Molecular and Genetic Medicine

Imaging of High and Low Resolution Ebola Envelope GP Structures Composited with in silico Models of Difficult-to-Resolve Sections

Abstract

Garry W Lynch, Stefanie S Portelli, Siu Wai Wong, Maria Rocha Costa, Ana Paula Mello Lemgruber, Peter Williamson, John S Sullivan, Robert Booy and Bret Church W

The Ebola surface glycoprotein, GP, facilitates receptor binding, cell infection and cytopathology, and is a principal target for immune protection. The structure of the GP central core structure and antibody target for the 1976 Ebola Zaire Mayinga strain of Ebola has been resolved by X-ray crystallography (e.g., pdb-ID: 3CSY). But other important GP regions have defied crystal structure determination. These include the apical mucin-like domain (MLD) that contains immuno-protective sites and is most distal to the membrane, and the membrane proximal C terminus region (meD) where GP is tethered to the Ebola surface. A molecular structure-based strategy in vaccine design necessitates detailed fine-structure knowledge of exposed sites for immuno-targeting. To address the lack of MLD and meD structures we have performed computational modeling of those regions using the programs iTasser, Phyre2 and CABS-flex. Candidate MLD model structures for the 1976 Mayinga strain were screened for continuity and fit with the 3CSY core and tested further for 3D compliance for its fit within the spatial boundaries of a lowresolution GP trimer cryoelectron tomograph (EMDB-ID: EMD-6003). Under these constraints only 1 of 6 initial MLD models generated by iTasser or Phyre2 met the required structural criteria of continuity, orientation and spatial fit. That best-fit structure (MLDm1p1) was additionally evaluated using the MolProbity geometric analysis, as well by the generation of highly similar and compatible structures (e.g., MLDm2c2) by the CABS-flex program. Notably, documented protective antibody sites of the MLD mapped to the MLDm1p1 apex surface, as anticipated for domain functionality or exposure to antibody attack. These studies describe best fit proximate in silico models of the MLD and meD regions of GP to for improved molecular understanding and therapy design. Biochemical and immunologic validation and refinements of the models are continuing, to establish to their biostructural compatibilities and value to inform on GP structure-function and immuno-target potential.