scholarly journals Hypothesized diprotomeric enzyme complex supported by stochastic modelling of palytoxin-induced Na/K pump channels

2018 ◽  
Vol 5 (3) ◽  
pp. 172155 ◽  
Author(s):  
Gabriel D. Vilallonga ◽  
Antônio-Carlos G. de Almeida ◽  
Kelison T. Ribeiro ◽  
Sergio V. A. Campos ◽  
Antônio M. Rodrigues
Keyword(s):  
Protein Interactions ◽  
Single Channel ◽  
Stochastic Modelling ◽  
Reaction Rates ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Conformational Substates ◽  
Pumping System ◽  
Electrophysiological Recordings ◽  
Probabilistic Queries

The sodium–potassium pump (Na + /K + pump) is crucial for cell physiology. Despite great advances in the understanding of this ionic pumping system, its mechanism is not completely understood. We propose the use of a statistical model checker to investigate palytoxin (PTX)-induced Na + /K + pump channels. We modelled a system of reactions representing transitions between the conformational substates of the channel with parameters, concentrations of the substates and reaction rates extracted from simulations reported in the literature, based on electrophysiological recordings in a whole-cell configuration. The model was implemented using the UPPAAL-SMC platform. Comparing simulations and probabilistic queries from stochastic system semantics with experimental data, it was possible to propose additional reactions to reproduce the single-channel dynamic. The probabilistic analyses and simulations suggest that the PTX-induced Na + /K + pump channel functions as a diprotomeric complex in which protein–protein interactions increase the affinity of the Na + /K + pump for PTX.

Swim-exercised mice show a decreased level of protein O-GlcNAcylation and expression of O-GlcNAc transferase in heart

2011 ◽  
Vol 111 (1) ◽  
pp. 157-162 ◽  
Author(s):  
Darrell D. Belke
Keyword(s):  
Protein Interactions ◽  
Contractile Function ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Training Exercise ◽  
General Protein ◽  
Exercise Induced ◽  
Glcnac Transferase ◽  
The Impact ◽  
Physiological Hypertrophy

Swim-training exercise in mice leads to cardiac remodeling associated with an improvement in contractile function. Protein O-linked N-acetylglucosamine ( O-GlcNAcylation) is a posttranslational modification of serine and threonine residues capable of altering protein-protein interactions affecting gene transcription, cell signaling pathways, and general cell physiology. Increased levels of protein O-GlcNAcylation in the heart have been associated with pathological conditions such as diabetes, ischemia, and hypertrophic heart failure. In contrast, the impact of physiological exercise on protein O-GlcNAcylation in the heart is currently unknown. Swim-training exercise in mice was associated with the development of a physiological hypertrophy characterized by an improvement in contractile function relative to sedentary mice. General protein O-GlcNAcylation was significantly decreased in swim-exercised mice. This effect was mirrored in the level of O-GlcNAcylation of individual proteins such as SP1. The decrease in protein O-GlcNAcylation was associated with a decrease in the expression of O-GlcNAc transferase (OGT) and glutamine-fructose amidotransferase (GFAT) 2 mRNA. O-GlcNAcase (OGA) activity was actually lower in swim-trained than sedentary hearts, suggesting that it did not contribute to the decreased protein O-GlcNAcylation. Thus it appears that exercise-induced physiological hypertrophy is associated with a decrease in protein O-GlcNAcylation, which could potentially contribute to changes in gene expression and other physiological changes associated with exercise.

scholarly journals Caveolins and cavins in the trafficking, maturation, and degradation of caveolae: implications for cell physiology

2017 ◽  
Vol 312 (4) ◽  
pp. C459-C477 ◽  
Author(s):  
Anna R. Busija ◽  
Hemal H. Patel ◽  
Paul A. Insel
Keyword(s):  
Protein Interactions ◽  
Conformational Stability ◽  
Cell Physiology ◽  
Adapter Proteins ◽  
Scaffolding Proteins ◽  
Protein Protein Interactions ◽  
Outer Coat ◽  
Ligand Affinity ◽  
Cellular Changes ◽  
Raft Domains

