C11 – Protein NMR I

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Key information

Next planned course: March 6-10, 2023
Registration deadline: February 24, 2023
Location: Partially on-site at UiB, partially digital
Course responsible: Professor Øyvind Halskau

Grading: Evaluation of lab reports (pass/fail)
Credits: 5 ECTS
Hotel Stay: If you are traveling to Bergen for this course, please book your hotel at Citybox Bergen City

Registration

Students must register in two steps:

  • First register toBioCat using the form at the bottom of the page, then:

Content

This course will provide students with sufficient knowledge in protein NMR to pursue structural characterization.

The two NMR courses within BioCat have a modular organization:

  • The first module is this course, C11; Protein NMR I, and is organized by UiB. It primarily concerns protein-NMR basics up to structure determination
  • The second module is C12: Protein NMR II, and is organized by NTNU. It focuses on functional enzyme characterization, including enzyme kinetics and dynamics.

Admission

Tentatively for 6-8 students, with a maximum number of 10 participants

Teaching

The course will be taught partially on-site at UiB and partially digitally over five intensive days. The students will acquire basic knowledge of structure determination and characterization by NMR through theoretical background, lectures and practical exercises.

The course’s overall aim is for the participants to set up and pursue a protein-NMR project. To this end, they will gain hands-on experience with data-acquisition, data-handling and data-analysis using the specialized software (TopSpin, CARA, CCPN). The first three days will cover lectures, practical demonstrations at the instrument and data analysis exercises using CARA program. It will cover sequence-specific assignment (Day 1 and Day 2), side-chain and NOE assignment (Day 3). The knowledge of the CARA program will be useful for the participants of the C12 course that will be held in April.

The remaining two days of C11 will contain an introduction to sequence-specific assignment and structural calculations using CCPN, a more advanced and current software package for biomolecular NMR analysis covering both assignment and structure calculations. CCPN-developing team member Dr. Vicky Higman will help to hold this part of the course.

Updated digital schedule

Day 1:

A short introduction of students/lecturers will be followed by a lecture on the fundamentals of NMR, the motivation for learning biomolecular NMR, and structural characterization using NMR. Hereafter, a lecture on fundamental building blocks of protein NMR spectroscopy will be held. This should provide the students with basic knowledge on what the most common NMR experiments employed in protein NMR do, and how they fit into each other. In the afternoon, the practical part will start. Before the end of the day, the students will have a demonstration at the instrument to show how to set up example experiments.

Day 2:

We begin the day by demonstrating data processing on the acquired overnight spectra and continuing with the sequence-specific backbone assignment (in CARA) throughout the day.

Day 3:

We move on to side-chain and NOE assignment (in CARA). This practical will then form the basis for introducing the theory of calculating protein structures. The proceeding steps for performing structure calculations will be presented and discussed.

Day 4:

Introduction to CCPN – setting up projects and getting started. Then, a sequence-specific assignment (in CCPN) as a practical exercise throughout the day.

Day 5:

Structure calculations (in CCPN) throughout the day. Concluding remarks.

Day 1Day 2Day 3Day 4Day 5
09.00 – 12.00Welcome word (OD). Introduction and fundamental biomolecular NMR (lecture, NÅF). Biomolecular NMR (lecture, OD).Data processing. NUS (JU) Sequence-specific assignment, backbone (OD)Sidechain and NOE assignments (OD)Installation of CCPN, setting up, getting started on assignment (OD, VH)CCPN
Structure calculation (OD, VH)
13.00 – 16.00Computer lab:
Set up CARA project, start assignment (OD)

Lab:
Acquisition of data overnight – HSQC, HNCA/HNCO /JU)		Computer lab:
Sequence-specific assignment, backbone (OD)		Sidechain and NOE assignments (OD)AssignmentStructure calculation
NÅF = Nils Åge Frøystein, OD = Olena Dobrovolska, JU = Jarl Underhaug, VH = Vicky Higman

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:

  • 35 hours: Preparation for lectures and lab exercises (before course and on site)
  • 15 hours: Lectures (on site)
  • 30 hours: Laboratory exercises (on site)
  • 15 hours: Self-study after each day on site
  • 35 hours: Post-course study, writing report

Exam and evaluation

Evaluation of lab report generated from results obtained during the practical part of the course (pass/not pass). All lab reports should be approved within 2 months in order to pass the course. 

Materials required

  • Pocket Guide to Biomol NMR, by Duckett (40 pages)
  • Manuals and theoretical cheat-sheets (30 pages)
  • Specialized work instructions for all days of practical work (40 pages)
  • Experimental articles and review articles (30 pages)
  • Lecture handouts (120-150 slides, 40-50 pages with 3 slides each)

Learning outcome

Knowledge

The student will gain:

  • some knowledge of the technological basis of an NMR instrument.
  • specialized knowledge regarding the theoretical basis of NMR as it applies to proteins.
  • specific knowledge of data acquisition requirements and processing for a biomolecular NMR project.
  • detailed and specialized knowledge on setting up and pursuing a protein-NMR project.
  • knowledge of which triple-resonance experiments are required to complete a sequence-specific assignment and side-chain protein assignments

Skills

The student will be able to:

  • use the software necessary for acquiring and processing NMR data
  • acquire simple and standardized triple-resonance NMR experiments
  • set up a CARA project for assignment
  • prepare chemical shift perturbation analyses and TALOS N outputs based on NMR data
  • pursue a CARA project and from it generate a set of files usable as input into a structural refinement
  • Set up CCPN project for assignment and structure calculations
  • use NMR-related databanks and tools for structural assessment, including the BMRB and PDB

General competence

The student will be able to:

  • understand the potential and difficulties of NMR as applied to proteins and other biomolecules
  • plan a project and pursue it from basic to detailed protein structure characterization in an independent manner
  • pursue more advance applications, such as structural refinement, under supervision or with more training

Registration