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The dark proteome is defined as proteins with no defined three-dimensional structure. It can not be detected or analyzed with the use of homologous modeling or analytical quantification for the molecular conformation is unknown.Perdigão, Nelson.
Dark Proteome Database: Studies on Dark Proteins
" Dark Proteome Database: Studies on Dark Proteins, March 27, 2019
10.20944/preprints201901.0198.v1
/ref> Dark proteins are mostly composed of unknown unknowns


History and Origin

It estimated to be about 14% of the proteome in archaea and bacteria, and as much as 44–54% of the proteome in eukaryotes and viruses, is dark. The origin of these dark proteins is unclear. Large portion of the dark proteome are of viral origin. Dark protein regions are dark due to originating from unusual organisms with no sufficient close relatives in current protein databases to provide protein to protein data on sequence alignments and structure determination.


Function

Dark proteins are not applicable to the structure-function paradigm the all proteins follow. They are predominately consisted of Intrinsically Disordered Proteins (IDP) that are necessary for certain biological function such as splicing, transcriptional and post-translational signaling, and signaling via protein networks. These processes are commonly executed intracellularly, however, dark proteins are over-represented in the extra-cellular matrix and on the endoplasmic reticulum. Dark proteins behave similarly to polymers and are capable of taking on many if not infinite conformations form due to the adaptability of the polypeptide chain. This is due to the lack of structure which provides flexibility and maneuverability which aids in certain ribosomal and cellular processes. They also are overrepresented in certain secretory tissues and exterior environment which aids the cell against harsh cellular environments. The function is not limited to only signaling and defense, though it is not fully understood. "Dark proteins are mostly unknown unknowns"


Methods for detection

Currently only computational and analytical techniques such
infrared Infrared (IR), sometimes called infrared light, is electromagnetic radiation (EMR) with wavelengths longer than those of visible light. It is therefore invisible to the human eye. IR is generally understood to encompass wavelengths from around ...
(IR), circular dichroism (CR),
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is use ...
(MS),
single-molecule experiment A single-molecule experiment is an experiment that investigates the properties of individual molecules. Single-molecule studies may be contrasted with measurements on an ensemble or bulk collection of molecules, where the individual behavior of mo ...
,
wide-angle X-ray scattering In X-ray crystallography, wide-angle X-ray scattering (WAXS) or wide-angle X-ray diffraction (WAXD) is the analysis of Bragg peaks scattered to wide angles, which (by Bragg's law) are caused by sub-nanometer-sized structures. It is an X-ray-diffr ...
,
small-angle X-ray scattering Small-angle X-ray scattering (SAXS) is a small-angle scattering technique by which nanoscale density differences in a sample can be quantified. This means that it can determine nanoparticle size distributions, resolve the size and shape of (monodis ...
,
wide-angle X-ray scattering In X-ray crystallography, wide-angle X-ray scattering (WAXS) or wide-angle X-ray diffraction (WAXD) is the analysis of Bragg peaks scattered to wide angles, which (by Bragg's law) are caused by sub-nanometer-sized structures. It is an X-ray-diffr ...
(WAXS),
Nuclear magnetic resonance Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
(NMR), and
gel filtration Size-exclusion chromatography (SEC), also known as molecular sieve chromatography, is a chromatographic method in which molecules in solution are separated by their size, and in some cases molecular weight. It is usually applied to large molecules ...
.Bhowmick, Asmist, David H. Brookes, Shane R. Yost, H. Jane Dyson, and Julie D. Forman-Kay. "Finding Our Way in the Dark Proteome." ACS Publication, July 7, 2016. Accessed April 08, 2019. doi:10.1021/jacs.6b06543. Coupled methodology with techniques are recommended if there are certain data points missing with the use of one method, the complementary method may serve to fill that gap.


See also

*
Intrinsically disordered proteins In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs rang ...
*
Protein dynamics Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these stat ...


References

{{Reflist Proteomics