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Rates of Peptide Folding

Rates of Peptide Folding. AP A 5 (A 3 RA) 3 A. Ref : Lednev I. K. et al. J. Am. Chem. Soc . 1999 , 121 , 8074-8086. A 21 amino acid, mainly alanine, α -helical peptide (AP). The folding/unfolding activating barriers based on an nanosecond UV resonance Raman study.

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Rates of Peptide Folding

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  1. Rates of Peptide Folding

  2. AP A5(A3RA)3A Ref: Lednev I. K. et al. J. Am. Chem. Soc. 1999, 121, 8074-8086. • 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

  3. AP A5(A3RA)3A Folding ~240±60 ns at 37 °C (310 K). !00 ns simulation Force field: GROMOS 45A3 Code: GROMACS 3.2.1. Solvent: SPC water. Box: Periodic Pressure: 1atm Temp: 310 K (Berendsen thermostat) Time step: 4fs (H atoms replaced by dummy atoms)

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

  5. Experimental Folding rates YGA YGG AP GB1 SES Curr. Opin. Struct. Biol. 2004, 14, 76-88

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

  7. Helical: From liner/coil YGA 2.0 μs YGG 0.7 μs AP 0.8 μs

  8. Hairpin: From native state GB1 6 μs SES 0.8 μs

  9. Hairpin: From liner/coil GB1 6μs SES 0.8μs

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