Density functional theory study of the dimer structure of amyloidogenic active sequence VQIVYK

Abstract

AbstractThe density functional theory calculations at the B3LYP/6‐31G(d) level were used to optimize the VQIVYK dimer complexes. In the stabilization energy calculations, the Complex 4 structure was calculated to be the most favorable structure among the Complex 1–5 geometries. The Complex 4 geometry was shown to be a more favorable geometry because of the less rigid geometry of the QIVY central part than the well‐ordered QIVY part of the Complex 1 parallel geometry. The central part of Complex 4 QIVY is optimized to the Y‐association structure of the Y5–Q2–Y5 interaction geometry. The Y5–Q2–Y5 interaction comprised two interactions, the Y5–Y5 pi–pi interaction and two cooperative H‐bonds. Both pi–pi interaction and the two cooperative H‐bonds contributed to the energy stabilization of Complex 4 geometry.