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The proteome is the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time. More specifically, it is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics
Proteomics
is the study of the proteome.

Contents

1 Systems 2 History 3 Size and contents

3.1 Dark proteome

4 Methods to study the proteome

4.1 Separation techniques and electrophoresis 4.2 Mass spectrometry 4.3 Protein
Protein
complementation assays and interaction screens

5 See also 6 References 7 External links

Systems[edit] The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome. History[edit] Marc Wilkins coined the term proteome [1] in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. It appeared in print in 1995,[2] with the publication of part of Wilkins's PhD thesis. Wilkins used the term to describe the entire complement of proteins expressed by a genome, cell, tissue or organism. Size and contents[edit] The proteome can be larger than the genome, especially in eukaryotes, as more than one protein can be produced from one gene due to alternative splicing (e.g. human proteome consists 92,179 proteins out of which 71,173 are splicing variants).[3] On the other hand, not all genes are translated to proteins, and many known genes encode only RNA which is the final functional product. Moreover, complete proteome size vary depending the kingdom of life. For instance, eukaryotes, bacteria, Archaea
Archaea
and viruses have on average 15145, 3200, 2358 and 42 proteins respectively encoded in their genomes.[4] Dark proteome[edit] Perdigão and co-workers surveyed the “dark” proteome – that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, they found that 44–54% of the proteome in eukaryotes and viruses was "dark", compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage.[5] Methods to study the proteome[edit] Main article: Proteomics Numerous methods are available to study proteins, sets of proteins, or the whole proteome. In fact, proteins are often studied indirectly, e.g. using computational methods and analyses of genomes. Only a few examples are given below. Separation techniques and electrophoresis[edit] Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. In the first dimension, the proteins are separated by isoelectric focusing, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight using SDS-PAGE. The gel is dyed with Coomassie Brilliant Blue
Coomassie Brilliant Blue
or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations. Mass spectrometry[edit] Mass spectrometry
Mass spectrometry
has augmented proteomics.[6] Peptide mass fingerprinting identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a non-reactive gas, and then cataloguing the fragment ions produced.[7] In May 2014, a draft map of the human proteome was published in Nature.[8] This map was generated using high-resolution Fourier-transform mass spectrometry. This study profiled 30 histologically normal human samples resulting in the identification of proteins coded by 17,294 genes. This accounts for around 84% of the total annotated protein-coding genes. Protein
Protein
complementation assays and interaction screens[edit] Protein
Protein
fragment complementation assays are often used to detect protein–protein interactions. The yeast two-hybrid assay is the most popular of them but there are numerous variations, both used in vitro and in vivo. See also[edit]

Metabolome Cytome Bioinformatics List of omics topics in biology Plant Proteome Database Transcriptome Interactome Human Proteome Project BioPlex

References[edit]

^ Wilkins, Marc (Dec 2009). " Proteomics
Proteomics
data mining". Expert review of proteomics. England. 6 (6): 599–603. doi:10.1586/epr.09.81. PMID 19929606.  ^ Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I (1995). "Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium". Electrophoresis. 16 (1): 1090–94. doi:10.1002/elps.11501601185. PMID 7498152.  ^ "UniProt: a hub for protein information". Nucleic Acids Research. 43 (D1): D204–D212. 2014. doi:10.1093/nar/gku989. ISSN 0305-1048. PMC 4384041 . PMID 25348405.  ^ Kozlowski, LP (26 October 2016). "Proteome-pI: proteome isoelectric point database". Nucleic Acids Research. 45: gkw978. doi:10.1093/nar/gkw978. PMC 5210655 . PMID 27789699.  ^ Perdigão, Nelson; et al. (2015). "Unexpected features of the dark proteome". PNAS. 112 (52): 15898–15903. doi:10.1073/pnas.1508380112. PMC 4702990 . PMID 26578815.  ^ Altelaar, AF; Munoz, J; Heck, AJ (January 2013). "Next-generation proteomics: towards an integrative view of proteome dynamics". Nature Reviews Genetics. 14 (1): 35–48. doi:10.1038/nrg3356. PMID 23207911.  ^ "Mass-Spectrometry-Based Draft of the Human Proteome". Nature.  ^ Kim, Min-Sik; et al. (May 2014). "A draft map of the human proteome". Nature. 509 (7502): 575–81. doi:10.1038/nature13302. PMC 4403737 . PMID 24870542. 

External links[edit]

PIR database UniProt database Pfam database

v t e

Proteins

Processes

Protein
Protein
biosynthesis Post-translational modification Protein
Protein
folding Protein
Protein
targeting Proteome Protein
Protein
methods

Structures

Protein
Protein
structure Protein
Protein
structural domains Proteasome

Types

List of types of proteins List of proteins Membrane protein Globular protein

Globulin Edestin Albumin

Fibrous protein

v t e

Proteins: key methods of study

Experimental

Protein
Protein
purification Green fluorescent protein Western blot Protein
Protein
immunostaining Protein
Protein
sequencing Gel electrophoresis/ Protein
Protein
electrophoresis Protein
Protein
immunoprecipitation Peptide mass fingerprinting/ Protein
Protein
mass spectrometry Dual-polarization interferometry Microscale thermophoresis Chromatin immunoprecipitation Surface plasmon resonance Isothermal titration calorimetry X-ray crystallography Protein
Protein
NMR Cryo-electron microscopy Freeze-fracture electron microscopy

Bioinformatics

Protein
Protein
structure prediction Protein–protein docking Protein
Protein
structural alignment Protein
Protein
ontology Protein–protein interaction
Protein–protein interaction
prediction

Assay

Enzyme assay Protein
Protein
assay Secretion
Secretion
assay

Display techniques

Bacterial display mRNA display Phage display Ribosome display Yeast display

Super-resolution microscopy

Photoactivated localization micr

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