Erik Lindahl

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Electrostatic strength Electrostatic interactions decay as 1/r (slow!) Example interaction energy: Two charges separated by ~1Å: 330 kcal/mol! (Compare to bond rotation, 2-4 kcal)
Semi-Empiric Modeling • Use simple interactions, but fit them to reproduce experimental properties • Compare to Ab initio: Use physics, and extrapolate 10-15 orders of magnitude • Arieh Warshel, Shneir Lifson, Michael Levitt
Page 1: Protein Physics 2012 Lecture 2, Jan
Page 6 and 7: Natural amino acids
Page 9 and 10: α R β α L
Page 11: Outline today • More on interacti
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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