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Dark Proteome Database: Studies on Dark Proteins

by 1,2,* and 1,2
Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
Instituto de Sistemas e Robótica, 1049-001 Lisbon, Portugal
Author to whom correspondence should be addressed.
High-Throughput 2019, 8(2), 8;
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)
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
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MDPI and ACS Style

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

AMA Style

Perdigão N, Rosa A. Dark Proteome Database: Studies on Dark Proteins. High-Throughput. 2019; 8(2):8.

Chicago/Turabian Style

Perdigão, Nelson, and Agostinho Rosa. 2019. "Dark Proteome Database: Studies on Dark Proteins" High-Throughput 8, no. 2: 8.

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