BioPlex

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The interaction network of MED1, one of the subunit of the Mediator complex. BioPlexMed1c.jpg
The interaction network of MED1, one of the subunit of the Mediator complex.

BioPlex (biophysical interactions of ORFeome-based complexes) is an open access resource for studying protein-protein interactions. [1] [2] [3] It is the result of collaborations between Harvard Medical School and Biogen. BioPlex 1.0 reported 23,744 interactions among 7,668 proteins. [4] BioPlex 2.0 extended those observations to detect over 29,000 new interactions. [5]

Contents

The basic technology is to express a "bait" protein in human cells. Those bait proteins interact with other proteins, and then the complexes of the bait and "prey" proteins are isolated by affinity purification. The interacting prey proteins are identified using mass spectrometry.

Use in research

Determining the interaction partners of poorly characterized proteins can provide clues to the function of those proteins, and knowing which "protein community" a disease gene resides in can give better context for its action. [5]

See also

Related Research Articles

TLE3

Transducin-like enhancer protein 3 is a protein that in humans is encoded by the TLE3 gene.

AKAP11

A-kinase anchor protein 11 is an enzyme that in humans is encoded by the AKAP11 gene.

TMTC4

Transmembrane and Tetratricopeptide repeat containing 4 is a protein that in humans is encoded by the TMTC4 gene. This protein crosses the plasma membrane 10 times, and resides in the ER lumen and cytosol. The predicted structure of the TMTC4 protein is a series of alpha-helices.

L2HGDH

L-2-hydroxyglutarate dehydrogenase, mitochondrial is an enzyme that in humans is encoded by the L2HGDH gene, also known as C14orf160, on chromosome 14.

C14orf80

Uncharacterized protein C14orf80 is a protein which in humans is encoded by the chromosome 14 open reading frame 80, C14orf80, gene.

The human interactome is the set of protein–protein interactions that occur in human cells. The sequencing of reference genomes, in particular the Human Genome Project, has revolutionized human genetics, molecular biology, and clinical medicine. Genome-wide association study results have led to the association of genes with most Mendelian disorders, and over 140 000 germline mutations have been associated with at least one genetic disease. However, it became apparent that inherent to these studies is an emphasis on clinical outcome rather than a comprehensive understanding of human disease; indeed to date the most significant contributions of GWAS have been restricted to the “low-hanging fruit” of direct single mutation disorders, prompting a systems biology approach to genomic analysis. The connection between genotype and phenotype remain elusive, especially in the context of multigenic complex traits and cancer. To assign functional context to genotypic changes, much of recent research efforts have been devoted to the mapping of the networks formed by interactions of cellular and genetic components in humans, as well as how these networks are altered by genetic and somatic disease.

A FFAT motif is a protein sequence motif of six defined amino acids plus neighbouring residues that binds to proteins in the VAP protein family.

Chromosome 8 open reading frame 82 is a protein encoded in humans by the C8orf82 gene.


Leukocyte Receptor Cluster Member 9 is an uncharacterized protein encoded by the LENG9 gene. In humans, LENG9 is predicted to play a role in fertility and reproductive disorders associated with female endometrium structures.

RTL6

Retrotransposon Gag Like 6 is a protein encoded by the RTL6 gene in humans. RTL6 is a member of the Mart family of genes, which are related to Sushi-like retrotransposons and were derived from fish and amphibians. The RTL6 protein is localized to the nucleus and has a predicted leucine zipper motif that is known to bind nucleic acids in similar proteins, such as LDOC1.

C12orf66 is a protein that in humans is encoded by the C12orf66 gene. The C12orf66 protein is one of four proteins in the KICSTOR protein complex which negatively regulates mechanistic target of rapamycin complex 1 (mTORC1) signaling.

The Family with sequence similarity 149 member B1 is an uncharacterized protein encoded by the human FAM149B1 gene, with one alias KIAA0974. The protein resides in the nucleus of the cell. The predicted secondary structure of the gene contains multiple alpha-helices, with a few beta-sheet structures. The gene is conserved in mammals, birds, reptiles, fish, and some invertebrates. The protein encoded by this gene contains a DUF3719 protein domain, which is conserved across its orthologues. The protein is expressed at slightly below average levels in most human tissue types, with high expression in brain, kidney, and testes tissues, while showing relatively low expression levels in pancreas tissues.

LCHN is a protein that in humans is encoded by the KIAA1147 gene located on chromosome 7. It is likely part of the tripartite DENN domain family of proteins that often function as Rab-GEFs to regulate vesicular trafficking. Both the mRNA and protein have been shown to be upregulated following ischemic stroke, and to be produced at altered levels in patients with FTD-ALS, however the gene's contribution to these states is not well understood.

RESF1

Retroelement silencing factor 1 is a protein that in humans is encoded by the RESF1 gene. RESF1 is broadly expressed in the lymph nodes, ovaries, appendix and spleen. RESF1 shows characteristics of being a minor histocompatibility antigen, as well as tumor suppressor capabilities. The high expression in the lymph nodes and spleen indicate function in the immune system.

Ccdc60

Coiled-coil domain containing 60 is a protein that in humans is encoded by the CCDC60 gene that is most highly expressed in the trachea, salivary glands, bladder, cervix, and epididymis.

C22orf31

C22orf31 is a protein which in humans is encoded by the C22orf31 gene. The C22orf31 mRNA transcript has an upstream in-frame stop codon, while the protein has a domain of unknown function (DUF4662) spanning the majority of the protein-coding region. The protein has orthologs with high percent similarity in mammals. The most distant orthologs are found in species of bony fish, but C22orf31 is not found in any species of birds or amphibians.

TMED5 Protein-coding gene in the species Homo sapiens

Transmembrane emp24 domain-containing protein 5 is a protein that in humans is encoded by the TMED5 gene.

SAAL1

Serum amyloid A-like 1 is a protein in humans encoded by the SAAL1 gene.

C5orf24

C5orf24 is a protein encoded by the C5orf24 gene (5q31.1) in humans. C5orf24 is primarily localized to the nucleus and is highly conserved with orthologs in mammals, birds, reptiles, amphibians, and fish.

UPF0602 Human gene

UPF0602 is a protein in humans that is encoded by the chromosome 4 open reading frame 47 (c4orf47) gene.

References

  1. anon. "BioPlex". harvard.edu. harvard.edu. Retrieved 24 May 2017.
  2. anon (2015-07-18). "Facebook for the Proteome". technology.org. technology.org. Retrieved 24 May 2017.
  3. anon. "New study maps protein interactions for a quarter of the human genome". phys.org/. phys.org. Retrieved 24 May 2017.
  4. Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP (2015). "The BioPlex Network: A Systematic Exploration of the Human Interactome". Cell. 162 (2): 425–40. doi:10.1016/j.cell.2015.06.043. PMC   4617211 . PMID   26186194.
  5. 1 2 Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW (2017). "Architecture of the human interactome defines protein communities and disease networks". Nature. 545 (7655): 505–509. Bibcode:2017Natur.545..505H. doi:10.1038/nature22366. PMC   5531611 . PMID   28514442.