Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context.
Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins (proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here.
Fiona Brinkman is a Professor in Bioinformatics and Genomics in the Department of Molecular Biology and Biochemistry at Simon Fraser University in British Columbia, Canada, and is a leader in the area of microbial bioinformatics. She is interested in developing "more sustainable, holistic approaches for infectious disease control and conservation of microbiomes".
The Database of Interacting Proteins (DIP) is a biological database which catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein–protein interactions. The data stored within DIP have been curated, both manually, by expert curators, and automatically, using computational approaches that utilize the knowledge about the protein–protein interaction networks extracted from the most reliable, core subset of the DIP data. The database was initially released in 2002. As of 2014, DIP is curated by the research group of David Eisenberg at UCLA.
InaD-like protein is a protein that in humans is encoded by the PATJ gene.
SCO2 cytochrome c oxidase assembly is a protein that in humans is encoded by the SCO2 gene. The encoded protein is one of the cytochrome c oxidase (COX)(Complex IV) assembly factors. Human COX is a multimeric protein complex that requires several assembly factors. Cytochrome c oxidase (COX) catalyzes the transfer of electrons from cytochrome c to molecular oxygen, which helps to maintain the proton gradient across the inner mitochondrial membrane that is necessary for aerobic ATP production. The encoded protein is a metallochaperone that is involved in the biogenesis of cytochrome c oxidase subunit II. Mutations in this gene are associated with fatal infantile encephalocardiomyopathy and myopia 6.
Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1, also known as UQCRFS1, Rieske iron-sulfur (Fe-S) protein, Cytochrome b-c1 complex subunit 5, or Complex III subunit 5 is a protein which in humans is encoded by the UQCRFS1 gene. UQCRFS1 is a subunit of the respiratory chain protein Ubiquinol Cytochrome c Reductase, which consists of the products of one mitochondrially encoded gene, MTCYTB and ten nuclear genes UQCRC1, UQCRC2, Cytochrome C1, UQCRFS1, UQCRB,UQCRQ, UQCRH, UCRC, and UQCR.
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification.
The PRIDE is a public data repository of mass spectrometry (MS) based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team.
MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides. MatrixDB takes into account the multimeric nature of the extracellular proteins. The database was initially released in 2009 and is maintained by the research group of Sylvie Ricard-Blum at UMR5246, Claude Bernard University Lyon 1.
The Death Domain database is a secondary database of protein-protein interactions (PPI) of the death domain superfamily. Members of this superfamily are key players in apoptosis, inflammation, necrosis, and immune cell signaling pathways. Negative death domain superfamily-mediated signaling events result in various human diseases which include, cancers, neurodegenerative diseases, and immunological disorders. Creating death domain databases are of particular interest to researchers in the biomedical field as it enables a further understanding of the molecular mechanisms involved in death domain interactions while also providing easy access to tools such as an interaction map that illustrates the protein-protein interaction network and information. There is currently only one database that exclusively looks at death domains but there are other databases and resources that have information on this superfamily. According to PubMed, this database has been cited by seven peer-reviewed articles to date because of its extensive and specific information on the death domains and their PPI summaries.
Dehydrogenase/reductase member 7B is an enzyme encoded by the DHRS7B gene in humans, found on chromosome 17p11.2. DHRS7B encodes a protein that is predicted to function in steroid hormone regulation. A deletion in the chromosomal region 17p11.2 has been associated with Smith-Magenis Syndrome, a genetic developmental disorder.
The PageRank algorithm has several applications in biochemistry.
Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center. and of Spanish National Bioinformatics Institute (INB-ISCIII). From 2015-2018, he was President of the International Society for Computational Biology. His research is focused on the study of biomedical systems with computational biology and bioinformatics approaches.
Succinate dehydrogenase complex assembly factor 2, formerly known as SDH5 and also known as SDH assembly factor 2 or SDHAF2 is a protein that in humans is encoded by the SDHAF2 gene. This gene encodes a mitochondrial protein needed for the flavination of a succinate dehydrogenase complex subunit required for activity of the complex. Mutations in this gene are associated with pheochromocytoma and paraganglioma.
SHLD1 or shieldin complex subunit 1 is a gene on chromosome 20. The C20orf196 gene encodes an mRNA that is 1,763 base pairs long, and a protein that is 205 amino acids long.
Cytochrome c oxidase assembly factor 5 is a protein that in humans is encoded by the COA5 gene. This gene encodes an ortholog of yeast Pet191, which in yeast is a subunit of a large oligomeric complex associated with the mitochondrial inner membrane, and required for the assembly of the cytochrome c oxidase complex. Mutations in this gene are associated with mitochondrial complex IV deficiency.
Chromosome 1 open reading frame 198 (C1orf198) is a protein that in humans is encoded by the C1orf198 gene. This particular gene does not have any paralogs in Homo sapiens, but many orthologs have been found throughout the Eukarya domain. C1orf198 has high levels of expression in all tissues throughout the human body, but is most highly expressed in lung, brain, and spinal cord tissues. Its function is most likely involved in lung development and hypoxia-associated events in the mitochondria, which are major consumers of oxygen in cells and are severely affected by decreases in available cellular oxygen.
Transmembrane protein 179 is a protein that in humans is encoded by the TMEM179 gene. The function of transmembrane protein 179 is not yet well understood, but it is believed to have a function in the nervous system.
