C12 – Protein NMR II
Key information
Next planned course: April 17-21, 2023
Registration deadline: March 17, 2023
Location: NTNU
Course responsible: Professor Finn L. Aachmann
Grading: Evaluation of lab reports (pass/fail)
Credits: 5 ECTS
Registration
Both of the steps below should be completed if you want to register and receive credits for this course:
- Register to BioCat using the form at the bottom of this page
- Contact Professor Finn Aachmann and inform him of your registration.
Admission
In order to attend this course, participants should document basic understanding of protein NMR, i.e. fulfill the learing outcome of C11 Protein NMR I, structure determination.
Tentatively for 6-8 students, with a maximum number of 10 participants.
Content
This course will provide students with sufficient basic knowledge in protein NMR to pursue dynamic applications; including relaxation measurements, kinetic tracking of enzyme-mediated substrate conversion.
The two NMR courses within BioCat have a modular organization, where the first module at UiB (C11 Protein NMR I, Structure determination) primarily concerns protein-NMR basics up to structural characterization, while the next module (C12 Protein NMR II, Functional characterization; this course) at NTNU, focuses on functional enzyme characterization, including enzyme kinetics and dynamics.
Teaching
The course will be taught intensively over five days. The students will acquire basic knowledge of functional characterization by NMR through a combination of theoretical background, lectures, practical exercises, as well as case studies from relevant literature.
Thus, the overall aim of the course is for the participants to gain hands-on experience while performing experiments. They will also learn how to set up real experiments that could then be implimented at their home institutions or other facilities.
On-site tentative schedule
Day 1:
Short icebreaker section followed by basic introduction and motivation for studing the function of proteins. Hereafter, a lecture on structural elucidation of carbohydrates. This should provide the students with basic knowledge on structural elucidation of different carbohydrates. In the afternoon, the students will have practical exercises where they will assign different carbohydrates. (Course material: Review articles and compendium)
Day 2-4:
Each day will deal with one subtopic within functional studies of proteins by NMR, where the theoretical background as well as case studies form literature will be taught in the moring section. The students will be divided into two groups and carry pratical exercises on theNMR instrument in the afternoon. (Course material: Articles, book {High-Resolution NMR Techniques in Organic Chemistry, 3rd Edition, Timothy D.W. Claridge} and compendium)
Day 5:
Introduction to time-resolved NMR and its application. Theoretical background for pseudo 2D and 3D experiments as well as their potential, limitation and pitfalls. In the afternoon, the students will set up and follow an enzymatic reaction over time by using the NMR instrument. They will learn how to extract and analyse the data form such experiments. (Course material: Articles and compendium).
| Monday | Tuesday | Wednesday | Thursday | Friday | |
|---|---|---|---|---|---|
| 09.00 – 12.00 | Introduction and motivation Carbohydrate assignment (Finn L. Aachmann) | Ligand NMR and chemical exchang (Rienhard Wimmer, Aalborg university) | Ligand NMR and pH (Finn L. Aachmann and Gaston Courtade) | Protein dynamics (Johan Isaksson, UiT) | Time-reesolved NMR (Finn L. Aachmann and Gaston Courtade) |
| 13.00 – 16.00 | Practical exercises | Set up STD, T1p, Waterlogsy | Setup Ligand and pH titrations | Set up T1, T2 and NH-NOE CEST, REX | Set up enzymatic reeaction and extract kinetic parameeteers |
The students are expected to spend 2-3 hours after class each afternoon to summarize the day and prepare for the following day.
Work requirement
According to generic ECTS guidelines, students should be prepared to dedicate 25-30 working hours pr. study point. In this course the workload is distributed into:
- 25 hours: Preparation for lectures and lab exercises (before course and on site)
- 15 hours: Lectures (on site)
- 15 hours: Laboratory exercises (on site)
- 80 hours: Finishing reports and exam preparations
Exam and evaluation
Evaluation of lab report generated from results obtained during the pratical part of the course. All lab reports should be approved within 2 months in order to pass the course.
Syllabus
Course material will be provided during the course
Learning outcome
This course aims to enable the candidate to propose a reasonable strategy for functional characterization of proteins by NMR spectroscopy. The candidates will gain hands-on experience through performing experiments as well as they will also learn the theoretical background from the lectures.
Knowledge
By the end of this course, the students will have:
- Knowledge of strategies for functional characterization of proteins by NMR spectroscopy and an understand of their strengths/limitations
- Basic knowledge on assignment strategies for small organic compounds (protein ligands).
- Familiarity with theoretical background and experimental setup for ligand interaction, pH, Chemical exchange and protein dynamics.
- Familiarity with the toolbox of programs for functional characterization of proteins
Skills
By the end of this course, the students will be able to:
- Evaluate the applicability of functional characterization of proteins by NMR spectroscopy, particularly for functional characterization of proteins
- Select the relevant experimental setup for functional characterization of proteins
- Evaluate the experimental data with programs and make graphical display
- Propose and design an experiment workflow for functional characterization of proteins
General competence
During this course, the student will gain experience in:
- Critical evaluation of literature of functional characterization of proteins by NMR spectroscopy and extraction of information from primary literature sources
- Scientific writing skills
- Experimental planning
