Showing papers by "James C. Phillips published in 2001"

Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane

Abstract: Vectorial proton translocation through membranes is a fundamental energy conversion process in biological cells. Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven, voltage-sensitive proton pump in the purple membrane (PM) of Halobacterium salinarumand achieves its biological function by cycling through a reaction sequence that includes ultrafast (500 fs) events, intermediate (Is) as well as slow (10 ms) steps. bR is of utmost simplicity in comparison with other proton translocating bioenergetic proteins and, therefore, constitutes an ideal model for the study of this process. The PM involves a highly structured supramolecular organization and is fundamental for the in vivo functioning of bR. Over the last 10 years, crystal structures of bR have become available at increasing resolution. The most recent structures resolve many of the lipids of the PM and provide atomic level detail of bR at below 2 A resolution. Fundamental for an understanding of the function of bR is internal water that participates in proton pumping. Several water molecules have been resolved now crystallographically in two channels, on the extracellular and on the intracellular side of bR. We show that free energy perturbation theory can place water molecules in bR, with results that compare well with the observed water molecules, and we apply the method to predict water movement during bR’s photocycle. A preliminary simulation illustrates that water molecules may indeed be displaced during the photocycle, after retinal undergoes an all-trans f 13-cis isomerization, and that this displacement may constitute a mechanism for proton pumping. A key advance reported in this feature article is the integration of the available bR structures into a model for the entire PM. This hexagonally periodic, lamellar model has been hydrated and refined through a constant pressure molecular dynamics simulation. The resulting structure connects extracellular bulk water with water molecules and key side groups in the interior of bR, permitting a seamless overall description of the proton path in the PM, from intracellular to extracellular space. For the first time, a complex cellular reaction can be accounted for in full atomic detail in its complete native environment.

NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License

Abstract: Description The NAMD User's Guide describes how to run and use the various features of the molecular dynamics program NAMD. This guide includes the capabilities of the program, how to use these capabilities, the necessary input files and formats, and how to run the program both on uniprocessor machines and in parallel. Introduction The University of Illinois at Urbana-Champaign has created its molecular dynamics software, NAMD, developed by the Theoretical Biophysics Group (" TBG ") at Illinois' Beckman Institute available free of charge for non-commercial use by individuals, academic or research institutions and corporations for in-house business purposes only, upon completion and submission of the online registration form available from the NAMD web site Commercial use of the NAMD software, or derivative works based thereon, REQUIRES A COMMERCIAL LICENSE. Commercial use includes: (1) integration of all or part of the Software into a product for sale, lease or license by or on behalf of Licensee to third parties, or (2) distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee. The University of Illinois will negotiate commercial-use licenses for NAMD upon request. These requests can be directed to namd@ks.uiuc.edu Registration Individuals may register in their own name or with their institutional or corporate affiliations. Registration information must include name, title, and e-mail of a person with signature authority to authorize and commit the individuals, academic or research institution, or corporation as necessary to the terms and conditions of the license agreement. All parts of the information must be understood and agreed to as part of completing the form. Completion of the form is required before software access is granted. Pay particular attention to the authorized requester requirements above, and be sure that the form submission is authorized by the duly responsible person. Registration will be administered by the NAMD development team. Upon execution of this Agreement by the party identified below (" Licensee "), The Board of Trustees of the University of Illinois (" Illinois "), on behalf of The Theoretical Biophysics Group (" TBG ") in the Beckman Institute, will provide the molecular dynamics software NAMD in Executable Code and/or Source Code form (" Software ") to Licensee, subject to the following terms and conditions. For purposes of this Agreement, Executable Code is the compiled code, which is ready to run on Licensee's computer. Source code consists …