Tag | Beckstein Lab

. . . . .
Tag Archives: rotation
Project: Simulation of transmembrane transport

Project: Simulation of transmembrane transport

A central process in maintaining life is the transport of ions or small molecules such as nutrients across the cell membrane by secondary active transporter proteins. In this project you will use molecular dynamics (MD) computer simulations to study some of the fundamental principles by which transporters act as molecular machines that transduce energy through macromolecular conformational changes. In particular, you will attempt to solve a molecular puzzle : how can a large transported molecule fit through a transporter protein that according to experimental structural data appears too narrow?

Comment [2] Continue Reading →
Project: Transport of divalent cations

Project: Transport of divalent cations

Divalent cations such as zinc or magnesium are essential for living organisms but the mechanisms by which they are transported into and out of the cell are not well understood at the molecular level. Classical molecular dynamics simulations of divalent ions are challenging because the high electric field strength near the ion leads to polarization effects that are not accurately accounted for in standard MD force fields. In this project you will explore alternative models for simulating divalent ions in order to find models that combine computational speed with sufficient accuracy to study transport of divalent ions with transporter proteins.

Comment Continue Reading →
Project: Predicting protonation states in proteins

Project: Predicting protonation states in proteins

In this rotation project you will predict known and unknown pKa values of key residues in proteins with a new method that combines molecular dynamics simulations with fast heuristic predictions. You will learn to write programs in the Python language and contribute to the open source MDAnalysis library.

Comment Continue Reading →