PhD-student: Ubiquitin-mediated protein processing at the single-molecule level, using optical tweezers and fluorescence

Date posted March 29, 2021
Type PhD positions

Protein chains undergo dramatic changes during their lifetime, beyond their initial folding. Eukaryotic cells possess an intricate ubiquitin protein ‘labelling’ system to regulate these changes. The aim of this project is to reveal the dynamics of this system at the single-molecule level for the first time. You will use advanced optical tweezers with combined single-molecule fluorescence and novel biochemical approaches to directly measure the striking hypothesized motor-like movements, complex interplay between protein chain folding, unfolding, and translocation, and to elucidate the mysterious role of the branched protein chain topology of these substrates. These experiments will provide unprecedented dynamic insights at the nanoscale level of this remarkable protein processing system.

This project has now become possible owing to recent technical advances, including the new in vitro assays of our collaborators, novel structural approaches, and optical tweezers techniques pioneered by our lab. The latter have previously shown how chaperones extend, clamp, confine, and processively pull on protein chains (Science 2007, Nature 2013, Nature 2016, Nature 2020). You will develop novel single-molecule approaches, automated data analysis methods, and help define innovative molecular biology methods, in order to enable this first dynamic view on ubiquitin-mediated protein chain processing.

Elucidating how this system works dynamically is of tremendous importance, given its central operation throughout the cell, for instance in regulating chromatin remodelers, key cell-cycle complexes, cytoskeletal organization, and more generally in maintaining the balance of protein error and repair, and is therefore also implicated in a wide spectrum of medical conditions. This project thus provides the opportunity to bridge the gap between single molecule events and crucial cellular function and malfunction.

About the group

Sandertanslab and Biophysics

Qualifications

We are looking for an outstanding experimental physicist or chemist with an interest in single-molecule techniques, programming skills to handle complex data, and a strong drive to excel in a competitive international environment. You will need to meet the requirements for an MSc-degree, to ensure eligibility for a Dutch PhD examination.

Terms of employment

The position is intended as full-time (40 hours / week, 12 months / year) appointment in the service of the Netherlands Foundation of Scientific Research Institutes (NWO-I) for the duration of four years, with a starting salary of gross € 2,441 per month and a range of employment benefits. After successful completion of the PhD research a PhD degree will be granted at Delft University of Technology. Several courses are offered, specially developed for PhD-students. AMOLF assists any new PhD-student with housing and visa applications and compensates their transport costs and furnishing expenses.

Contact info

Prof.dr. ir. Sander Tans
Group leader Biophysics
E-mail: tans@amolf.nl
Phone: +31 (0)20-754 7100

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