Protein Research Lab

Course content

This is a research-integrating experimental laboratory course. It is based on a seven weeks teaching period with 3 x 8 hours/week of student directed research on intrinsically disordered proteins (IDPs) including protein expression and purification, followed by experimentally addressing a self-defined testable hypothesis through biophysical studies.

The course totals 80 hours of obligatory laboratory work and introductory part on IDPs and 2 weeks of presentations (planning and execution).

The two weeks at the end of the course are reserved for oral presentations of scientific data through a scientific poster session in which suggestions for further research are presented. The students will additionally communicate their research, focusing on a non-specialized audience, via either a web-doc or a podcast presentation to which introductions are given. 

Experimental part
The course focuses exclusively on intrinsically disordered proteins (IDPs), and integrates ongoing IDP research with teaching. It follows the concept of student-directed research. The student can choose between different IDPs, either with an academic interest or with an industrial partner, and will define a project based on a hypothesis, that includes recombinant expression of the chosen proteins, design of purification strategies, purification and characterization. Methods include fractionation methods, electrophoresis, chromatography (size exclusion, affinity, heparin columns, ion exchange, reversed phase, protease-driven tag-release etc.), Western blot (antibody based) analysis, pull-down and immune precipitation assays, peptide mass finger printing, protein crystallization with partners, applied bioinformatics, chemical modification, and mass spectrometry. It also includes CD-, fluorescence-, and NMR-spectroscopy, isothermal titration calorimetry, small-angle X-ray scattering, molecular graphics and modelling, ligand binding, pKa determination and dataprocessing and presentation. The laboratory course of 80 hours is distributed over seven weeks and students work in research teams of 3-4 student researchers. An inspirational lecture from an international expert in the IDP field as well as an introduction to entrepreneurship and innovation are included. Given the nature of research-integrating teaching, risk assessment and data-based experimental re-design are included aspects.

At the end of the laboratory course, each group presents its data by an oral presentation with discussion and at a scientific poster session of 3 hours where they present their own poster, which will include suggestions for further research. A scientific board consisting of external evaluators will discuss the poster. Additionally, each group produces either a web-doc or a podcast on their findings where the international expert is available for interviews.

Education

MSc Programme in Biochemistry

Learning outcome

Knowledge:

  • Understand and describe IDPs in terms of biophysical properties and  functional advantages
  • Describe and understand details of the chemical and physical properties of IDPs, and how this can be exploited for their isolation
  • Describe how NMR, SAXS and CD can be used to characterize IDPs
  • Explain mechanism of folding-upon-binding, and describe and apply methods for studies of IDPs
  • Describe physical forces in terms of energy, range and dependence on geometry, environments and  other parameters of importance
  • Describe and understand the principle of SDS-PAGE including the stacking effect
  • Describe and understand basic chromatographic theory
  • Describe thermodynamically the underlying physical chemistry in protein interactions and calculate thermodynamic parameters from selected graphical presentations
  • Participate in a seminar on latest topics in IDPs
  • Knowledge on entrepreneurship and innovation


Skills:

  • Evaluate the relative advantages and disadvantages of NMR, CD, SAXS and ITC approaches for IDP analysis
  • Demonstrate a thorough understanding of a selection of modern protein biophysical, spectroscopic and chemical experimental and analytical methods and assessment of when to use which method for solving a specific problem
  • Understand and evaluate thermodynamics of protein folding and interactions involving IDPs
  • Describe and evaluate methods for protein quantification
  • Design purification procedures based on predefined protein properties
  • Evaluate and conclude on protein purity from appropriate methods
  • Analyze experimental data from protein purification protocols
  • Quantitatively analyze and evaluate IDP interactions
  • Describe and understand the use of methods applied in IDP interactions including ITC, surface plasmon resonance, fluorescence, SAXS and NMR spectroscopy
  • Evaluate methods and theoretical approaches to address questions in relation to this research topic
  • Execute protein purification and characterization experiments
  • Define testable hypotheses in relation to experimental protein science involving IDPs


Competences:

  • Critically evaluate experimental results from studies of protein primary and secondary structure using protein chemistry
  • Differentiate between physical forces in terms of energy, range and dependence on geometry, environments and other parameters of importance
  • Critically evaluate advantages and disadvantages of different procedures used for purification and characterization of IDPs
  • Cite, evaluate and understand various heterologous protein expression systems including various tags
  • Critically evaluate experimental biophysical results
  • Critically evaluate experimental data on ensembles
  • Analyze, evaluate and condense experimental data in protein science from combinations of all possible areas of the curriculum to solve relevant research questions in relation to IDPs
  • Demonstrate written- and oral communication in a protein scientific language
  • Define, attack and present a scientific problem regarding IDPs (oral presentation)
  • Communicate verbally in a scientific language and present published scientific results in power points in a clear and informative way
  • Design strategies to test scientific hypotheses experimentally
  • Design, execute, critically evaluate, and present experiments in protein chemistry
  • Design a scientific poster of the students own scientific results and present this in front of an audience
  • Design and deliver either a podcast or a web-doc of own results

An 80 hours obligatory lab-course disseminated over 7 weeks. A total of 14 hours of obligatory oral presentations and scientific discussions.

See Absalon

It is recommended that the student has passed a basic course in protein science such as Protein Videnskab og Enzymology (PVEt) (Biochemistry), Protein structure and function (Chemistry), Protein Chemistry and Enzymology I and II (Molecular Biomedicine), Protein Chemistry and Enzymology for Biologists (Biology) or Bio-structural chemistry (Pharmaceutical sciences).

As the course require some knowledge on protein chemistry, we do not recommend that the student has passed only a basic biochemistry course. A prior course in protein science/​biophysics/​physical chemistry is highly recommended.

Students who have passed all first-year courses and half of the second year courses (corresponding to a total of 90 ECTS) of their curriculum would have obtained competencies that would enable them to follow the course, including the recommendations for basic courses listed above.

Academic qualifications equivalent to a BSc degree is recommended.

If you have passed or followed Protein Science A, you are not eligible for attending this course.

Oral
Individual
Collective

Oral feedback both individually and in groups on oral presentations and written presentations in the form of a scientific poster presenting the results of the laboratory work.

ECTS
7,5 ECTS
Type of assessment
Continuous assessment
80% attendance in laboratory exercises.
In the end of the course you have to make an oral presentation of your results in a powerpoint and a written presentation in the form of a poster. The poster must also be orally presented individually in front of an internal censor and if relevant, the industrial partner. Deliver either a podcast or a web-doc of the obtained results.
Aid
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
Several internal examiners.
Criteria for exam assessment

See Learning Outcome.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 10
  • Preparation
  • 80
  • Practical exercises
  • 80
  • Project work
  • 36
  • Exam
  • 0
  • English
  • 206