Caveolins (Cavs) are ~20 kDa scaffolding proteins that assemble as oligomeric complexes in lipid raft domains to form caveolae, flask-shaped plasma membrane (PM) invaginations. Caveolae (“little caves”) require lipid-lipid, protein-lipid, and protein-protein interactions that can modulate the localization, conformational stability, ligand affinity, effector specificity, and other functions of proteins that are partners of Cavs. Cavs are assembled into small oligomers in the endoplasmic reticulum (ER), transported to the Golgi for assembly with cholesterol and other oligomers, and then exported to the PM as an intact coat complex. At the PM, cavins, ~50 kDa adapter proteins, oligomerize into an outer coat complex that remodels the membrane into caveolae. The structure of caveolae protects their contents (i.e., lipids and proteins) from degradation. Cellular changes, including signal transduction effects, can destabilize caveolae and produce cavin dissociation, restructuring of Cav oligomers, ubiquitination, internalization, and degradation. In this review, we provide a perspective of the life cycle (biogenesis, degradation), composition, and physiologic roles of Cavs and caveolae and identify unanswered questions regarding the roles of Cavs and cavins in caveolae and in regulating cell physiology.1

scholarly journals Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome

2021 ◽  
Author(s):  
Caroline Benz ◽  
Muhammad Ali ◽  
Izabella Krystkowiak ◽  
Leandro Simonetti ◽  
Ahmed Sayadi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Human Proteome ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Linear Motif ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Wide Range ◽  
Disordered Regions

Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies using a wide range of experimental approaches have identified tens of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional and cell type-specific interactions are likely to be disproportionately under-represented. Moreover, for most known protein-protein interactions the binding regions remain uncharacterized. We previously developed proteomic peptide phage display (ProP-PD), a method for simultaneous proteome-scale identification of short linear motif (SLiM)-mediated interactions and footprinting of the binding region with amino acid resolution. Here, we describe the second-generation human disorderome (HD2), an optimized ProP-PD library that tiles all disordered regions of the human proteome and allows the screening of ~1,000,000 overlapping peptides in a single binding assay. We define guidelines for how to process, filter and rank the results and provide PepTools, a toolkit for annotation and analysis of identified hits. We uncovered 2,161 interaction pairs for 35 known SLiM-binding domains and confirmed a subset of 38 interactions by biophysical or cell-based assays. Finally, we show how the amino acid resolution binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the human proteome. The HD2 ProP-PD library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.

scholarly journals Characterization of Dominantly Negative Mutant ClyA Cytotoxin Proteins in Escherichia coli

2003 ◽  
Vol 185 (18) ◽  
pp. 5491-5499 ◽  
Author(s):  
Sun Nyunt Wai ◽  
Marie Westermark ◽  
Jan Oscarsson ◽  
Jana Jass ◽  
Elke Maier ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Interactions ◽  
Single Channel ◽  
Dominant Negative ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Protein Protein Interactions ◽  
Mutant Proteins ◽  
Negative Feature

ABSTRACT We report studies of the subcellular localization of the ClyA cytotoxic protein and of mutations causing defective translocation to the periplasm in Escherichia coli. The ability of ClyA to translocate to the periplasm was abolished in deletion mutants lacking the last 23 or 11 amino acid residues of the C-terminal region. A naturally occurring ClyA variant lacking four residues (183 to 186) in a hydrophobic subdomain was retained mainly in the cytosolic fraction. These mutant proteins displayed an inhibiting effect on the expression of the hemolytic phenotype of wild-type ClyA. Studies in vitro with purified mutant ClyA proteins revealed that they were defective in formation of pore assemblies and that their activity in hemolysis assays and in single-channel conductance tests was at least 10-fold lower than that of the wild-type ClyA. Tests with combinations of the purified proteins indicated that mutant and wild-type ClyA interacted and that formation of heteromeric assemblies affected the pore-forming activity of the wild-type protein. The observed protein-protein interactions were consistent with, and provided a molecular explanation for, the dominant negative feature of the mutant ClyA variants.

scholarly journals Synthetic Protein Circuits and Devices Based on Reversible Protein-Protein Interactions: An Overview

