Computational study of the interaction of amolecular photoswitch with the human Nav1.4 ion channel

Palmisano, Vito Federico, VF (2020) Computational study of the interaction of amolecular photoswitch with the human Nav1.4 ion channel. Master's Thesis / Essay, Chemistry.

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Abstract

A non-invasive and orthogonal force which can induce motion is light. The ability to deliver infor-mation wrapped in form of wavelength and intensity, makes it a perfect stimulus for turning “on”and “off” molecules. At the molecular level, light can induce reversible phototransformations ofchemical species causing changes in geometry, flexibility and polarity. Those transformations canoccur with an high spatial and temporal precision, requirements needed to interact in a biologicalenvironment avoiding alteration of the biomolecular activity. Ion channels are ideal targets forphotoswitches since the transport of ions through these membrane proteins can be regulated withlight. In this computation work, the interactions of a molecular photoswitch inside a human’sbrain ion channel were identified, as well as the vertical excitation energy of the photoswitch inthe presence of an environment. An accelerated atomistic molecular dynamics method is employedto search for available binding pockets in a human’s brain voltage gated ion channel (Nav1.4) forp-diaminoazobenzene, a molecular photoswtich. An end state free energy method is used to char-acterize the binding free energy of the ligand and the pairwise decomposition energy of interactionof the ligand with surrounding residues. Three distinct binding pockets are identitifed and themajor interactions of p-diaminoazobenzene are characterized as van der Walls interactions withhydrophobic side chain aminoacids.

Item Type:	Thesis (Master's Thesis / Essay)
Supervisor name:	Faraji, S.S. and Vries, A.H. de
Degree programme:	Chemistry
Thesis type:	Master's Thesis / Essay
Language:	English
Date Deposited:	23 Jul 2020 10:05
Last Modified:	23 Jul 2020 10:05
URI:	https://fse.studenttheses.ub.rug.nl/id/eprint/22796

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