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Tag Archives: binding
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?

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Molecular mechanism of ligand recognition by the Mhp1 transporter

Molecular mechanism of ligand recognition by the Mhp1 transporter

The hydantoin transporter Mhp1 is a sodium?coupled secondary active transport protein of the nucleobase?cation?symport family and shares the widespread 5?helix inverted repeat transporter architecture. Our previous work showed Mhp1 functions according to the alternating access mechanism. In our new paper in EMBO J , we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site?directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands.

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Protein hydration

Protein hydration

Proteins interact with the surrounding water, and water molecules influence the binding of ligands and drugs to proteins profoundly. Coarse-grained analysis of water dynamics can be facilitated with a network model of hydration as shown here for the retinol binding protein CRBPII.

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