Learning outcomes
Deepened knowledge on the biophysical chemistry of proteins with emphasis on
properties rather than methods. Upon completion of the course, the student shall be
able to:

Knowledge and understanding
• Describe the structures and functions of several protein families
• Describe physical properties of proteins including surface properties and
hydrodynamics
• Define the molecular driving forces that govern the, structure, folding and stability of
proteins
• Demonstrate acquaintance with the literature in the area, including classical as well as
recent papers

Skills and abilities
• Calculate accessible surface area and other properties for proteins with known
structure
• Analyse ligand binding and protein stabilitet
• Use the literature and databases to improve the scientific level of protein research
projects.

Evaluation ability and approach•
Explain protein properties and phenomena from a physicochemical perspective
• Discuss and evaluate both fundamental texts and advanced applications in the area.
• Summarize the knowledge level in classical as well as modern literature in the area.

Syllabus (pdf)

The course is set up around the following topics:

Protein sequences
- Physicochemical properties of the amino acid side chains
- Ionizable groups in side chains and backbone
- Chemical properties of the amino acid side chains (reactivity and modifications)
- Benefits and constraints imposed by the covalent chain

Protein targeting and modification
- Signal peptides, membrane anchors
- Post translational modification
- Non-canonical amino acids, glycosylation, protein splicing, intein-mediated ligation

Protein structure taxonomy
- What folds are represented in nature?
- What are the dominant folds?
- Structure and relation to Function. What folds are used for what function
- Modular proteins and protein modules

Structure of Folded proteins
- Topology
- Symmetry
- Multi-protein assemblies
- Geometry of proteins: packing, shape etc

Protein stability- Inter- and intra-molecular interactions
- Hydrogen bonding geometry, aromatic interactions, pH dependence, dielectric
properties of proteins
- The role of water, hydrophobic effect
- Thermodynamic signatures of folding
- Entropy/enthalpy compensation

Extremophiles- Thermophiles
- Halofiles
- Alkalofiles
- Can we distinguish cause form consequence?

Hydrodynamic properties
- Protein as polymers
- Protein solubility
- Radius of gyration and other measures of dimensions
- Diffusion
- Rotation
- Electrophoretic mobility of single proteins and non-covalent complexes
- Chromatographic properties of single proteins and non-covalent complexes
- Sedimentation properties of single proteins and non-covalent complexes

Protein folding and aggregation
- Folding mechanisms
- Aggregation propensity
- Aggregation mechanisms

Ligand Binding
- Equilibrium processes
- Allostery
- Cooperativity
- Rates of association and dissociation

The relation between sequence and structure
- Secondary structure propensity
- Structure prediction
- Protein design

Protein Dynamics
- Local and global fluctuations
- Time scales
- Connection to protein function

Membrane proteins
- Structural universe of membrane proteins
- Physical properties of membranes and its consequence for protein structure
- Membrane-spanning sequences
- Transporters and channels

Evolution
- Evolution of protein structure and function