Molecular dynamics study of the conformational behavior of a representative elastin building block: Boc-Gly-Val-Gly-Gly-Leu-OMe.
The conformational behavior of the synthetic peptide, Boc-Gly-Val-Gly-Gly-Leu-OMe, containing the X-Gly-Gly and Gly-Gly-X (X = Val or Leu) repeating sequences and constituting a fragment of elastin was investigated by molecular mechanics and molecular dynamics (MD) simulation. The results suggest that, irrespective of the approximations used, the molecule shows a manifold of low energy conformations characterized by gamma-turns and type II beta-turns. Furthermore, MD simulations point out a conformational floppiness due to very low barriers between different conformations. Experimental CD measurements in a virtually apolar medium (dioxane--epsilon = 2.209), which better mimics the vacuum conditions of the simulation, support the theoretical results. The general emerging picture, indicating the molecule as characterized by a combination of flexibility with conformational preferences, is in agreement with previous experimental findings and enriches of new aspects the description of the microscopic behavior of this molecule suggesting more detailed interpretation of previous data.
Lelj
F
F
Dipartimento di Chimica, Universitá degli Studi della Basilicata, Potenza, Italy.
Tamburro
A M
AM
Villani
V
V
Grimaldi
P
P
Guantieri
V
V
D000595:Amino Acid Sequence; D002942:Circular Dichroism; D004146:Dioxanes; D004549:Elastin / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation
D004146:Dioxanes; D004549:Elastin