Minimalist molecular model for nanopore selectivity.

Authors:
Dr. Mauricio Carrillo-Tripp, PhD
Dr. Mauricio Carrillo-Tripp, PhD
Biomolecular Diversity Laboratory, Cinvestav
Associate Profesor
Computational Biophysics
Irapuato, Guanajuato | México

Phys Rev Lett 2004 Oct 14;93(16):168104. Epub 2004 Oct 14.

Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62210 Cuernavaca, Morelos, México.

Using a simple model it is shown that the cost of constraining a hydrated potassium ion inside a narrow nanopore is smaller than the cost of constraining the smaller hydrated sodium ion. The former allows for a greater distortion of its hydration shell and can therefore maintain a better coordination. We propose that in this way the larger ion can go through narrow pores more easily. This is relevant to the molecular basis of ion selective nanopores and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes, from biological to synthetic.

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.93.168104DOI Listing
October 2004
12 Reads
4 PubMed Central Citations(source)
7.51 Impact Factor

Publication Analysis

Top Keywords

cost constraining
8
greater distortion
4
molecular basis
4
pore operate
4
distortion hydration
4
details pore
4
hydration shell
4
allows greater
4
operate sorts
4
hydrated sodium
4
sorts nanotubes
4
sodium ion
4
basis ion
4
ion allows
4
shell maintain
4
smaller hydrated
4
ion narrow
4
larger ion
4
mechanism depend
4
narrow pores
4

Similar Publications

Ion hydration in nanopores and the molecular basis of selectivity.

Biophys Chem 2006 Dec 3;124(3):243-50. Epub 2006 May 3.

Chemistry Department, Wabash College, P.O. Box 352, Crawfordsville, IN 47933, USA.

Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2. Read More

View Article
December 2006

Factors governing the Na(+) vs K(+) selectivity in sodium ion channels.

J Am Chem Soc 2010 Feb;132(7):2321-32

Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.

Monovalent Na(+) and K(+) ion channels, specialized pore-forming proteins that play crucial biological roles such as controlling cardiac, skeletal, and smooth muscle contraction, are characterized by a remarkable metal selectivity, conducting the native cation while rejecting its monovalent contender and other ions present in the cellular/extracellular milieu. Compared to K(+) channels, the principles governing Na(+) vs K(+) selectivity in both epithelial and voltage-gated Na(+) channels are much less well understood due mainly to the lack of high-resolution 3D structures. Thus, many questions remain. Read More

View Article
February 2010

Density functional theory investigations on the chemical basis of the selectivity filter in the K+ channel protein.

J Am Chem Soc 2004 Apr;126(14):4711-6

Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3.

The chemical-physical basis of loading and release of K(+) and Na(+) ions in and out of the selectivity filter of the K(+) channel has been investigated using the B3LYP method of density functional theory. We have shown that the difference between binding free energies of K(+) and Na(+) to the cavity end of the filter is smaller than the difference between the K(+) and Na(+) solvation free energies. Thus, the loading of K(+) ions into the cavity end of the selectivity filter from the solution phase is suggested to be selective prior to the subsequent conduction process. Read More

View Article
April 2004

Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels.

J Gen Physiol 2007 Feb 16;129(2):135-43. Epub 2007 Jan 16.

Institute for Molecular Pediatric Sciences, Gordon Center for Integrative Sciences, University of Chicago, IL 60637, USA.

Fundamental concepts governing ion selectivity in narrow pores are reviewed and the microscopic factors responsible for the lack of selectivity of the NaK channel, which is structurally similar to the K+-selective KcsA channel, are elucidated on the basis of all-atom molecular dynamics free energy simulations. The results on NaK are contrasted and compared with previous studies of the KcsA channel. Analysis indicates that differences in hydration of the cation in the pore of NaK is at the origin of the lack of selectivity of NaK. Read More

View Article
February 2007