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Evidence for existence of thirty hypothetical proteins in rat brain.

ABSTRACT: BACKGROUND: The rapid completion of genome sequences has created an infrastructure of biological information and provided essential information to link genes to gene products, proteins, the building blocks for cellular functions. In addition, genome/cDNA sequences make it possible to predict proteins for which there is no experimental evidence. Clues for function of hypothetical proteins are provided by sequence similarity with proteins of known function in model organisms. RESULTS: We constructed a two-dimensional protein map and searched for expression of hypothetical proteins in rat brain. Two-dimensional electrophoresis (2-DE) with subsequent in-gel digestion of spots and matrix-assisted laser desorption/ionization (MALDI) spectrometric identification were applied. In total about 3700 spots were analysed, which resulted in the identification of about 1700 polypeptides, that were the products of 190 different genes. A number of hypothetical gene products were detected (30 of 190, 15.8%) and are considered brain proteins. CONCLUSIONS: A major finding of this study is the demonstration of the existence of putative proteins that were so far only deduced from their nucleic acid structure by a protein chemical method independent of antibody availability and specificity and unambiguously identifying proteins.

SUBMITTER: Shin JH

PROVIDER: S-EPMC373456 | biostudies-literature | 2004 Jan

REPOSITORIES: biostudies-literature

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Evidence for existence of thirty hypothetical proteins in rat brain.

Shin Joo-Ho JH Yang Jae-Won JW Juranville Jean-François JF Fountoulakis Michael M Lubec Gert G

Proteome science 20040130 1

BACKGROUND: The rapid completion of genome sequences has created an infrastructure of biological information and provided essential information to link genes to gene products, proteins, the building blocks for cellular functions. In addition, genome/cDNA sequences make it possible to predict proteins for which there is no experimental evidence. Clues for function of hypothetical proteins are provided by sequence similarity with proteins of known function in model organisms. RESULTS: We construct ...[more]

PMID: 14754459

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Project description:BackgroundMonkeypox virus is a small, double-stranded DNA virus that causes a zoonotic disease called Monkeypox. The disease has spread from Central and West Africa to Europe and North America and created havoc in some countries all around the world. The complete genome of the Monkeypox virus Zaire-96-I-16 has been sequenced. The viral strain contains 191 protein-coding genes with 30 hypothetical proteins whose structure and function are still unknown. Hence, it is imperative to functionally and structurally annotate the hypothetical proteins to get a clear understanding of novel drug and vaccine targets. The purpose of the study was to characterize the 30 hypothetical proteins through the determination of physicochemical properties, subcellular characterization, function prediction, functional domain prediction, structure prediction, structure validation, structural analysis, and ligand binding sites using Bioinformatics tools.ResultsThe structural and functional analysis of 30 hypothetical proteins was carried out in this research. Out of these, 3 hypothetical functions (Q8V547, Q8V4S4, Q8V4Q4) could be assigned a structure and function confidently. Q8V547 protein in Monkeypox virus Zaire-96-I-16 is predicted as an apoptosis regulator which promotes viral replication in the infected host cell. Q8V4S4 is predicted as a nuclease responsible for viral evasion in the host. The function of Q8V4Q4 is to prevent host NF-kappa-B activation in response to pro-inflammatory cytokines like TNF alpha or interleukin 1 beta.ConclusionsOut of the 30 hypothetical proteins of Monkeypox virus Zaire-96-I-16, 3 were annotated using various bioinformatics tools. These proteins function as apoptosis regulators, nuclease, and inhibitors of NF-Kappa-B activator. The functional and structural annotation of the proteins can be used to perform a docking with potential leads to discover novel drugs and vaccines against the Monkeypox. In vivo research can be carried out to identify the complete potential of the annotated proteins.

Dataset Information

Evidence for existence of thirty hypothetical proteins in rat brain.

Publications

Evidence for existence of thirty hypothetical proteins in rat brain.

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