Rates of Peptide Folding

AP A 5 (A 3 RA) 3 A Ref: Lednev I. K. et al. J. Am. Chem. Soc. 1999, 121, A 21 amino acid, mainly alanine, α-helical peptide (AP). The folding/unfolding activating barriers based on an nanosecond UV resonance Raman study. ~8 kcal/mol activation barrier; reciprocal rate constant ~240±60 ns at 37 °C (310 K). Strand Helix ? Direct comparison to experiment

!00 ns simulation AP A 5 (A 3 RA) 3 A Folding ~240±60 ns at 37 °C (310 K). Force field: GROMOS 45A3 Code: GROMACS Solvent: SPC water. Box:Periodic Pressure:1atm Temp:310 K (Berendsen thermostat) Time step:4fs (H atoms replaced by dummy atoms)

N-ter C-ter 0 ns (starting structure) N-ter C-ter 10 ns N-ter C-ter 30 ns C-ter N-ter 50 ns N-ter C-ter 75 ns N-ter C-ter 70 ns N-ter C-ter 80 ns N-ter C-ter 85 ns N-ter C-ter 100 ns

Curr. Opin. Struct. Biol. 2004, 14, GB1 SES AP YGG YGA Experimental Folding rates

Helical: From native state AP 0.8 μs YGA 2.0 μs YGG 0.7 μs

Helical: From liner/coil YGG 0.7 μ s AP 0.8 μ s YGA 2.0 μ s

Hairpin: From native state GB1 6 μs SES 0.8 μs

Hairpin: From liner/coil GB1 6 μ s SES 0.8 μ s