, 2012. It is designed for students and researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 20 participants.

Klaus Schulten and Emad Tajkhorshid are members of the Computational Modeling core. Tajkhorshid also collaborates in the Structural Dynamics of ABC Transporter and Conformational Dynamics in the CLC Channel/Transporter Family projects.

Find out more information and apply »