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Enzyme dynamics: NMR spectroscopy and kinetics (EDNMR)

Vak
2020-2021

Admission requirements

Core course in MSc Chemistry - Chemical Biology, core course in MSc Life Science and Technology (Biophysical Sciences series), elective course.
For students with a BSc MST, LST or equivalent. Good understanding of protein structure (primary – quaternary structure, amino acids), basics of Michaelis Menten kinetics, concept of Boltzmann equilibrium is needed.

Description

Proteins carry out most functions in the cell. These molecules are not rigid, but are mobile on a wide range of timescales. The course aims to convey the concept of protein dynamics in relation to biological function. The focus is on enzyme catalysis and two techniques will be discussed in detail: nuclear magnetic resonance (NMR) spectroscopy to study protein mobility and kinetic measurements to characterise enzyme activity. NMR spectroscopy is a versatile analytical technique with many applications. We will discuss the fundamentals of NMR (chemical shift, dipolar coupling, J-coupling, relaxation), as well as multidimensional NMR and relaxation experiments to characterize molecular mobility on nanosecond and millisecond timescale. It provides a basis in NMR spectroscopy that is of use for any chemist. The study of kinetics will comprise steady state and pre-steady state theory and methods to measure enzyme characteristics such as k(cat) and K(M), as well as inhibitor kinetics. The theory will be placed into context by studying several papers from the literature.

Course objectives

Learning goals:

  • the student understands the fundamentals of NMR spectroscopy and can explain the concepts of chemical shift, dipolar coupling, J-coupling, relaxation and chemical exchange

  • the student understands how NMR spectroscopy can be used to study protein dynamics on different timescales and can critically discuss possibilities and limitations

  • the student understands and can apply the theory of steady state and pre-steady state kinetics for the characterisation of enzyme-catalysed reactions in calculations and simulations

  • the student can explain how kinetic experiments are performed and analysed, both for steady state and stopped-flow measurements

  • the student understands the concept of dynamics in enzymology and can apply this knowledge to explain results described in the literature as well as to address questions concerning new systems

Timetable

Schedule information can be found on the website of the programmes. Assignment deadlines are communicated via Brightspace.

Mode of instruction

Lectures, exercises, discussions and simulations. We will work with a flipped class-room approach for some aspects of the course. If necessary, the course can be given in online modus, using narrated Powerpoint slides or recorded lectures, computer tutorials and discussion in online classrooms and breakout rooms.

Assessment method

Exercises and an on-line test need to be completed and handed in to be allowed to participate in the written exam at the end of the course.
Written exam (closed book) with admission requirement.
If an exam on campus is not possible, the exam will be an online, open book version.

Reading list

Required book: Peter Hore, Nuclear Magnetic Resonance, Second Edition, ISBN: 9780198703419, Oxford Chemistry Primers.
Links to the relevant literature articles will be published on Brightspace.

Registration

Register for this course via uSis

Contact

Prof. Dr. M. Ubbink

Remarks

According to OER article 4.8, students are entitled to view their marked examination for a period of 30 days following the publication of the results of a written examination. Students should contact the lecturer to make an appointment for such an inspection session.