Master Projects

1) Intrinsically Disordered Proteins: Function by Dynamics 

The Spaghetti Protein Project

 

Contact: Enrico Zurlo HL 821c tel. 527 5567 This email address is being protected from spambots. You need JavaScript enabled to view it.  Martina Huber HL 816a tel. 527 5560 This email address is being protected from spambots. You need JavaScript enabled to view it.

          

Recently discovered proteins use flexibility to perform essential functions, such as regulating protein production in the cell. How can such pieces of nano-spaghetti perform such specific tasks? And how flexible is flexible?

 Does the structure and conformation of the protein follow a random chain model or are there sections that possess residual structure?

 A special interest derives from the finding that these proteins also occur in neurodegenerative diseases. 

 

Master projects 2016 1

  

  The project: Compare random chain models and predict experimental observables.

 

Experiment: Measure properties of flexible proteins by electron paramagnetic resonance methods

Theory: Compare results to different model of random chains and derive flexibility parameters of the proteins

 

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 2) Nano-EPR  

 

Contact: Enrico Zurlo HL 821c tel. 527 5567 This email address is being protected from spambots. You need JavaScript enabled to view it.  Martina Huber HL 816a tel. 527 5560 This email address is being protected from spambots. You need JavaScript enabled to view it.

  

Pulses and Spins to Make the Invisible Visible –

Pulse Sequences for Nano-meter Distances in Electron Paramagnetic Resonance

The dipolar interaction of unpaired electron spins is a powerful way to determine the structure of nano-scopic systems that are too small for microscopy. Pulsed EPR is particularly useful to measure nano-meter distances and reveal the inner structure of nano-objects.

Distance distributions can be determined, showing whether the ensemble is structured or disordered. 

The project: Experiment with pulses and spins to size up proteins 

 

 Mater projects 2016 2

 

Come see us at the 8th floor of the Huygens

Experiment: Implement the sequences on existing hardware and test on model and real systems.

Theory: Use product-operator formalism to describe pulse sequences.

 

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3)  Temperature-cycle Electron Paramagnetic Resonance

taking part in an exciting new development

 

Supervisors: Gabriele Panarelli MSc, Prof. dr E.J.J. Groenen

 

A new approach to the study of paramagnetic transient species in the condensed phase is being developed: T-cycle EPR. The sample is in the microwave cavity of our unique EPR spectrometer, which operates with microwaves of 275 GHz and magnetic fields up to 13 Tesla. An infrared pulse of a diode laser, which induces a temporary temperature increase, is used to start and stop a (bio)chemical process. 


 



 

Recently, the first successful experiments have been performed and research has been started to demonstrate the applicability of T-cycle EPR in the study of reaction kinetics and the detection of short-lived reaction intermediates. An ideal moment for a master student to hop on.

 

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 

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4) Rapid freeze-quench EPR at multiple microwave frequencies

a well-defined, challenging and rewarding master project

 

Supervisors: Dr P. Gast, Prof. dr E.J.J. Groenen

 

 

A way to study the kinetics of (bio)chemical reactions is to freeze a reacting mixture at different times. This technique is called rapid freeze-quench and can be used to characterize intermediate states by spectroscopic methods. Often paramagnetic species are involved, which makes electron-paramagnetic-resonance (EPR) spectroscopy the method of choice. In our research group, we have pioneered EPR at high microwave frequencies, and successfully developed a spectrometer operating at 275 GHz in magnetic fields up to 13 Tesla and at low temperatures.

 


 


In a recent development, we have shown that EPR from 9 up to 275 GHz can be combined with the rapid freeze-quench technique, which allows the study of transients at multiple microwave frequencies. A convincing demonstration of this powerful approach for reaction times down to the millisecond range is lacking. An ideal master project, as the proof of the pudding is in the eating.

 

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 

Bachelor projects

 

    1)  What can peptides do to membranes?

 Supervisors: P. Kumar and Dr. M. Huber

 

 

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by formation of clumps of Aβ-peptides in the brain of AD patients. Aβ-peptides are natively unfolded and cause deformation of the membrane of brain cells. The possible mechanism is still not clear. 

Master 2014martina 1

Fig. 1 Left: a membrane structure called vesicle and a schematic of the protein.

Rright: change of EPR lineshape because of immobilization of protein

We want to study the interaction of the Aβ-peptide with membranes by Electron Paramagnetic Resonance (EPR). 

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Our group is always interested in accommodating physics or chemistry students who want to do their bachelor or master research project with us. If you are interested, please contact: Prof. Edgar Groenen or Dr. Martina Huber 

 

 

Courses given by EPR members

 

  • Natuurkunde voor Biologen (1st year Biology Course)
  • Quantummechica 1(2nd year Physics Course)
  • EPR in chemistry and biochemistry (Chemistry Master Course)
  • Molecular Physics (2nd year Life science and Technology students)

 

Recently discovered proteins use flexibility to perform essential functions, such as regulating protein production in the cell. How can such pieces of nano-spaghetti perform such specific tasks? And how flexible is flexible?

Does the structure and conformation of the protein follow a random chain model or are there sections that possess residual structure?

A special interest derives from the finding that these proteins also occur in neurodegenerative diseases.

 

 

 

IMGP1546

The project: Compare random chain models and predict experimental observables.

Experiment: Measure properties of flexible proteins by electron paramagnetic resonance methods

Theory: Compare results to different model of random chains and derive flexibility parameters of the proteins