Biomaterial Database

Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A. 1989

J Aqvist, and A Warshel

Department of Chemistry, University of Southern California, Los Angeles 90089-1062.

Calculations of the solvation energetics for a Na+ ion inside the Gramicidin A channel and in water are presented. The protein dipoles Langevin dipoles (PDLD) method is used to obtain an electrostatic free energy profile for ion permeation through the channel. To gauge the quality of the PDLD results the solvation free energy of a Na+ ion in water and in the center of the channel is also calculated using free energy perturbation (FEP) simulations. The effect of the polarisability of the surrounding lipid membrane is taken into account by representing the membrane by a large grid of polarisable point dipoles. The two methods give similar solvation energies in the interior of the channel and these are less than 5 kcal/mol above the solvation free energy for Na+ in water, in good agreement with experimental data on the activation barriers for ion permeation. It appears that the problems associated with previous calculations of energy profiles in membrane channels can be overcome by a consistent treatment of all the relevant electrostatic contributions. In particular, we find that the induced dipoles of the membrane and the protein contributes with approximately 10 kcal/mol to the solvation energy inside the channel and can therefore not be discarded in a realistic description of ion solvation in the Gramicidin channel.

UI	MeSH Term	Description	Entries
D007473	Ion Channels	Gated, ion-selective glycoproteins that traverse membranes. The stimulus for ION CHANNEL GATING can be due to a variety of stimuli such as LIGANDS, a TRANSMEMBRANE POTENTIAL DIFFERENCE, mechanical deformation or through INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS.	Membrane Channels,Ion Channel,Ionic Channel,Ionic Channels,Membrane Channel,Channel, Ion,Channel, Ionic,Channel, Membrane,Channels, Ion,Channels, Ionic,Channels, Membrane
D008433	Mathematics	The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)	Mathematic
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D008962	Models, Theoretical	Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.	Experimental Model,Experimental Models,Mathematical Model,Model, Experimental,Models (Theoretical),Models, Experimental,Models, Theoretic,Theoretical Study,Mathematical Models,Model (Theoretical),Model, Mathematical,Model, Theoretical,Models, Mathematical,Studies, Theoretical,Study, Theoretical,Theoretical Model,Theoretical Models,Theoretical Studies
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D006096	Gramicidin	A group of peptide antibiotics from BACILLUS brevis. Gramicidin C or S is a cyclic, ten-amino acid polypeptide and gramicidins A, B, D are linear. Gramicidin is one of the two principal components of TYROTHRICIN.	Gramicidin A,Gramicidin A(1),Gramicidin B,Gramicidin C,Gramicidin D,Gramicidin Dubos,Gramicidin J,Gramicidin K,Gramicidin NF,Gramicidin P,Gramicidin S,Gramicidins,Gramoderm,Linear Gramicidin,Gramicidin, Linear
D012964	Sodium	A member of the alkali group of metals. It has the atomic symbol Na, atomic number 11, and atomic weight 23.	Sodium Ion Level,Sodium-23,Ion Level, Sodium,Level, Sodium Ion,Sodium 23
D013816	Thermodynamics	A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)	Thermodynamic