scholarly journals Identifying Optimal Lipid Raft Characteristics Required To Promote Nanoscale Protein-Protein Interactions on the Plasma Membrane

2006 ◽  
Vol 26 (1) ◽  
pp. 313-323 ◽  
Author(s):  
Dan V. Nicolau ◽  
Kevin Burrage ◽  
Robert G. Parton ◽  
John F. Hancock
Keyword(s):  
Plasma Membrane ◽  
Long Range ◽  
Protein Interactions ◽  
Small Diameter ◽  
Equilibrium Concentration ◽  
Membrane Microdomains ◽  
Small Scale ◽  
Protein Protein Interactions ◽  
Protein Mobility ◽  
Dynamic Partitioning

ABSTRACT The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raft-excluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.

scholarly journals Interdependent assembly of specific regulatory lipids and membrane fusion proteins into the vertex ring domain of docked vacuoles

2004 ◽  
Vol 167 (6) ◽  
pp. 1087-1098 ◽  
Author(s):  
Rutilio A. Fratti ◽  
Youngsoo Jun ◽  
Alexey J. Merz ◽  
Nathan Margolis ◽  
William Wickner
Keyword(s):  
Membrane Fusion ◽  
Protein Interactions ◽  
Fusion Proteins ◽  
Membrane Microdomains ◽  
Rab Gtpase ◽  
Protein Protein Interactions ◽  
Px Domain ◽  
Protein Partitioning ◽  
Membrane Fusion Proteins ◽  
Rab Effector

Membrane microdomains are assembled by lipid partitioning (e.g., rafts) or by protein–protein interactions (e.g., coated vesicles). During docking, yeast vacuoles assemble “vertex” ring-shaped microdomains around the periphery of their apposed membranes. Vertices are selectively enriched in the Rab GTPase Ypt7p, the homotypic fusion and vacuole protein sorting complex (HOPS)–VpsC Rab effector complex, SNAREs, and actin. Membrane fusion initiates at vertex microdomains. We now find that the “regulatory lipids” ergosterol, diacylglycerol and 3- and 4-phosphoinositides accumulate at vertices in a mutually interdependent manner. Regulatory lipids are also required for the vertex enrichment of SNAREs, Ypt7p, and HOPS. Conversely, SNAREs and actin regulate phosphatidylinositol 3-phosphate vertex enrichment. Though the PX domain of the SNARE Vam7p has direct affinity for only 3-phosphoinositides, all the regulatory lipids which are needed for vertex assembly affect Vam7p association with vacuoles. Thus, the assembly of the vacuole vertex ring microdomain arises from interdependent lipid and protein partitioning and binding rather than either lipid partitioning or protein interactions alone.

scholarly journals The NHR1 Domain of Neuralized Binds Delta and Mediates Delta Trafficking and Notch Signaling

2007 ◽  
Vol 18 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Cosimo Commisso ◽  
Gabrielle L. Boulianne
Keyword(s):  
Plasma Membrane ◽  
Notch Signaling ◽  
Ubiquitin Ligase ◽  
Protein Interactions ◽  
Neural Development ◽  
Ring Domain ◽  
Protein Protein Interactions ◽  
Necessary And Sufficient ◽  
Conserved Residue ◽  
Notch Ligands

Notch signaling, which is crucial to metazoan development, requires endocytosis of Notch ligands, such as Delta and Serrate. Neuralized is a plasma membrane-associated ubiquitin ligase that is required for neural development and Delta internalization. Neuralized is comprised of three domains that include a C-terminal RING domain and two neuralized homology repeat (NHR) domains. All three domains are conserved between organisms, suggesting that these regions of Neuralized are functionally important. Although the Neuralized RING domain has been shown to be required for Delta ubiquitination, the function of the NHR domains remains elusive. Here we show that neuralized1, a well-characterized neurogenic allele, exhibits a mutation in a conserved residue of the NHR1 domain that results in mislocalization of Neuralized and defects in Delta binding and internalization. Furthermore, we describe a novel isoform of Neuralized and show that it is recruited to the plasma membrane by Delta and that this is mediated by the NHR1 domain. Finally, we show that the NHR1 domain of Neuralized is both necessary and sufficient to bind Delta. Altogether, our data demonstrate that NHR domains can function in facilitating protein–protein interactions and in the case of Neuralized, mediate binding to its ubiquitination target, Delta.

scholarly journals The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication

2019 ◽  
Author(s):  
Jonas Defoort ◽  
Yves Van de Peer ◽  
Lorenzo Carretero-Paulet
Keyword(s):  
Protein Interactions ◽  
Specific Property ◽  
Small Scale ◽  
Biological Interactions ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Functional Dynamics ◽  
Dosage Balance ◽  
Gene Duplicates ◽  
The Impact

