Lab meeting will take place on
Monday, November 2, 2020
10:00am
Presenter: James Eastwood, Ph.D. Candidate, NYU
A Graph Interpretation of the Cyclic Peptoid Conformational Energy Landscape
Cyclic peptoids are known to adopt various stable conformations, but the details of their complex energy landscape have been poorly understood. Molecular dynamics simulations of an exhaustive set of idealized possible starting conformations for various sizes of cyclic peptoids produced a limited set of populated conformations, demonstrating the limited number of local minima in the energy landscape due to the geometric constraint of cyclization. Sets of three adjacent dihedral angles (phi, psi, omega) demonstrate correlated motion over the course of simulation for macrocycles of six residues and larger. This correlated motion suggests a transition pathway between nearby minima: inversion of one amide bond and the concerted rotation of the preceding phi and psi angles to their mirror-image conformation. The energy landscape of cyclic peptoids can therefore be described as a network of conformations interconnected by individual concerted motions.
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