Protein folding - 2I9M

2I9M sequence SAAEAYAKRIAEAMAKG

Conditions

Force field AMBER-i
Water Implicit (GB)
Charge reduction factor 0.5
Method Replica exchange molecular dynamics (REMD)
Number of replicas 8
Attempt to exchange every 16 steps
Exchange attempts 32
Temperature range 273.15 - 370.00 K
Total simulated process time 30 ns for each replica
Computation time 67 hours on 4-core processor


Starting conformation - linear

Results

Folding events 25
Time to the first folding event 300 ps

 

2I9M experimental (NMA) 2I9M experimental (pdb2I9M NMR)

2I9M protein folding after 300 ps replica-4 after 300 ps

Literature

Duan LL, Mei Y, Zhang D, Zhang QG, Zhang JZ.
Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds.
J Am Chem Soc. 2010 Aug 18;132(32):11159-64

 

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