Course Learning Outcomes:

The learners will be able to:
Explain the chemical and physical principles underlying protein structure, stability, flexibility, and conformational behavior.
Explain the thermodynamic and kinetic principles governing protein folding and conformational transitions.
Analyze protein structures, dynamics and binding and describe major techniques to determine them.
Interpret spectroscopic, structural, and biophysical data to characterize protein conformation, stability, and dynamics.
Explain the molecular basis of protein–ligand and protein–protein interactions, including binding energetics, cooperativity, and allostery.

Course Contents:

Chemical Properties of Proteins: Polypeptide backbone, types of amino acids, protein ionization, pKa, isoelectric point, biosynthesis of proteins, protein purification methods (affinity, size-exclusion and ion-exchange), determining molecular size and amino acid composition.

Physical Interactions and Conformational Properties in Proteins: Non-covalent interactions in proteins, conformational restrictions and flexibility, Ramachandran plot, regular conformations, secondary and tertiary structure of proteins.

Proteins in Solution and Membranes: Physical and chemical properties of soluble proteins and membrane proteins, flexibility of protein structure, Anfinsen’s hypothesis and Levinthal’s paradox, protein folding models, thermodynamics and kinetics of protein folding.

Interaction with Other Molecules: Structures of protein–ligand complexes, energetics and dynamics of binding, relationship between protein conformation and binding, allostery.

Biophysical Techniques:

Structure: Circular dichroism, X-ray crystallography, nuclear magnetic resonance (NMR), cryo-electron microscopy (cryo-EM).

Dynamics: Electrophoresis, scattering methods, optical spectroscopy (absorption and fluorescence spectroscopy), single-molecule force spectroscopy (AFM, optical tweezers and magnetic tweezers) and fluorescence spectroscopy (FRET, FCS), molecular dynamics simulations.

Thermodynamics and Kinetics: Stopped-flow techniques, isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), surface plasmon resonance (SPR), biolayer interferometry (BLI) and analytical ultracentrifugation (AUC).

References:

1. Proteins: Structures and Molecular Properties, 2nd ed. Thomas E. Creighton, W. H. Freeman and Company, New York, 1993.
2. Proteins: Structure and Function, 2nd ed. David Whitford, John Wiley & Sons, 2013.
3. Biophysical Chemistry, 2nd ed. D. Klostermeier and M. G. Rudolph, CRC Press, 2025.
4. Molecular Modelling: Principles and Applications, 2nd ed. Andrew R. Leach, Pearson Education, 2001. (For molecular dynamics simulations).