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Inferring functional units in ion channel pores via relative entropy

Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay (2021):
Inferring functional units in ion channel pores via relative entropy.
In: European biophysics journal : EBJ, ISSN 1432-1017,
DOI: 10.1007/s00249-020-01480-7,
[Article]

Abstract

Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.

Item Type: Article
Erschienen: 2021
Creators: Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay
Title: Inferring functional units in ion channel pores via relative entropy
Language: English
Abstract:

Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.

Journal or Publication Title: European biophysics journal : EBJ
Divisions: 10 Department of Biology
10 Department of Biology > Plant Membrane Biophysics
10 Department of Biology > Computational Biology and Simulation
Date Deposited: 09 Feb 2021 06:33
DOI: 10.1007/s00249-020-01480-7
Identification Number: pmid:33523249
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