Next Article in Journal
Mass Spectrometry-Based Methodologies for Targeted and Untargeted Identification of Protein Covalent Adducts (Adductomics): Current Status and Challenges
Previous Article in Journal
Vertical Scanning Interferometry for Label-Free Detection of Peptide-Antibody Interactions
Article Menu

Export Article

Open AccessArticle

Dark Proteome Database: Studies on Dark Proteins

1
Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
2
Instituto de Sistemas e Robótica, 1049-001 Lisbon, Portugal
*
Author to whom correspondence should be addressed.
High-Throughput 2019, 8(2), 8; https://doi.org/10.3390/ht8020008
Received: 1 December 2018 / Revised: 12 March 2019 / Accepted: 15 March 2019 / Published: 27 March 2019
(This article belongs to the Special Issue Algorithms and Tools in Computational Proteomics)
  |  
PDF [5982 KB, uploaded 21 May 2019]
  |  

Abstract

The dark proteome, as we define it, is the part of the proteome where 3D structure has not been observed either by homology modeling or by experimental characterization in the protein universe. From the 550.116 proteins available in Swiss-Prot (as of July 2016), 43.2% of the eukarya universe and 49.2% of the virus universe are part of the dark proteome. In bacteria and archaea, the percentage of the dark proteome presence is significantly less, at 12.6% and 13.3% respectively. In this work, we present a necessary step to complete the dark proteome picture by introducing the map of the dark proteome in the human and in other model organisms of special importance to mankind. The most significant result is that around 40% to 50% of the proteome of these organisms are still in the dark, where the higher percentages belong to higher eukaryotes (mouse and human organisms). Due to the amount of darkness present in the human organism being more than 50%, deeper studies were made, including the identification of ‘dark’ genes that are responsible for the production of so-called dark proteins, as well as the identification of the ‘dark’ tissues where dark proteins are over represented, namely, the heart, cervical mucosa, and natural killer cells. This is a step forward in the direction of gaining a deeper knowledge of the human dark proteome. View Full-Text
Keywords: dark proteome; molecular structure; homology modelling dark proteome; molecular structure; homology modelling
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary materials

SciFeed

Share & Cite This Article

MDPI and ACS Style

Perdigão, N.; Rosa, A. Dark Proteome Database: Studies on Dark Proteins. High-Throughput 2019, 8, 8.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
High-Throughput EISSN 2571-5135 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top