Abstract
BackgroundTrp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns.ResultsHigh-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg) and Root Mean Square Deviation (RMSD) have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles.ConclusionThree ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE), shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.
Highlights
Trp cage is a recently-constructed fast-folding miniprotein
Molecular dynamics simulations of the Trp-cage miniprotein construct (PDB ID: 1L2Y) were carried out using the OPLS-AA force-field incorporated in the freely available program, GROMACS
It can be seen that the Root Mean Square Deviation (RMSD) of the evolving structure with reference to the starting structure increases rapidly in the first 40 ps, during which time the only structural change observed is denaturation of the 3,10 helix
Summary
Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. Recent developments in instrumentation and methodology have enabled us to take major steps forward in comprehending the dynamics of proteins and peptides at the molecular level. Protein engineering methods such as Phi-value analysis [1] and various spectroscopic techniques such as NMR have made the task more practicable. A 20-residue Trp-cage miniprotein has been designed [2]. D9 and R16 are involved in a stabilizing salt-bridge interaction
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