Abstract Gene duplicates, generated either through whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary novelty. Previous studies reported contrasting evolutionary and functional dynamics of duplicate genes depending on the mechanism of origin, a behaviour that is hypothesized to stem from constraints to maintain the relative dosage balance between the genes concerned and their interaction context. However, the mechanisms ultimately influencing loss and retention of gene duplicates over evolutionary time are not yet fully elucidated. Here, by using a robust classification of gene duplicates in Arabidopsis thaliana, Solanum lycopersicum and Zea mays, large RNAseq expression compendia and an extensive protein-protein interaction (PPI) network from Arabidopsis, we investigated the impact of PPIs on the differential evolutionary and functional fate of WGD and SSD duplicates. In all three species, retained WGD duplicates show stronger constraints to diverge at the sequence and expression level than SSD ones, a pattern that is also observed for shared PPI partners between Arabidopsis duplicates. PPIs are preferentially distributed among WGD duplicates and specific functional categories. Furthermore, duplicates with PPIs tend to be under stronger constraints to evolve than their counterparts without PPIs regardless of their mechanism of origin. Our results support dosage balance constraint as a specific property of genes involved in biological interactions, including physical PPIs, and suggest that additional factors may be differently influencing the evolution of genes following duplication, depending on the species, time and mechanism of origin.

scholarly journals The Lipid Raft Component Stomatin Interacts with the Na+ Taurocholate Cotransporting Polypeptide (NTCP) and Modulates Bile Salt Uptake

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 986
Author(s):  
Monique D. Appelman ◽  
Marion J.D. Robin ◽  
Esther W.M. Vogels ◽  
Christie Wolzak ◽  
Winnie G. Vos ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Bile Salt ◽  
Protein Interactions ◽  
Basolateral Membrane ◽  
Sodium Taurocholate ◽  
Salt Transport ◽  
Protein Protein Interactions ◽  
Cell Surface Biotinylation ◽  
Detergent Resistant Membranes ◽  
Entry Receptor

The sodium taurocholate cotransporting polypeptide (NTCP) is expressed at the basolateral membrane of hepatocytes, where it mediates the uptake of conjugated bile acids and forms the hepatocyte entry receptor for the hepatitis B and D virus. Here, we aimed to identify novel protein–protein interactions that could play a role in the regulation of NTCP. To this end, NTCP was precipitated from HA-tagged hNTCP-expressing HepG2 cells, and chloride channel CLIC-like 1 (CLCC1) and stomatin were identified as interacting proteins by mass spectrometry. Interaction was confirmed by co-immunoprecipitation. NTCP, CLCC1 and stomatin were found at the plasma membrane in lipid rafts, as demonstrated by a combination of immunofluorescence, cell surface biotinylation and isolation of detergent-resistant membranes. Neither CLCC1 overexpression nor its knockdown had an effect on NTCP function. However, both stomatin overexpression and knockdown increased NTCP-mediated taurocholate uptake while NTCP abundance at the plasma membrane was only increased in stomatin depleted cells. These findings identify stomatin as an interactor of NTCP and show that the interaction modulates bile salt transport.

scholarly journals Subcellular Targeting of Plant Sucrose Transporters Is Affected by Their Oligomeric State

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 158 ◽  
Author(s):  
Varsha Garg ◽  
Aleksandra Hackel ◽  
Christina Kühn
Keyword(s):  
Protein Interactions ◽  
Subcellular Distribution ◽  
Sucrose Transporter ◽  
Membrane Microdomains ◽  
Protein Protein Interactions ◽  
Subcellular Targeting ◽  
Oligomeric State ◽  
Sucrose Transporters ◽  
Interaction Partners ◽  
The Impact

Post-translational regulation of sucrose transporters represents one possibility to adapt transporter activity in a very short time frame. This can occur either via phosphorylation/dephosphorylation, oligomerization, protein–protein interactions, endocytosis/exocytosis, or degradation. It is also known that StSUT1 can change its compartmentalization at the plasma membrane and concentrate in membrane microdomains in response to changing redox conditions. A systematic screen for protein–protein-interactions of plant sucrose transporters revealed that the interactome of all three known sucrose transporters from the Solanaceous species Solanum tuberosum and Solanum lycopersicum represents a specific subset of interaction partners, suggesting different functions for the three different sucrose transporters. Here, we focus on factors that affect the subcellular distribution of the transporters. It was already known that sucrose transporters are able to form homo- as well as heterodimers. Here, we reveal the consequences of homo- and heterodimer formation and the fact that the responses of individual sucrose transporters will respond differently. Sucrose transporter SlSUT2 is mainly found in intracellular vesicles and several of its interaction partners are involved in vesicle traffic and subcellular targeting. The impact of interaction partners such as SNARE/VAMP proteins on the localization of SlSUT2 protein will be investigated, as well as the impact of inhibitors, excess of substrate, or divalent cations which are known to inhibit SUT1-mediated sucrose transport in yeast cells. Thereby we are able to identify factors regulating sucrose transporter activity via a change of their subcellular distribution.

