The aim of this module is to discuss the application of basic physical chemistry concepts for describing protein structure and dynamics and to show how advanced physical chemistry methods are used for investigating these important aspects of proteins.

By the end of the module, students should be able to

• discuss the importance of protein structure and dynamics for understanding biological processes;
• describe the experimental methods that are used to study structure, folding and fast dynamics of proteins;
• describe and discuss some of the theoretical methods that are used to predict protein structure and and model protein folding/dynamics;
• discuss the physical chemistry principles underlying these methods and apply the basic equations needed for the analysis of such data.

This lecture course deals with topics at the interface between physical chemistry and biology, which is of increasing importance as physical chemical methods and ideas are being applied to understanding biological processes. The course is split into three sections. Section A deals with protein structure determination, Section B discusses protein folding, and Section C briefly outlines the importance of fast protein dynamics.

A Protein Structure

• Protein structure classification: Primary, secondary, tertiary, quaternary
• Ramachandran plot
• Secondary structural elements: alpha-helix, beta-sheets, turns, others
• Importance of 3D structure for function
• Methods for protein structure determination: diffraction methods, NMR, CD, FTIR/Raman
• Protein data bank
• Physical chemistry background: protein crystallisation, diffraction of X-rays electrons and neutrons, 2D-NMR, dipole interactions, electronic and vibrational spectroscopies
• Methods of protein structure prediction: reference data sets, ab initio, Zimm-Bragg statistical mechanics model of helix formation

B Protein Folding

• Levinthal paradoxon
• Forces relevant for protein folding; hydrophobic interaction and its thermodynamic consequence: cold- and heat denaturation
• Basic kinetic schemes encountered in protein folding, protein folding models
• Observing the folding process - initialisation methods:
  rapid mixing, photochemical methods, temperature and pH jumps
• Observing the folding process - detection:
  Fluorescence (Förster transfer, FRET, spectral shifts), UV/vis-absorbance, CD, FTIR/Raman, NMR, H/D-exchange, EPR
• Folding kinetics analysis: Chevron plot, Phi-value analysis

C Protein Dynamics

• Examples and timescales of protein dynamics - femtoseconds to minutes
• Examples of methods for investigating fast protein dynamics: H/D-exchange and Molecular Dynamics

This module consists of 15 50-minute lectures covering theoretical aspects and experimental approaches to protein structure, folding and dynamics. The lectures will be supported by 2 tutorials, in which problem questions on the lecture material (which students will have been given in advance) will be discussed in detail, and one workshop, in which the use of a molecular visualisation program for displaying, animating and analysing protein structures is demonstrated.

Biophysics Textbook online (Biophysical Society):
http://www.biophysics.org/btol/

Mechanisms of Protein Folding (R.H. Pain, ed.), Oxford University Press, 1994