PerMemDB: A database for eukaryotic peripheral membrane proteins.

08:00 EDT 17th October 2019 | BioPortfolio

Summary of "PerMemDB: A database for eukaryotic peripheral membrane proteins."

The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and/or lipids, via non-covalent interactions and are of outmost importance, due to numerous cellular functions in which they participate. In an effort to collect data regarding this heterogeneous group of proteins we designed and constructed a database, called PerMemDB. PerMemDB is currently the most complete and comprehensive repository of data for eukaryotic peripheral membrane proteins deposited in UniProt or predicted with the use of MBPpred - a computational method that specializes in the detection of proteins that interact non-covalently with membrane lipids, via membrane binding domains. The first version of the database contains 231,770 peripheral membrane proteins from 1009 organisms. All entries have cross-references to other databases, literature references and annotation regarding their interactions with other proteins. Moreover, additional sequence annotation of the characteristic domains that allow these proteins to interact with membranes is available, due to the application of MBPpred. Through the web interface of PerMemDB, users can browse the contents of the database, submit advanced text searches and BLAST queries against the protein sequences deposited in PerMemDB. We expect this repository to serve as a source of information that will allow the scientific community to gain a deeper understanding of the evolution and function of peripheral membrane proteins via the enhancement of proteome-wide analyses. The database is available at:


Journal Details

This article was published in the following journal.

Name: Biochimica et biophysica acta. Biomembranes
ISSN: 1879-2642
Pages: 183076


DeepDyve research library

PubMed Articles [13830 Associated PubMed Articles listed on BioPortfolio]

S-Acylation of Proteins.

Palmitoylation or S-acylation is the posttranslational attachment of fatty acids to cysteine residues and is common among integral and peripheral membrane proteins. Palmitoylated proteins have been fo...

Proteomic analysis of Escherichia coli detergent-resistant membranes (DRM).

Membrane microdomains or lipid rafts compartmentalize cellular processes by laterally organizing membrane components. Such sub-membrane structures were mainly described in eukaryotic cells, but, recen...

Why do eukaryotic proteins contain more intrinsically disordered regions?

Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins. Methods predicting intrinsic disorder are based on the amino acid sequence of a protein. Therefore, there must exist an und...

Visualizing membrane trafficking through the electron microscope: cryo-tomography of coat complexes.

Coat proteins mediate vesicular transport between intracellular compartments, which is essential for the distribution of molecules within the eukaryotic cell. The global arrangement of coat proteins o...

An intrinsic compartmentalization code for peripheral membrane proteins in photoreceptor neurons.

In neurons, peripheral membrane proteins are enriched in subcellular compartments, where they play key roles, including transducing and transmitting information. However, little is known about the mec...

Clinical Trials [5624 Associated Clinical Trials listed on BioPortfolio]

ObseRvation of PeripHEral rEtinal Morphology in Normals

To develop a database of the peripheral retinal circulation using ultra widefield fluorescein angiography (UWF-FA) imaging for the Optos COE platform. This database will serve as a quanti...

Mandibular Furcation III Regeneration (FURC-III-REGEN)

Teeth with furcation grade III defects will be treated with open flap debridement and regenerative therapy with biphasic calcium phosphate combined with either enamel matrix proteins or a ...

Mandibular Furcation II Regeneration

Teeth with furcation grade II defects will be treated with open flap debridement and regenerative therapy with biphasic calcium phosphate combined with either enamel matrix proteins or a c...

Test of the Nipro ELISIO H Dialyzer in Different Dialysis Treatment Procedures

A current trend in dialysis membrane engineering is to maximize the permeability for larger low-molecular weight proteins while retaining albumin. Protein-leaking dialysis membranes do not...

Effects of Internal Limiting Membrane Peeling on Visual Function in Epiretinal Membrane Surgery

The patients who are diagnosed with idiopathic epiretinal membrane and scheduled to undergo epiretinal membrane removal will be treated with conventional vitrectomy and the epiretinal memb...

Medical and Biotech [MESH] Definitions

Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.

Lipids, predominantly phospholipids, cholesterol and small amounts of glycolipids found in membranes including cellular and intracellular membranes. These lipids may be arranged in bilayers in the membranes with integral proteins between the layers and peripheral proteins attached to the outside. Membrane lipids are required for active transport, several enzymatic activities and membrane formation.

A group of three related eukaryotic phyla whose members possess an alveolar membrane system, consisting of flattened membrane-bound sacs lying beneath the outer cell membrane.

A high molecular weight (220-250 kDa) water-soluble protein which can be extracted from erythrocyte ghosts in low ionic strength buffers. The protein contains no lipids or carbohydrates, is the predominant species of peripheral erythrocyte membrane proteins, and exists as a fibrous coating on the inner, cytoplasmic surface of the membrane.

The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.

Quick Search

DeepDyve research library

Searches Linking to this Article