Protein folding - Trp-Cage

Trp-Cage sequence NLYIQWLKDGGPSSGRPPPS

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 40 ns for each replica
Computation time 93 hours on 4-core processor

 

Protein folding Trp-Cage line
Starting conformation - linear

Results

Folding events 7
Time to the first folding event 10 ns

 

Trp-Cage experimental (NMA) Trp-Cage experimental (pdb1L2Y NMR)

Trp-Cage protein folding after 10 ns replica-5 after 10 ns

Literature

Neidigh J.W., Fesinmeyer R.M. and Andersen N.H.
Designing a 20-residue protein.
Nat. Struct. Biol. 2002, 9, 425-430

Qiu L, Pabit S.A., Roitberg A.E. and Hagen S.J.
Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 μs.
J. Am. Chem. Soc. 2002, 124, 12952-12953
The experimental folding rate.

Simmerling C., Strockbine B. and Roitberg A.E.
All-Atom Structure Prediction and Folding Simulations of a Stable Protein.
J. Am. Chem. Soc. 2002, 124, 11258-11259
10 ns folding in modified AMBER99 force field. MD at 325 K. Solvation effects were incorporated using the Generalized Born model.

 

Conditions 2

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 12 ns for each replica
Computation time 41 hours on 4-core processor

Results

Folding events 3
Time to the first folding event 8 ns
Exchange accepted 20 %

 

back

 

 

 

 

Software for


Tutor

 

Manual