Browsing by Author "Penny ED"

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    Beyond BLASTing: How 3D structural prediction can support or refute BLAST results
    (2015-09) Daly TK; Sutherland-Smith AJ; Penny ED
    Biologists know that not all BLAST results are homologs and that trees lose information at deep times. We have therefore developed a pipeline to bring increased confidence to the BLAST result. We use structural prediction to support or refute the inclusion of protein sequences into multiple sequence alignments. Ancestral sequence reconstruction (ASR) together with structural prediction can be used to create seed sequences to help find remote homologs. The process can be used to help with annotation.
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    In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes
    (Oxford University Press, 25/07/2013) Daly TK; Sutherland-Smith AJ; Penny ED
    Vaults are very large oligomeric ribonucleoproteins conserved among a variety of species. The rat vault 3D structure shows an ovoid oligomeric particle, consisting of 78 major vault protein monomers, each of approximately 861 amino acids. Vaults are probably the largest ribonucleoprotein structures in eukaryote cells, being approximately 70 nm in length with a diameter of 40 nm--the size of three ribosomes and with a lumen capacity of 50 million Å(3). We use both protein sequences and inferred ancestral sequences for in silico virtual resurrection of tertiary and quaternary structures to search for vaults in a wide variety of eukaryotes. We find that the vault's phylogenetic distribution is widespread in eukaryotes, but is apparently absent in some notable model organisms. Our conclusion from the distribution of vaults is that they were present in the last eukaryote common ancestor but they have apparently been lost from a number of groups including fungi, insects, and probably plants. Our approach of inferring ancestral 3D and quaternary structures is expected to be useful generally.