Archive by category: In The Press

First issue of MPSDC e-newsletter released

Fresh off the press: the first edition of the semi-annual Membrane Protein Structural Dynamics Consortium (MPSDC) e-newsletter!

The MPSDC e-newsletter brings together announcements, updates, features, new publications, and other MPSDC-relevant news blurbs in one email.

In the Winter 2013 newsletter, we announced the Frontiers in Membrane Protein Dynamics 2014 conference, and shared the exciting news of two scientists joining the Protein Expression / Purification core team. Additionally, we reviewed consortium progress and scientific advances discussed at 2013 Annual Meeting, and featured ongoing collaborative research in the laboratories of Hassane Mchaourab, Benoît Roux, and Emad Tajkhorshid.

View the Winter 2013 e-newsletter »

Do you want to receive the latest MPSDC updates via email? Sign up here!

Remember, you can also stay up the date with the MPSDC through our active Facebook page!

MPSDC Director to give plenary lecture at 2014 International Biophysics Congress

The 2014 International Biophysics Congress, which is taking place in Brisbane, Australia this year, will have the pleasure of hosting none other than MPSDC Director Dr. Eduardo Perozo.

Along with three other scientists, Perozo has been nominated as a plenary speaker for this conference hosted by the Australian Society for Biophysics (ASB) and the International Union of Pure and Applied Biophysics (IUPAB).

“IUPAB 2014″ will feature an outstanding scientific program and a stimulating social program. Attending this Congress will be highly scientifically rewarding, as well as a terrific opportunity to visit Australia. The meeting will be held from August 3 – 7, 2014 at the Brisbane Convention & Exhibition Centre.

Visit the IUPAB 2014 Conference website »

Transporter linked to autism risk

Membrane Protein Structural Dynamics Consortium (MPSDC) team member Hassane Mchaourab was recently featured in the Vanderbilt University Medical Center Reporter, along with a team of scientists who have linked a non-inherited, de novo mutation in the dopamine transporter to autism spectrum disorder (ASD).

The research was partially funded by the MPSDC, and contributes to the overall objectives of the Transport Cycle in Neurotransmitter Uptake Systems project in which Mchaourab is an active collaborator.

The group’s research was published in the journal Molecular Psychiatry, with Mchaourab as one of the senior authors. You can read more about the publication here.

Read the Vanderbilt University Medical Center Reporter after the jump.

Heiner Matthies, Ph.D., at the white board, leads a “seminar” for colleagues who hold vials of their fruit fly model that for the first time linked a non-inherited mutation in the dopamine transporter to autism. Seated at right, from the back, are Nicholas Campbell, Aurelio Galli, Ph.D., and P.J. Hamilton. Seated at left are Hassane Mchaourab, Ph.D., and James Sutcliffe, Ph.D. (photo by Susan Urmy)

Read more »

Collaborative MPSDC team develops innovative computational simulation technique

With our 2013 annual meeting less than a month away, we are delighted to share with you the news about a new computational simulation technique developed by several MPSDC team members that was first presented at last year’s Frontiers in Membrane Protein Dynamics conference. The development of this technique speaks to the significant scientific collaborations that take place under the umbrella of the Consortium, as well as the scientific conversations that began in Chicago last year.

At the conference, Benoît Roux from our Computational Modeling Core introduced his team’s findings obtained from DEER (Double Electron-Electronic Resonance) data. At the conference, Roux and his team received helpful feedback from a number of scholars affiliated with the MPSDC as well as external invitees. After the conference, Roux and his team collaborated with a number of other scientists, including consortium colleague Hassane Mchaourab, to develop a novel computational simulation technique for exploiting the information from distance distribution data obtained from ESR/DEER spectroscopy for the refinement of membrane protein structures. This simulation technique, called the Restrained-Ensemble Molecular Dynamics (REMD) simulation method, uses a global ensemble-based energy restraint to force the spin-spin distance distribution histograms calculated from a multiple-copy molecular dynamics simulation to match those obtained from ESR/DEER experiments.