Protein-Protein Interactions in the Tetraspanin Web

Physiology ◽  
2005 ◽  
Vol 20 (4) ◽  
pp. 218-224 ◽  
Author(s):  
Shoshana Levy ◽  
Tsipi Shoham
Keyword(s):  
Signal Transduction ◽  
Cell Proliferation ◽  
Protein Interactions ◽  
Membrane Microdomains ◽  
Protein Protein Interactions ◽  
Host Parasite Interactions ◽  
Evolutionarily Conserved ◽  
And Migration ◽  
Host Parasite ◽  
Partner Proteins

Tetraspanins are evolutionarily conserved membrane proteins that tend to associate laterally with one another and to cluster dynamically with numerous partner proteins in membrane microdomains. Consequently, members of this family are involved in the coordination of intracellular and intercellular processes, including signal transduction; cell proliferation, adhesion, and migration; cell fusion; and host-parasite interactions.

scholarly journals Membrane Binding of HIV-1 Matrix Protein: Dependence on Bilayer Composition and Protein Lipidation

2016 ◽  
Vol 90 (9) ◽  
pp. 4544-4555 ◽  
Author(s):  
Marilia Barros ◽  
Frank Heinrich ◽  
Siddhartha A. K. Datta ◽  
Alan Rein ◽  
Ioannis Karageorgos ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Protein Interactions ◽  
Matrix Protein ◽  
Full Length ◽  
Protein Protein Interactions ◽  
Binding Studies ◽  
Protein Protein Interaction ◽  
Gag Polyprotein ◽  
Protein Lipidation ◽  
Hiv 1

ABSTRACTBy assembling in a protein lattice on the host's plasma membrane, the retroviral Gag polyprotein triggers formation of the viral protein/membrane shell. The MA domain of Gag employs multiple signals—electrostatic, hydrophobic, and lipid-specific—to bring the protein to the plasma membrane, thereby complementing protein-protein interactions, located in full-length Gag, in lattice formation. We report the interaction of myristoylated and unmyristoylated HIV-1 Gag MA domains with bilayers composed of purified lipid components to dissect these complex membrane signals and quantify their contributions to the overall interaction. Surface plasmon resonance on well-defined planar membrane models is used to quantify binding affinities and amounts of protein and yields free binding energy contributions, ΔG, of the various signals. Charge-charge interactions in the absence of the phosphatidylinositide PI(4,5)P2attract the protein to acidic membrane surfaces, and myristoylation increases the affinity by a factor of 10; thus, our data do not provide evidence for a PI(4,5)P2trigger of myristate exposure. Lipid-specific interactions with PI(4,5)P2, the major signal lipid in the inner plasma membrane, increase membrane attraction at a level similar to that of protein lipidation. While cholesterol does not directly engage in interactions, it augments protein affinity strongly by facilitating efficient myristate insertion and PI(4,5)P2binding. We thus observe that the isolated MA protein, in the absence of protein-protein interaction conferred by the full-length Gag, binds the membrane with submicromolar affinities.IMPORTANCELike other retroviral species, the Gag polyprotein of HIV-1 contains three major domains: the N-terminal, myristoylated MA domain that targets the protein to the plasma membrane of the host; a central capsid-forming domain; and the C-terminal, genome-binding nucleocapsid domain. These domains act in concert to condense Gag into a membrane-bounded protein lattice that recruits genomic RNA into the virus and forms the shell of a budding immature viral capsid. In binding studies of HIV-1 Gag MA to model membranes with well-controlled lipid composition, we dissect the multiple interactions of the MA domain with its target membrane. This results in a detailed understanding of the thermodynamic aspects that determine membrane association, preferential lipid recruitment to the viral shell, and those aspects of Gag assembly into the membrane-bound protein lattice that are determined by MA.

scholarly journals Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

2020 ◽  
Vol 37 (8) ◽  
pp. 2394-2413 ◽  
Author(s):  
Tao Shi ◽  
Razgar Seyed Rahmani ◽  
Paul F Gugger ◽  
Muhua Wang ◽  
Hui Li ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Flowering Plants ◽  
Expression Level ◽  
Small Scale ◽  
Whole Genome ◽  
Functional Constraints ◽  
Expression Divergence ◽  
Protein Protein Interactions ◽  
Methylation Patterns ◽  
The Impact

Abstract For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.

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