Paper Citing NAMD - Abstract
Sinicropi, Adalgisa; Bernini, Caterina; Basosi, Riccardo; Olivucci, Massimo
A novel biomimetic photochemical switch at work: design of a photomodulable peptide
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 8:1639-1649, 2009
We report the outcomes of our recent computational and experimental work for the development of a novel biomimetic molecular switch. Furthermore, we present the new results on the design and computational characterization of a "functional" cyclic peptidomimetic formed by the switch conjugated to a biologically active peptide: the RGD sequence involved in the control of cell adhesion. Structural properties of the construct are investigated in aqueous solution using molecular dynamics (MD) simulations. Analysis of MD trajectories reveals that, for each diastereoisomer of the switch (E or Z), different conformations are stabilized. Electrostatic and spectroscopic properties of such conformers are evaluated by means of ab initio multiconfiguration quantum chemical method implemented in a quantum-mechanical/molecular-mechanic (CASPT2//CASSCF/6-31G*/AMBER) scheme.
