Download - Protein folding kinetics and more
Protein folding kinetics and more
Chi-Lun Lee (李紀倫 )
Department of Physics
National Central University
Introduction
Protein (polypeptide chain): chain of amino
acid residues
Primary structure : sequence of amino acid residues
Secondary structure : locally folded three-dimensional structure ( helix, sheet, etc.)
Tertiary structure : fully-folded compact structure
For a single domain globular protein (~100 amid acid residues), its diameter ~ 5nm and molecular mass ~ 10000 daltons (compact structure)
Features of protein folding :
• Volume exclusion and chain connectivity
• Van der Waals interactions
• Hydrogen bond
• Hydrophobic interactions
• …
Concepts from chemical reactions
Transition state theory
F
Reaction coordinate
Unfolded
Transition state
Folded
F*
Arrhenius relation : kAB ~ exp(-F*/T)
Energy surface may be rough at times…
• Traps from local minima
• Non-Arrenhius relation
• Non-exponential relaxation
• Glassy dynamics?
• Defining an order parameter
• Specifying a network
• Assigning energy distribution P(E,)
• Projecting the network on the order parameter c
ontinuous time random walk (CTRW)
Statistical Energy Landscape Theory
Generalized master equation