[toc]Protein structure determination using Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three core techniques in Structural Biology. This module will provide an in-depth introduction to the technique. No similar module is offered at this level anywhere in South Africa.
Lecturer
Dr David Pugh (Deputy Programme Co-ordinator, UWC) has a background in Applied Mathematics and Physics, and has experience of determining protein structures using nuclear magnetic resonance (NMR) spectroscopy. Dr Pugh is the leader of the Structural Biology Group at UWC. He will also co-ordinate the NMR component of the Masters Programme in Structural Biology, as well as contribute lectures on mathematical techniques and NMR spectroscopy.
Main Outcomes
The aim of this module is to introduce you to the practice and some of the theory of protein structure determination using Nuclear Magnetic Resonance Spectroscopy. By the end you should be able to:
- understand the principles of NMR spectroscopy,
- be able to use appropriate software to process and analyse spectra,
- be able to analyse one, two and three-dimensional spectra in order to assign chemical shifts and NOE’s,
- interpret NOE’s as spatial restraints between atoms
- be able to use molecular dynamics calculations to determine protein structures using NOE-derived distance restraints.
- use NMR-based methods for analyzing protein-protein interactions and the dynamical behaviour of proteins in solution
- use NMR to measure substrate binding to proteins
Main Content
- Principles of biomolecular NMR spectroscopy
- Spectral processing
- Multi-dimensional experiments
- Chemical shift assignment
- Structure determination
- NMR-based interaction studies
- Backbone dynamics
This module descriptor document also can be downloaded as an MS-Word document.
| Home Department: | Biotechnology, UWC |
| Module description (Header): | Protein NMR spectroscopy |
| Generic module name: | Structural Biology |
| Alpha-numeric code: | STB705 |
| Credit Value: | 15 Credits |
| Duration: | 6 Weeks |
| Module Type: | P |
| Level: | 8 |
| Prerequisites: | , , and |
| Co-requisites: | None |
| Prohibited combinations: | None |
| Learning time breakdown (hours): | |
| Contact with lecturer/tutor: | 60 |
| Assignments & tasks: | 40 |
| Tests & examinations: | 5 |
| Practicals: | 0 |
| Selfstudy: | 35 |
| Project: | 10 |
| Total Learning Time | 150 |
| Methods of Student Assessment: | Tutorial sheets will be handed out approximately once a week. Tutorials will count approximately equally towards a tutorial mark, which will make up 40% of the final mark for the module. A 3-hour exam will be scheduled at the end of the course. 40% Tutorials 20% Project 40% Exam |
Syllabus
- Week 1 Introduction to Biomolecular NMR
- Week 2 Spectral processing
- Fourier Transformation of a Lorentzian signal
- NMRPipe and NMRDraw
- Phasing
- Window functions
- Spectral width; the Nyquist theorem; folding
- Referencing
- Tutorial: Processing of HSQC spectrum
- Week 3 Spectral assignment
- NMRView
- Working with 3D datasets; strip plots
- Tutorial: Working with HNCO, HNCA, HN(CO)CA spectra
- Tutorial: Backbone assignment using CBCA(CO)NH
- Side-chain assignment using HCCH-TOCSY and HSQC-TOCSY
- Week 4 Structure determination
- Aria-CNS
- Molmol
- Week 1-3 1-D NMR
- acquire 1-D spectrum of protein
- vector model of NMR, coherence, T1 and T2
- data processing, window functions, sweep width, resolution
- saturation, pulsed field gradients
- software tools
- data simulations and analysis using MATLAB
- Week 4-5 2-D NMR
- coherence transfer
- COSY, TOCSY, NOESY
- assignment of spin systems
- Week 6 Heteronuclear experiments
- isotope enrichment
- 15N-separated NOESY, TOCSY
- inter-residue coherence transfer experiments, HNCA, HN(CO)CA
- Week 7-8 Structure calculations
- chemical shifts and secondary structure
- generation of spatial restraints
- calculations using CNS, Dyanna
Online Lectures
Introduction to Biomolecular NMR
References
[bibliplug category=”NMR” order_by=”last_name, year, title”]