Structure-based functional inference of hypothetical proteins from Mycoplasma hyopneumoniae

Abstract

Enzootic pneumonia caused by Mycoplasma hyopneumoniae is a major constraint to efficient pork production throughout the world. This pathogen has a small genome with 716 coding sequences, of which 418 are homologous to proteins with known functions. However, almost 42% of the 716 coding sequences are annotated as hypothetical proteins. Alternative methodologies such as threading and comparative modeling can be used to predict structures and functions of such hypothetical proteins. Often, these alternative methods can answer questions about the properties of a model system faster than experiments. In this study, we predicted the structures of seven proteins annotated as hypothetical in M. hyopneumoniae, using the structure-based approaches mentioned above. Three proteins were predicted to be involved in metabolic processes, two proteins in transcription and two proteins where no function could be assigned. However, the modeled structures of the last two proteins suggested experimental designs to identify their functions. Our findings are important in diminishing the gap between the lack of annotation of important metabolic pathways and the great number of hypothetical proteins in the M. hyopneumoniae genome.

Fructose-bisphosphate aldolase and enolase from Echinococcus granulosus: Genes, expression patterns and protein interactions of two potential moonlighting proteins

“…Search for templates and generation of molecular models were conducted as described elsewhere (da Fonsêca et al, 2011). Templates used for EgFBA1 modeling were FBAs from Drosophila melanogaster (Hester et al, 1991) (PDB code: 1FBA), from rabbit muscle (Blom and Sygusch, 1997) (PDB code: 1ADO) and liver (PDB code: 1FDJ), and from human muscle (Dalby et al, 1999) (PDB code: 4ALD).…”

Towards New Drug Targets? Function Prediction of Putative Proteins ofNeisseria meningitidisMC58 and Their Virulence Characterization

“…For structure-based drug design and discovery, we need some of the potential drug targets (Hassan et al, 2007a;2007b;2008b;2013a;Naz et al, 2013;Thakur and Hassan, 2011;Thakur et al, 2013). Hence, HPs are also potential markers and targets for therapeutic agents in drug design and discovery (da Fonseca et al, 2012;Lubec et al, 2005;Minion et al, 2004).…”

Functional Annotation and Curation of Hypothetical Proteins Present in A Newly Emerged Serotype 1c of Shigella flexneri: Emphasis on Selecting Targets for Virulence and Vaccine Design Studies

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