Schematic representation of the alanine dipeptide, along with definition of the and dihedral angles.
Schematic representation of the , hari, and selection subspaces, using TYR residue with an internal rotation axis going through atoms and , as an example. The selected atoms are shown in bold.
Acyclic isomerization paths of the alanine dipeptide in the gas phase: comparison of the line interpolation and two interpolation-free guesses. Columns 1 through 3 correspond to paths 1-2, 1-3, and 2-3, respectively. Rows are as follows: (a) projection of the paths on PES, in degrees; (b) projection of the paths in the representation (7) as described in the text , , in Å.
Flow chart for exploration of the (a) PES and (b) path reconstruction. LM, TS, and DB stand for local minima(um), transition state and database, respectively.
(Color online) Representative peptide structures: (a) the optimized native hairpin from protein G, (b) the most stable structure from sampled PES , (c) the lowest energy structure in the basin near the native structure from the shortest-link path, (d) the extended structure, and [(e) and (f)] the two minima in the topological bottleneck (see text for description). In (a) the eight native hydrogen bonds are shown with solid lines. All atoms and bonds are shown in ball and stick. The side chains of the four hydrophobic residues are also shown with van der Waals spheres.
Summary of the structural and energetic parameters for the CPR refined folding path. In (a) 1 represents the with the scale on the right axis, 2 the radius of gyration for the hydrophobic core, and 3 the RMSD to the optimized structure of the native hairpin from protein G; in (b) the solid line represents the energy profile along the path including all intermediates and transition states.
Optimization summary for gas phase cyclic paths of the alanine dipeptide. Unless otherwise specified in all entries the interaction parameter .
Optimization summary for the GBMV implicit solvent cyclic paths of the alanine dipeptide. Interaction parameter .
Optimization summary for the GBORn implicit solvent cyclic paths of the alanine dipeptide. Interaction parameter .
Optimization summary for gas phase acyclic paths of the alanine dipeptide with linear and interpolation free initial guess. The data corresponds to No. of ; ; .
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