Protein Research Lab - Intrinsically Disordered Proteins

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 and how this related to function
• 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 data presented in graphics

Skills:

• Evaluate the relative advantages and disadvantages of NMR, CD, and SAXS 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 CD, ITC, fluorescence, SAXS and NMR spectroscopy
• Evaluate methods and theoretical approaches to address questions in relation to research on IDPs
• Execute protein purification and characterization experiments
• Define testable hypotheses in relation to experimental protein science involving IDPs
• Perform an ensemble modeling of an IDP using computational tools.
• Integrate experimental data to reweight computationally generated proteins ensembles
• Use different digital tools to fit, model and present the data and evaluate the appropriateness of the model(s)
• Use graphical digital tools to produce figures that present scientific data in a communicative way.

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 and poster 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 personally generated scientific data and present this in front of an audience