Department of Chemistry

Lund University

The biophysical chemistry of proteins (NAKE 008) 15.0 ECTS

Course description

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
• Define the molecular driving forces that govern the, structure, folding and stability of
• 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
• Analyse ligand binding and protein stabilitet
• Use the literature and databases to improve the scientific level of protein research

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)

Course content

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

- 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 of protein structure and function


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