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1171
Author(s):  
Stefano Rosa ◽  
Chiara Bertaso ◽  
Paolo Pesaresi ◽  
Simona Masiero ◽  
Andrea Tagliani
Keyword(s):  
Protein Interactions ◽  
De Novo ◽  
Cell Metabolism ◽  
Building Blocks ◽  
New Drugs ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Genetic Circuits ◽  
Cellular Targets ◽  
Synthetic Protein

Protein-protein interactions (PPIs) contribute to regulate many aspects of cell physiology and metabolism. Protein domains involved in PPIs are important building blocks for engineering genetic circuits through synthetic biology. These domains can be obtained from known proteins and rationally engineered to produce orthogonal scaffolds, or computationally designed de novo thanks to recent advances in structural biology and molecular dynamics prediction. Such circuits based on PPIs (or protein circuits) appear of particular interest, as they can directly affect transcriptional outputs, as well as induce behavioral/adaptational changes in cell metabolism, without the need for further protein synthesis. This last example was highlighted in recent works to enable the production of fast-responding circuits which can be exploited for biosensing and diagnostics. Notably, PPIs can also be engineered to develop new drugs able to bind specific intra- and extra-cellular targets. In this review, we summarize recent findings in the field of protein circuit design, with particular focus on the use of peptides as scaffolds to engineer these circuits.

Zinc transport in mammalian cells

1996 ◽  
Vol 270 (2) ◽  
pp. C401-C410 ◽  
Author(s):  
J. G. Reyes
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Enzyme Catalysis ◽  
Mammalian Cells ◽  
Cell Types ◽  
Future Research ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Cell Interior ◽  
Intracellular Organelles

The importance of zinc in cell physiology is related mainly to its intracellular involvement in enzyme catalysis, protein structure, protein-protein interactions, and protein-oligonucleotide interactions. The mechanisms by which Zn2+ enters mammalian cells have been studied in a variety of cell systems. A review of this literature indicates that, in all cells, Zn2+ interacts with extracellular binding sites, which are likely to include binding sites involved in the subsequent translocation of this ion to the cell interior. Inside the cell, Zn2+ binds to cytosolic and organelle binding sites or is taken up by intracellular organelles. Despite these general conclusions, the mechanisms of the different transport and binding steps are, for most cell types, only partially solved. This review critically discusses the literature on mammalian Zn2+ transport and outlines some critical points for future research of the mechanisms of transport of this ion.

scholarly journals Improved Photocleavable Proteins with Faster and More Efficient Dissociation

2020 ◽  
Author(s):  
Xiaocen Lu ◽  
Yurong Wen ◽  
Shuce Zhang ◽  
Wei Zhang ◽  
Yilun Chen ◽  
...  
Keyword(s):  
Protein Interactions ◽  
First Generation ◽  
Fluorescent Protein ◽  
Cultured Cells ◽  
Protein Localization ◽  
Contrast Ratio ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
X Ray ◽  
Chain Cleavage

AbstractThe photocleavable protein (PhoCl) is a green-to-red photoconvertible fluorescent protein that, when illuminated with violet light, undergoes main chain cleavage followed by spontaneous dissociation of the resulting fragments. The first generation PhoCl (PhoCl1) exhibited a relative slow rate of dissociation, potentially limiting its utilities for optogenetic control of cell physiology. In this work, we report the X-ray crystal structures of the PhoCl1 green state, red state, and cleaved empty barrel. Using structure-guided engineering and directed evolution, we have developed PhoCl2c with higher contrast ratio and PhoCl2f with faster dissociation. We characterized the performance of these new variants as purified proteins and expressed in cultured cells. Our results demonstrate that PhoCl2 variants exhibit faster and more efficient dissociation, which should enable improved optogenetic manipulations of protein localization and protein-protein interactions in living cells.

Protein-protein interactions of the p53 family with the Bcl-2 family in hepatocellular carcinoma

2011 ◽  
Vol 49 (08) ◽  
Author(s):  
LC König ◽  
M Meinhard ◽  
C Sandig ◽  
MH Bender ◽  
A Lovas ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
P53 Family
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