Fold Prediction of VP24 Protein of Ebola and Marburg Viruses using de novo Fragment Assembly
ARMY MEDICAL RESEARCH INST OF INFECTIOUS DISEASES FORT DETRICK MD
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Virus particle 24 VP24 is one of the least understood proteins of the small genomes of Ebola and Marburg virus. Recent experiments show that Ebola VP24 blocks binding of tyrosine-phosphorylated STAT-1 homodimer PY-STAT1 to the NPI-1 subfamily of importin alpha, thereby preventing nuclear accumulation of this interferon-promoting transcription factor which, in turn, reduces the immune response of the host target. Because of the lack of crystallographic structures for VP24, we applied a bioinformatics analysis and de novo protein structure prediction to classify its fold topology and better understand its biological function. Structure predictions were carried out using the fragment-based Rosetta method. Our scoring function for filtering and ranking structures consisted of a combined approach of an all-atom statistical potential and the CHARMM22 force field with a generalized Born solvent model. From 40,000 Rosetta-generated structures and selective comparisons with the SCOP database, a structural match to two of our top 10-ranking models was the Armadillo repeat fold topology, which is part of the alpha-alpha superhelix fold cluster. Specific members of the Armadillo repeat family include importin alpha, importin beta, and exportin. We predict that a large segment of the VP24 topology is not unique, but rather represents an ancestral homolog of this existing repertoire of structures. We propose that, unlike the nuclear import of host cargo, VP24 lacks a classical nuclear localization signal NLS and targets importin alpha by structural complementarity similar to that observed with the heterodimeric complex with exportin, whereby interfering with the auto-inhibitory NLS on importin alpha and blocking peripheral docking sites for PY-STAT1 assembly. In addition to the dominant helical classification of VP24, a beta sheet is predicted near the C-terminus.
- Genetic Engineering and Molecular Biology