AP A5A3RA3A

1
AP A5(A3RA)3A
Ref Lednev I. K. et al. J. Am. Chem. Soc. 1999,
121, 8074-8086.

• A 21 amino acid, mainly alanine, a-helical
  peptide (AP).
• The folding/unfolding activating barriers based
  on an nanosecond UV resonance Raman study.
• 8 kcal/mol activation barrier reciprocal rate
  constant 24060 ns at 37 C (310 K).

Strand
?
Helix
2
YGA Ac-YG(AKA3)2AG-NH2
Ref Wang T. et al. Chem. Phys. Lett. 2003, 370,
842-848.

• 14-residue helical peptides (YGA).
• Time-resolved IR spectroscopy coupled with
  laser induced T-jump technique.
• Existence of an enthalpic barrier for the
  nucleation process.

Strand
Helix
3
YGG Ac-YGG(KA4)3K-NH2
Ref Werner J. H. et al. J. Phys. Chem. B 2002,
106, 487-494

• Baldwins YGG-3X series of peptides (YGG-3Ai).
• Laser-induced T-jumps to rapidly perturb the
  helix/coil equilibrium from a predominantly
  unfolded to a more folded ensemble.
• a-helix nucleation occurs on a sub-microsecond
  time-scale with a substantial enthalpic barrier.

Strand
Helix
4
Detailed simulation conditions
Ref Kubelka J. et al. Curr. Opin. Struct. Biol.
2004, 14, 76-88.
GROMOS 53A6 force field, GROMACS package version
3.2.1. The SPC water model. Initial structures
are linear coil states, surrounded by 1.0-nm
solvent wall Pressure at 1 bar using LINCS Dummy
atom approximation for side-chain H to accelerate
the simulations.
5
AP A5(A3RA)3A
Ref Lednev I. K. et al. J. Am. Chem. Soc. 1999,
121, 8074-8086.

• A 21 amino acid, mainly alanine, a-helical
  peptide (AP).
• The folding/unfolding activating barriers based
  on an nanosecond UV resonance Raman study.
• 8 kcal/mol activation barrier reciprocal rate
  constant 24060 ns at 37 C (310 K).

MD simulation start from the a-helix
structure The GROMOS 45A3 force field was adopted
6
AP A5(A3RA)3A
Secondary structure
Residue
Time (ps)
7
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