Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Benoit Roux Applicant's institution: ANL Applicant's division: BSD Project Name: kcsa Project title: Computational study of ion selectivity in the KcsA channel Associated funding: NIH-GM062342 Other Systems: Science: The selective binding of small ions (e.g., Na+, K+, Ca2+, Mg2+) to protein sites plays a key functional role in many important biological processes. The selectivity for is governed by the free energy landscape encountered by the different ions when they associated with the binding site. This, in turn, reflects the balance of ion-protein and ion-solvent interactions. Project description: The binding of small ions is a fundamental to the structure and function of biological systems. Ions are involved in the folding of proteins and nucleic acids, enzyme catalysis, and in numerous cellular signaling processes. Monovalent cations such as Na+ and K+ play an important role in the homeostasis and electric activity of living cells and in modulating biomolecular stability through both specific and non-specific interactions. The importance of those small cations is most strikingly examplified by their implication in a wide variety of membrane transport proteins, e.g., ion channels, transporters, and ATP-driven pumps. Understanding quantitatively the microscopic factors controlling ion selectivity using molecular dynamics (MD) simulations remains a great challenge. In simple terms, the concept of selectivity means that the "correct" ion, is able to binding more favorably than an "incorrect" ion. At a physical level, it is to be anticipated that energetics and solvation play a key role in this process, although different aspects of energetics may be highlighted by the various experimental methods used to probe the system. Some experimental measurements are more sensitive to the relative depth of free energy wells, while others are more sensitive to the relative height of free energy barriers. In the case of ion channels, the large hydration energy of the ions contrasts with the small free energy barriers necessary for the fast conduction observed experimentally. This implies that ion-protein association is ultimately controlled by a delicate balance of very strong interactions. Frequently, permeation involves the partial dehydration of an ion, followed by the binding to a proteinaceous environment. This archetype is well illustrated by the crystal structure of the KcsA channel. The pore of the KcsA channel comprises a wide aqueous vestibular entryway, lined by non-polar residues on the intracellular side, leading up on the extracellular side to a narrow region lined by backbone carbonyl oxygens. This region of the pore, formed by the residues corresponding to the signature sequence TTVGYG common to all K+ channels, acts as a "selectivity filter" by allowing only the passage of nearly dehydrated K+ ions across the cell membrane. Such fundamental characteristi cs of ion conduction through narrow pores are also exemplified by the gramicidin A channel (gA), where tight interactions between the permeating ion and the protein are critical. In such narrow molecular pores, a permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with the backbone carbonyl oxygens. The best strategy to address such issues is to compute the multi-ion PMF corresponding to the microscopic process in question (Berneche and Roux, Nature 2001). In particular, the calculation of the PMF enables us to pin-point the location of the largest barrier opposing the passage of a single Na+ ion while there are two K+ ions elsewhere in the pore. We carry those type of calculations using umbrella sampling MD simulations. Our plan is to compute the multi-ion free energy landscape for Na+ permeation through the KcsA channel using the open state structure that was recently determined by X-ray crystallography in the Perozo laboratory. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/research.html Requested allocation: 452832 Justification: The umbrella sampling calculations described here constitute a major part of the PhD thesis of David Medovoy, a graduate student in Biophysics at the University of Chicago. The goal of the umbrella sampling MD simulation is to obtain W(z1,z2,z3) the 3-ion PMF function of the coordinate of the 3 ions in the selectivity filter. To understand the effect of selectivity, two systems must be considered: with 3 K+ ions, and with 1 Na+ and 2 K+ ions. Based on our experience with similar computations, we know that a grand total of 3931 MD window simulations is needed for two systems. Each window should be simulated for 0.6 ns, the first 0.1 ns being used for equilibration and the last 0.5 ns for sampling proper, for total aggregate MD simulation time of 2.4 microseconds for each of the two systems. The unbiased 3D PMFs are then calculated using the weighted histogram method (WHAM). The simulations are generated with NAMD, which is the most efficient program for classical MD. The total requested allocation is: 452,832 SU = (3931 windows) * (0.6 ns/window) * ((8*cores)*(12 hour)/ns) The requester has used 0 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System