Erik Lindahl

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Amino acids & structure • All amino acids are not equal • Proline is very rare in alpha helices • Glycine is common in tight turns • Some residues common at helix ends • Differences inside/surface of proteins • What is the cause of these differences, and can it be useful?
Outline today • More on interactions, charges & electrostatics • Hydrogen bonds • The peptide group/bond properties • Boltzmann distribution • Why is it so hard to keep your kids’ rooms tidy? • Definitions of entropy, temperature, etc.
Page 1: Protein Physics 2012 Lecture 2, Jan
Page 6 and 7: Natural amino acids
Page 9: α R β α L
Page 13 and 14: Semi-Empiric Modeling • Use simpl
Page 15 and 16: Bond stretching • Vibration aroun
Page 17 and 18: Torsions/dihedrals Frequently calle
Page 19 and 20: Nonbonded interactions Packing effe
Page 21 and 22: Lennard-Jones • Simpler form than
Page 23 and 24: Hydrophobic effect
Page 25: The Boltzmann Distribution ⇢ / e
Page 28 and 29: Formulating Boltzmann • Clapeyron
Page 30 and 31: Which shape is best energy-wise? Vo
Page 32 and 33: Free Energy • Use V=exp{ln(V)}
Page 34 and 35: How many states does this correspon
Page 36 and 37: Phase Transitions Explained • Sys
Page 38 and 39: Partitioning • Consider transfer

Erik Lindahl

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