2008
DOI: 10.1063/1.2931568
|View full text |Cite
|
Sign up to set email alerts
|

Comment on “Free energy simulations of single and double ion occupancy in gramicidin A” [J. Chem. Phys. 126, 105103 (2007)]

Abstract: In a recent article published by Bastug and Kuyucak [J. Chem. Phys.126, 105103 (2007)] investigated the microscopic factors affecting double ion occupancy in the gramicidin channel. The analysis relied largely on the one-dimensional potential of mean force of ions along the axis of the channel (the so-called free energy profile of the ion along the channel axis), as well as on the calculation of the equilibrium association constant of the ions in the channel binding sites. It is the purpose of this communicati… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
3

Citation Types

0
28
0

Year Published

2008
2008
2021
2021

Publication Types

Select...
8
1
1

Relationship

4
6

Authors

Journals

citations
Cited by 21 publications
(28 citation statements)
references
References 18 publications
0
28
0
Order By: Relevance
“…As with the alchemical methods described above, restraining potentials of different shape may be introduced to carry out a calculation, as long as their contributions are correctly accounted for in the final equilibrium binding constant. 70 The PMF-based method is illustrated schematically in Figure 2.…”
Section: Theory and Methodsmentioning
confidence: 99%
“…As with the alchemical methods described above, restraining potentials of different shape may be introduced to carry out a calculation, as long as their contributions are correctly accounted for in the final equilibrium binding constant. 70 The PMF-based method is illustrated schematically in Figure 2.…”
Section: Theory and Methodsmentioning
confidence: 99%
“…The p K a of E148 was estimated using the equation for calculating the equilibrium constant of binding of the substrate at the binding site of the protein, based on the one-dimensional PMF for the substrate moving along the channel axis with the cylindrical potential applied at the channel entrance: 36 where the substrate is the excess proton and the binding site is E148. Here, C 0 is the standard state concentration (1 M = 1/1660 Å –3 ), and Δ G site is the free energy cost introduced by the cylindrical potential at the substrate binding site (the CEC is at E148.).…”
Section: Methodsmentioning
confidence: 99%
“…This is needed to construct mathematically well-defined PMFs along the channel axis28,54. Other choices of restraining potential could be used, although the final results will be independent of such choice only if the computations are properly unbiased54.…”
Section: Methodsmentioning
confidence: 99%