Protein folding - Chignolin

Chignolin sequence GYDPETGTWG

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 15 ns for each replica
Computation time 22 hours on 4-core processor

 

Protein folding Chignolin line
Starting conformation - linear

Results

Folding events 6
Time to the first folding event 3.5 ns

 

Chignolin experimental (NMA) Chignolin experimental (pdb1UAO NMR)

Chignolin protein folding after 3.5 ns replica-1 after 3.5 ns

Chignolin protein folding after 4 ns replica-4 after 4 ns

Chignolin protein folding after 15 ns replica-2 after 15 ns

Literature

Honda S, Yamasaki K, Sawada Y, Morii H.
10 residue folded peptide designed by segment statistics.
Structure. 2004 Aug;12(8):1507-18

Suenaga A, Narumi T, Futatsugi N, Yanai R, Ohno Y, Okimoto N and Taiji M.
Folding Dynamics of 10-Residue β-Hairpin Peptide Chignolin.
Chem. Asian J. 2007, 2, 591-598
MD simulations in an explicit solvent. Typical time is 500 ns.

Honda S, Akiba T, Kato Y S, Sawada Y, Sekijima M, Ishimura M, Ooishi A, Watanabe H, Odahara T and Harata K.
Crystal Structure of a Ten-Amino Acid Protein.
J. Am. Chem. Soc. 2008, 130, 15327-15331
A novel protein, CLN025, was designed based on the sequence of chignolin.

 

Conditions 2

Force field AMBER-i
Water Implicit (GB)
Charge reduction factor 0.5
Method Replica exchange molecular dynamics (REMD)
Number of replicas 4
Attempt to exchange every 16 steps
Exchange attempts 32
Temperature range 273.15 - 370.00 K
Total simulated process time 135 ns for each replica
Computation time 65 hours on 4-core processor

Results

Folding events 23
Time to the first folding event 1.7 ns

 

Conditions 3

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 - 350.00 K
Total simulated process time 18 ns for each replica
Computation time 18 hours on 4-core processor

Results

Folding events 15
Time to the first folding event 1.3 ns
Exchange accepted 34 %

 

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