Thermal unfolding simulations of apo-calmodulin using leap-dynamics.
The simulation method leap-dynamics (LD) has been applied to protein thermal unfolding simulations to investigate domain-specific unfolding behavior. Thermal unfolding simulations of the 148-residue protein apo-calmodulin with implicit solvent were performed at temperatures 290 K, 325 K, and 360 K and compared with the corresponding molecular dynamics trajectories in terms of a number of calculated conformational parameters. The main experimental results of unfolding are reproduced in showing the lower stability of the C-domain: at 290 K, both the N- and C-domains are essentially stable; at 325 K, the C-domain unfolds, whereas the N-domain remains folded; and at 360 K, both domains unfold extensively. This behavior could not be reproduced by molecular dynamics simulations alone under the same conditions. These results show an encouraging degree of convergence between experiment and LD simulation. The simulations are able to describe the overall plasticity of the apo-calmodulin structure and to reveal details such as reversible folding/unfolding events within single helices. The results show that by using the combined application of a fast and efficient sampling routine with a detailed molecular dynamics force field, unfolding simulations of proteins at atomic resolution are within the scope of current computational power.
Kleinjung
Jens
J
Division of Mathematical Biology, National Institute for Medical Research, London, United Kingdom. jkleinj@nimr.mrc.ac.uk
Fraternali
Franca
F
Martin
Stephen R
SR
Bayley
Peter M
PM
D001059:Apoproteins / Q000737:chemistry*; D002147:Calmodulin / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D011489:Protein Denaturation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D012997:Solvents / Q000737:chemistry; D013696:Temperature
D001059:Apoproteins; D002147:Calmodulin; D012997:Solvents