RESUMEN

Novel adjustments are introduced to the docking algorithm, DOCK/PIERR, for the purpose of predicting structures of transmembrane protein complexes. Incorporating knowledge about the membrane environment is shown to significantly improve docking accuracy. The extended version of DOCK/PIERR is shown to perform comparably to other leading docking packages. This membrane version of DOCK/PIERR is applied to the prediction of coiled-coil homodimer structures of the transmembrane region of the C-terminal peptide of amyloid precursor protein (C99). Results from MD simulation of the C99 homodimer in POPC bilayer and docking are compared. Docking results are found to capture key aspects of the homodimer ensemble, including the existence of three topologically distinct conformers. Furthermore, the extended version of DOCK/PIERR is successful in capturing the effects of solvation in membrane and micelle. Specifically, DOCK/PIERR reproduces essential differences in the homodimer ensembles simulated in POPC bilayer and DPC micelle, where configurational entropy and surface curvature effects bias the handedness and topology of the homodimer ensemble.

Asunto(s)

Algoritmos , Precursor de Proteína beta-Amiloide/química , Membrana Celular/química , Simulación del Acoplamiento Molecular/métodos , Precursor de Proteína beta-Amiloide/metabolismo , Membrana Celular/metabolismo , Entropía , Membrana Dobles de Lípidos , Micelas , Simulación de Dinámica Molecular , Fosfatidilcolinas/química , Multimerización de Proteína

RESUMEN

In the present paper, the authors focus on proton conduction pathways in a cubic perovskite KTaO(3) and an orthorhombic perovskite SrZrO(3). Density functional theory with a generalized gradient approximation is used to find proton binding sites. The nudged elastic band method is used to find transition states between minima. With this potential energy map of binding and transition states, adjacency matrices and their analogs identify four types of conduction paths in KTaO(3). Distortions from these paths are seen in SrZrO(3). In both cases, the lowest energy path has an intraoctahedral transfer rate-limiting barrier. A Fourier analysis of the OH stretch in ab initio molecular dynamics simulations revealed a strongly redshifted OH stretch in SrZrO(3) relative to KTaO(3). Hence, an orthorhombic system with a lowest energy conduction path limited by an intraoctahedral barrier can exhibit a redshifted OH stretch.