Conformational analysis of [Met5]-enkephalin: solvation and ionization considerations.
[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II' bend, G-G Type II' bend, and G-G Type I' bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by phi/psi-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 degrees C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.
Carlacci
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Department of Chemistry, University of South Florida, Tampa 33620-5250, USA.
D004734:Energy Metabolism; D004744:Enkephalin, Methionine / Q000737:chemistry* / Q000494:pharmacology; D007477:Ions; D008432:Mathematical Computing; D010449:Peptide Mapping; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012997:Solvents; D013237:Stereoisomerism; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D007477:Ions; D012997:Solvents; D004744:Enkephalin, Methionine