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Spectroscopy and Modeling to Infer Channel Structure and Function

By Vishwanath Jogini

University of Chicago

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Abstract

We are particularly interested in issues about ion permeation, ion selectivity, gating, and channel inhibitors. We are currently working on the KcsA channel, the OmpF porin, and the gramicidin A> channel. We are also spending our efforts in the development of new computational approaches for studying biological macromolecular systems.

The computational approach called "molecular dynamics" (MD) is central to our work. It consists of constructing detailed atomic models of the macromolecular system and, having described the microscopic forces with a potential function, using Newton's classical equation, F=MA, to literally "simulate" the dynamical motions of all the atoms as a function of time. The calculated trajectory, though an approximation to the real world, provides detailed information about the time course of the atomic motions, which is impossible to access experimentally.

In addition, other computational approaches, at different level of complexity and sophistication, can be very useful. In particular, Poisson-Boltzmann (PB) continuum electrostatic models, in which the influence of the solvent is incorporated implicitly, plays an increasingly important role in estimating the solvation free energy of macromolecular assemblies.

Credits

Breezed and Uploaded by Omar Sobh
University of Illinois at Urbana-Champaign.

Cite this work

Researchers should cite this work as follows:

  • Nano-Bio Workshop and nanoHUB Summer School,
    NCSA, University of Illinois at Urbana-Champaign, July 30-31, 2007
  • Vishwanath Jogini (2008), "Spectroscopy and Modeling to Infer Channel Structure and Function," http://nanohub.org/resources/4173.

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