8.592 - HST.452J (Spring 2024)

Statistical Physics in Biology

Lecture 10

Protein Structure & Folding

1. Biomolecular Forces                                                                  
   • van der Waals interactions
   • hydrogen bonds
   • hydrophobic effect
     • Notes on hydrogen bonding and hydrophobicity
     • Article by David Chandler, Nature 437, 640 (2005) (offline)
2. Protein structure
   • secondary
   • 3D structure
3. Protein Folding Problem(s)
• Understand the physics of the folding problem (unique and reachable ground state) 
• Anfinsen Experiment
• Predict the native structure, given the sequence 
• Sequence-structure mapping and fold prediction
4. Lattice proteins
5. Random Energy Model (REM) [B. Derrida, Physics Reports 67, 29 (1980)]
6. Application of REM to protein folding
• Bryngelson and Wolynes
• Need a well defined native state competing with a continuum of competing (decoy) compact states
• Designed REM

(Slides on force from)

(Slides on Folding)

   (Mirny Lecture notes from 2013)

   (Mirny Lecture notes from 2022)

(Kardar notes on lattice models)