26 research outputs found
University Magazine Spring 2002
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
Ion Permeation in the NanC Porin from Escherichia coli: Free Energy Calculations along Pathways Identified by Coarse-Grain Simulations
Using
the X-ray structure of a recently discovered bacterial protein,
the <i>N</i>-acetylneuraminic acid-inducible channel (NanC),
we investigate computationally K<sup>+</sup> and Cl<sup>–</sup> ions’ permeation. We identify ion permeation pathways that
are likely to be populated using coarse-grain Monte Carlo simulations.
Next, we use these pathways as reaction coordinates for umbrella sampling-based
free energy simulations. We find distinct tubelike pathways connecting
specific binding sites for K<sup>+</sup> and, more pronounced, for
Cl<sup>–</sup> ions. Both ions permeate the porin preserving
almost all of their first hydration shell. The calculated free energy
barriers are <i>G</i><sup>#</sup> ≈ 4 kJ/mol and <i>G</i><sup>#</sup> ≈ 8 kJ/mol for Cl<sup>–</sup> and K<sup>+</sup>, respectively. Within the approximations associated
with these values, discussed in detail in this work, we suggest that
the porin is slightly selective for Cl<sup>–</sup> versus K<sup>+</sup>. Our suggestion is consistent with the experimentally observed
weak Cl<sup>–</sup> over K<sup>+</sup> selectivity. A rationale
for the latter is suggested by a comparison with previous calculations
on strongly anion selective porins
University Magazine Fall 2006
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Winter 2003
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Fall 2010
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Winter 2012
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Fall 2014
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Spring 2014
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Winter 2013
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999
University Magazine Winter 2014
This is the official magazine for RIT Alumni. Issued thrice a year in spring, fall and winter. Printing began in 1999