Protein Science A (ProtSciA)

Knowledge:

• Describe and understand details of the chemical and physical properties, reactivity and experimental analysis of amino acids, both in isolation and in the context of protein structures
• Explain and describe methods for the determination of protein structures
• Describe the basic methods and principles of NMR including its applications for protein characterization
• Describe and understand basic principles in small-angle X-ray scattering
• Explain the principles of cryo-electron microscopy and X-ray crystallopgraphy and how it is applied in protein structure analysis
• Explain the principles of single-molecule FRET and optical tweezers and how it is applied in protein science
• Understand and describe intrinsically disordered proteins in terms of biophysical properties and functional advantages
• Explain mechanism of folding, and describe and apply methods for studies of protein folding and stability in vitro
• Describe and understand mechanisms for protein misfolding
• 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
• Describe and understand basic concepts in protein engineering and protein design
• Describe selected methods for high-throughput protein science

Skills:

• Integrate amino acid properties and modifications in relation to chemistry, disease and protein design
• Explain the practical matters of small angle X-ray scattering in relation to protein structure and disorder
• Evaluate data from small angle X-ray scattering
• Evaluate Guinier, Kratky plots and distribution functions
• Evaluate the relative advantages and disadvantages of crystallographic, cryo-EM and NMR approaches for protein structure analysis
• Evaluate qualities of experimental protein structures
• Evaluate data from single-molecule FRET including transfer efficiency histograms.
• 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 stability for two-state folders and understand protein folding intermediates
• Evaluate free energy landscapes and folding funnels
• Analyse phi-values in relation to transition states for protein folding
• Understand how changes in protein stability can cause disease
• Describe and evaluate methods for protein quantification
• Design purification procedures based on predefined protein properties
• Evaluate and conclude on protein purity from appropriate methods
• Analyse experimental data from protein purification protocols
• Quantitatively analyse and evaluate protein-ligand and protein-protein interactions including enzyme reactions
• Understand and differentiate between agonism, antagonism and inverse antagonism
• Evaluate principles of protein regulation, active site chemistry and binding
• Diagnose binding reactions qualitatively and quantitatively and analyse these
• Describe and understand the use of methods applied in protein-ligand interactions including ITC, surface plasmon resonance, fluorescence and NMR spectroscopy
• Use of AlphaFold and ColabFold and assessment of reliablity and outputs
• Describe simple protein structures
• Evaluate methods and theoretical approaches to address questions in relation to protein science 
• Execute protein purification and characterization experiments
• Define testable hypotheses in relation to experimental protein science
• Describe and understand the concept of hydrogen exchange in proteins
• Describe and understand interacting forces leading to higher-order protein assemblies including amyloids, fibers, condensates

Competences:

• Critically evaluate experimental results from studies of protein primary and secondary structure using protein chemistry
• Integrate and evaluate protein structure-function and disorder-function relationships
• 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 proteins purification and characterization
• Cite, evaluate and understand various heterologous protein expression systems
• Understand and differentiate between negative and positive cooperativity in binding
• Demonstrate insight into isotope labelling, sequential assignments and evaluate the quality of NMR spectra
• Critically evaluate experimental data from single-molecule techniques including smFRET and optical tweezers
• Analyze, evaluate and condense experimental data in protein science from combinations of all possible areas of curriculum to solve relevant protein science problems
• Demonstrate written- and oral communication in a protein scientific language
• Defining, attacking and presenting a scientific problem in protein chemistry (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