Tag | Beckstein Lab

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Tag Archives: protein
Bidstrup Foundation Undergraduate Fellowship for Kacey Clark

Bidstrup Foundation Undergraduate Fellowship for Kacey Clark

Physics freshwoman undergraduate student Kacey Clark was selected as a Bidstrup Undergraduate Fellow for the 2016-2017 academic year. The Bidstrup Fellowship is awarded by Barrett, The Honors College at Arizona State University where Kacey is a student.

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Bedabrata Choudhury

Bedabrata Choudhury

In Fall 2014, Bedabrata started a rotation project on the molecular mechanism of temperature sensing. The goal of this project is to study the heat-sensitive TRPV1 ion channel with molecular dynamics (MD) simulations and identify regions or conformations of the protein that are sensitive to temperature changes. The work will be carried out in collaboration with the experimental lab of Dr van Horn in the Department of Chemistry and Biochemistry.

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Tutorial: MDAnalysis

Tutorial: MDAnalysis

A short introductory tutorial on MDAnalysis

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Tutorial: Simulating AdK with Gromacs

Tutorial: Simulating AdK with Gromacs

A tutorial that teaches you to perform and analyze a molecular dynamics simulation of the the enzyme adenylate kinase (AdK) with the Gromacs simulation package.

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David Dotson

David Dotson

David worked as a research software engineer in the lab. He left in June 2017 for industry.

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Atomically detailed molecular dynamics simulations

Atomically detailed molecular dynamics simulations

Using molecular dynamics (MD) computer simulations we can study membrane proteins in atomic detail, down to the movements of individual water molecules. For example, the Mhp1 transporter protein shown here switches between three different functional states: A: outward facing; B: occluded; C: inward facing — as predicted byt the alternating access model.

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Ion channels

Ion channels

Ion channels are membrane proteins that play major roles in fast signal conduction in nerve cells and the brain. They consist of a water filled pore through which ions can flow. An external signal, such as a change in membrane potential or the binding of a neurotransmitter, can switch the pore from “open” to “closed”, a process termed gating.

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Transporters

Transporters

Transporter proteins are used by cells to “pump” molecules or ions into or out of the cell. They are present in all cells (digestive system, nervous system, blood, …) with important roles in metabolism. Secondary active transporters move their substrates against a electrochemical potential gradient and therefore couple uptake/excretion to an energetically favourable flow of sodium ions or protons into the cell.

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