Titlebook: Structure and Function of Membrane Proteins; Ingeborg Schmidt-Krey,James C. Gumbart Book 2021 Springer Science+Business Media, LLC, part o

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NMR Spectroscopic Studies of Ion Channels in Lipid Bilayers: Sample Preparation Strategies Exemplifdies, respectively, as exemplified by the human voltage dependent anion channel 1 (hVDAC1). Here, we report protocols for the preparation of homogenous samples of recombinant hVDAC1 in detergent micelles and lipid two-dimensional crystals yielding high resolution NMR spectra. Procedures are describe

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Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins,. Conventional molecular dynamics simulations employ fixed protonation states, thus neglecting the coupling between protonation and conformational equilibria. Here we describe the membrane-enabled hybrid-solvent continuous constant pH molecular dynamics method for capturing atomic details of proton-

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,Molecular Dynamics–Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformatiosample functionally important conformational transitions of membrane proteins such as those involved in active membrane transport or channel activation process. Here we describe a combination of multiple MD based techniques that allows for a rigorous characterization of energetics and kinetics of la

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Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamicsain insights in understanding allosteric regulation in biomolecules. In this chapter, we introduce the basic theories and protocols used in protein dynamics network analysis through a series of interactive python Jupyter notebook scripts. While various network analysis methods exist in the literatur

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