Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins

Biological characteristics and agonists of GPR120 (FFAR4) receptor: the present status of research

GPR120 receptor functions as a receptor for ω-3 fatty acid, involving regulating the secretion of gastrointestinal peptide hormone, adipogenesis, adipogenic differentiation and anti-inflammatory process and the like in the aspect of biological functions. In view that the dysfunction of GPR120 receptor is closely correlated with metabolic disorders, GPR120 may act as a novel potential therapeutic target for the treatment of obesity, insulin resistance, Type 2 diabetes and so on. Therefore, mounting scientists devote themselves to probing the molecular mechanism of the biological function of GPR120 receptor and their ligands for the treatment of impaired metabolic health. Herein, we summarize the mechanisms of signal transduction through GPR120 receptor, and discovery and development of GPR120 agonists thereof.

Specific domains in anterior pharynx-defective 1 determine its intramembrane interactions with nicastrin and presenilin

γ-Secretase, a multisubunit transmembrane protease comprised of presenilin, nicastrin, presenilin enhancer 2, and anterior pharynx-defective one, participates in the regulated intramembrane proteolysis of Type I membrane proteins including the amyloid precursor protein (APP). Although Aph-1 is thought to play a structural role in the assembly of γ-secretase complex and several transmembrane domains (TMDs) of Aph-1 have been shown to be critical for its function, the importance of the other domains of Aph-1 remains elusive. We screened a series of Aph-1 mutants and focused on nine mutations distributed in six different TMDs of human APH-1aS, assessing their ability to complement mouse embryonic fibroblasts lacking Aph-1. We showed that mutations in TMD4 (G126) and TMD5 (H171) of Aph-1aS prevented the formation of the Nct/Aph-1 subcomplex. Importantly, although mutations in TMD3 (Q83/E84/R85) and TMD6 (H197) of APH-1aS did not affect Nct/Aph-1 subcomplex formation, both mutations prevented further association/endoproteolysis of PS1. We propose a model that identifies critical TMDs of Aph-1 for associations with Nct and PS for the stepwise assembly of γ-secretase components.

MTP1 mops up excess zinc in Arabidopsis cells

The MTP1 protein of Arabidopsis thaliana belongs to a ubiquitous family of transition metal transporters that extrude metal ions from the cytoplasm. In a recent publication, Yoshihiro Kobae and colleagues show that AtMTP1 localizes to the vacuolar membrane in Arabidopsis roots and suspension-cultured cells. They demonstrate that the mtp1-1 mutant is hypersensitive to zinc and complement the mutant by transforming it with the MTP1 coding sequence downstream of a constitutive (35S) promoter.

Adaptive evolution of MRGX2, a human sensory neuron specific gene involved in nociception

MRGX2, a G-protein-coupled receptor, is specifically expressed in the sensory neurons of the human peripheral nervous system and involved in nociception. Here, we studied DNA polymorphism patterns and evolution of the MRGX2 gene in world-wide human populations and the representative nonhuman primate species. Our results demonstrated that MRGX2 had undergone adaptive changes in the path of human evolution, which were likely caused by Darwinian positive selection. The patterns of DNA sequence polymorphisms in human populations showed an excess of derived substitutions, which against the expectation of neutral evolution, implying that the adaptive evolution of MRGX2 in humans was a relatively recent event. The reconstructed secondary structure of the human MRGX2 revealed that three of the four human-specific amino acid substitutions were located in the extra-cellular domains. Such critical substitutions may alter the interactions between MRGX2 protein and its ligand, thus, potentially led to adaptive changes of the pain-perception-related nervous system during human evolution.

Building protein diagrams on the web with the residue-based diagram editor RbDe

The residue-based diagram editor (RbDe) is web-based software that greatly simplifies the construction of schematic diagrams of proteins. Residue-based diagrams display the sequence of a given protein in the context of its secondary and tertiary structure. Such diagrams are frequently used to summarize mutations or sequence features, in the context of the overall topology of a protein. The initial version of RbDe was designed for transmembrane proteins and has enabled many users to create diagrams of large systems such as G protein-coupled receptors or transporters. We present an extended diagram editor that supports other families of proteins. Users can now import custom-diagram layouts, use them to render members of any protein family and generate high-quality output for publication purposes. RbDe is available free over the web, at http://icb.mssm.edu/crt/RbDe

Interactive construction of residue-based diagrams of proteins: the RbDe web service

We announce the Residue-based Diagram Editor (RbDe) web service that allows online construction of residue-based diagrams and the creation of stored diagram libraries. The service has been tuned for the construction of snake-like diagrams (for transmembrane proteins) but can be used to render any protein for which defined secondary structure data or hypotheses are available. RbDe is freely available through the Internet from our web site: http://transport.physbio. mssm.edu/rbde/RbDe.html. Licenses for intranet uses can be obtained upon request.