Archive by date: March

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 »

Membrane Protein Modeling workshop to take place at the University of Chicago on May 7th

During the week of the Membrane Protein Structural Dynamics Consortium (MPSDC)’s Annual Meeting, a workshop specifically dedicated to Membrane Protein Modeling will be held at the University of Chicago on Tuesday, May 7th. This Workshop is designed to provide an introduction to the most important computational tools and techniques used in molecular dynamics simulations of membrane proteins, including utilization of the programs NAMD and VMD, as well as the CHARMM-GUI Membrane Builder. We will also cover the use of force field parameterization tools. The workshop will include a practical “hands-on” session.

The Workshop is co-organized by the Computational Modeling Core (CMC) of the MPSDC and the Theoretical and Computational Biophysics Group (TCBG) of the University of Illinois at Urbana-Champaign.

Register for the CMC Membrane Protein Workshop (required) »

Last year’s CMC Workshop, also held at the University of Chicago.

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