Already, the method has yielded three unique publications detailing the results of these experiments:

  • Islam, S. M.; Stein, R.; Mchaourab, H.; Roux, B. Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme, J. Phys. Chem. B 117(17): 4740-54, 2013. (link)
  • Roux, B.; Islam, S. M. Restrained-Ensemble Molecular Dynamics Simulations Based on Histograms from Double Electron-Electron Resonance Spectroscopy, J. Phys. Chem. B 117(17): 4733-9, 2013, In Press. (link)
  • Roux, B.; Weare, J. On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method, J. Chem. Phys. 138(8): 084107, 2013. (link)

The article co-authored by Benoît Roux and Jeane Weare was highlighted by the Journal of Chemical Physics on their Top 20 Most Read in March 2013.

Roux and his team have also gone on to apply this method to VSD (voltage-sensing domain) data with Eduardo Perozo, and Glt(Ph) data with Olga Boudker. Additionally, Wonpil Im is also implementing an easy setup of this method with dummy spin-labels on his CHARMM-GUI generator.

Shahidul M. Islam from Roux’s team, who co-authored two of the above papers and has been deeply involved in the scientific process, provided the MPSDC with an overview of the technique and its utility. We invite you to read his overview here »

Congratulations to all involved in the development of this exciting and important new method!

Benoît Roux receives Great Lakes Consortium award access to Blue Waters supercomputer

The Great Lakes Consortium for Petascale Computation has awarded access to the Blue Waters supercomputer — which is capable of performing quadrillions of calculations every second and of working with quadrillions of bytes of data — to 10 diverse science and engineering projects, including a project titled “The mechanism of the sarco/endoplasmic reticulum ATP-driven calcium pump”, spearheaded by Benoît Roux and his team.

Blue Waters supercomputer. Click to enlarge.

The Great Lakes Consortium for Petascale Computation is a collaboration among colleges, universities, national research laboratories, and other educational institutions that facilitates the widespread and effective use of petascale computing. The computing and data capabilities of Blue Waters will assist researchers in addressing questions of biology, nanoelectronics, ecological and economic impacts of climate change, and more.

Roux’s work with the Blue Waters supercomputer will make a significant contribution to the Conformational Transitions in P-class ATPases Project of the Membrane Protein Structural Dynamics Consortium (MPSDC), in which Roux collaborates with Francisco Bezanilla. Roux’s team provided the following description of their research plans with Blue Waters:

Maintaining optimum concentration gradients of monovalent (Na+, K+) and divalent (Ca2+) ions across cell membranes is a crucial part of signaling and regulation of many biological processes. Positively charged ions, being impermeable to largely hydrophobic cell membranes, need special passages to travel in and out of the living cell. Nature’s answer to this problem is two classes of membrane proteins called ion channels and ion pumps. Ion channels are responsible for the passive transport of selected ions, while ion pumps consume ATP to transport ions against their gradient.

Understanding the detailed molecular mechanism of ion pumps has been a long standing problem. In the early parts of the previous decade, a major breakthrough came in the form of determination of atomic resolution X-ray crystal structures of calcium transporting pump of sarcoplasmic reticulum of skeletal muscles (SERCA) that uses ATP hydrolysis as a source of free energy. Detailed structural studies of the pump under different conditions provided analogues of various intermediates in the reaction cycle and revealed important changes in the tertiary structure of the protein both in the cytoplasmic and in the transmembrane parts. Two major outstanding issues are the pathways of the ions to and from the transmembrane binding sites and a detailed understanding of the large scale conformational changes among various functionally relevant states. We will apply all-atom molecular dynamics (MD) and string method with swarms-of-trajectories to study transition pathways among various experimental structures.

The allocations provided on the Blue Waters supercomputer will allow us to study this important membrane protein with unprecedented detail. This study will reveal the molecular mechanism of an important step in the ion pumping process of a P-type ATPase and will provide a solid ground to understand other ATP-driven ion pumps such as the sodium-potassium pump, which shares very high sequence similarity with SERCA.

Congratulations to Benoît and his team for receiving this important award!

Learn more about the Blue Waters supercomputer »

Categories
Recent Posts
Archives
Recent Comments
Recent Photos