scholarly journals Proteomic analysis of exported chaperone/co-chaperone complexes of P. falciparum reveals an array of complex protein-protein interactions

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Qi Zhang ◽  
Cheng Ma ◽  
Alexander Oberli ◽  
Astrid Zinz ◽  
Sonja Engels ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Proteomic Analysis ◽  
Protein Protein Interactions ◽  
Complex Protein

scholarly journals Protein–protein interactions in intracellular Ca2+-release channel function

1999 ◽  
Vol 337 (3) ◽  
pp. 345-361 ◽  
Author(s):  
John J. MACKRILL
Keyword(s):  
Protein Interactions ◽  
Ryanodine Receptors ◽  
Accessory Proteins ◽  
Protein Protein Interactions ◽  
Release Channel ◽  
Specific Effects ◽  
Complex Protein ◽  
A Cell ◽  
And Function ◽  
Opposing Effects

Release of Ca2+ ions from intracellular stores can occur via two classes of Ca2+-release channel (CRC) protein, the inositol 1,4,5-trisphosphate receptors (InsP3Rs) and the ryanodine receptors (RyRs). Multiple isoforms and subtypes of each CRC class display distinct but overlapping distributions within mammalian tissues. InsP3Rs and RyRs interact with a plethora of accessory proteins which modulate the activity of their intrinsic channels. Although many aspects of CRC structure and function have been reviewed in recent years, the properties of proteins with which they interact has not been comprehensively surveyed, despite extensive current research on the roles of these modulators. The aim of this article is to review the regulation of CRC activity by accessory proteins and, wherever possible, to outline the structural details of such interactions. The CRCs are large transmembrane proteins, with the bulk of their structure located cytoplasmically. Intra- and inter-complex protein–protein interactions between these cytoplasmic domains also regulate CRC function. Some accessory proteins modulate channel activity of all CRC subtypes characterized, whereas other have class- or even isoform-specific effects. Certain accessory proteins exert both direct and indirect forms of regulation on CRCs, occasionally with opposing effects. Others are themselves modulated by changes in Ca2+ concentration, thereby participating in feedback mechanisms acting on InsP3R and RyR activity. CRCs are therefore capable of integrating numerous signalling events within a cell by virtue of such protein–protein interactions. Consequently, the functional properties of InsP3Rs and RyRs within particular cells and subcellular domains are ‘customized ’ by the accessory proteins present.

scholarly journals Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Likui Feng ◽  
Matthew T. Gordon ◽  
Ying Liu ◽  
Kari B. Basso ◽  
Rebecca A. Butcher
Keyword(s):  
Protein Interactions ◽  
Biosynthetic Pathway ◽  
Polyketide Synthase ◽  
Carrier Protein ◽  
Nonribosomal Peptides ◽  
Direct Transfer ◽  
Protein Protein Interactions ◽  
Nonribosomal Peptide ◽  
Peptide Synthetase ◽  
Complex Protein

AbstractPolyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis.

scholarly journals The Protein Interaction Network of the Epithelial Junctional Complex: A System-Level Analysis

2008 ◽  
Vol 19 (12) ◽  
pp. 5409-5421 ◽  
Author(s):  
Luca Paris ◽  
Gianfranco Bazzoni
Keyword(s):  
Protein Interactions ◽  
Random Network ◽  
Interaction Network ◽  
Small World ◽  
System Level ◽  
Junctional Complex ◽  
Protein Protein Interactions ◽  
Complex Protein ◽  
Organizing Principles

To acquire system-level understanding of the intercellular junctional complex, protein–protein interactions occurring at the junctions of simple epithelial cells have been examined by network analysis. Although proper hubs (i.e., very rare proteins with exceedingly high connectivity) were absent from the junctional network, the most connected (albeit nonhub) proteins displayed a significant association with essential genes and contributed to the “small world” properties of the network (as shown by in vivo and in silico deletion, respectively). In addition, compared with a random network, the junctional network had greater tendency to form modules and subnets of densely interconnected proteins. Module analysis highlighted general organizing principles of the junctional complex. In particular, two major modules (corresponding to the tight junctions and to the adherens junctions/desmosomes) were linked preferentially to two other modules that acted as structural and signaling platforms.

Piezo Dispensed Microarray of Multivalent Chelating Thiols for Dissecting Complex Protein−Protein Interactions

2006 ◽  
Vol 78 (11) ◽  
pp. 3643-3650 ◽  
Author(s):  
Goran Klenkar ◽  
Ramûnas Valiokas ◽  
Ingemar Lundström ◽  
Ali Tinazli ◽  
Robert Tampé ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Complex Protein

scholarly journals Peptide Signals Encode Protein Localization

2007 ◽  
Vol 189 (21) ◽  
pp. 7581-7585 ◽  
Author(s):  
Jay H. Russell ◽  
Kenneth C. Keiler
Keyword(s):  
Protein Interactions ◽  
Fluorescent Protein ◽  
Protein Localization ◽  
Protein Protein Interactions ◽  
Helical Structures ◽  
Bacterial Proteins ◽  
Complex Protein ◽  
Peptide Signals ◽  
Green Fluorescent ◽  
Localization Information

ABSTRACT Many bacterial proteins are localized to precise intracellular locations, but in most cases the mechanism for encoding localization information is not known. Screening libraries of peptides fused to green fluorescent protein identified sequences that directed the protein to helical structures or to midcell. These peptides indicate that protein localization can be encoded in 20-amino-acid peptides instead of complex protein-protein interactions and raise the possibility that the location of a protein within the cell could be predicted from bioinformatic data.

scholarly journals Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan

2021 ◽  
Author(s):  
Likui Feng ◽  
Matthew T. Gordon ◽  
Ying Liu ◽  
Kari B. Basso ◽  
Rebecca A. Butcher
Keyword(s):  
Protein Interactions ◽  
Biosynthetic Pathway ◽  
Polyketide Synthase ◽  
Carrier Protein ◽  
Direct Transfer ◽  
Protein Protein Interactions ◽  
Nematode Caenorhabditis Elegans ◽  
Nonribosomal Peptide ◽  
Peptide Synthetase ◽  
Complex Protein

Hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between megasynthases. In the nematode Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides in animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional stand-alone enzymes that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes in the biosynthetic pathway and discover a novel mechanism of trafficking intermediates between a PKS and an NRPS. Specifically, we show that the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis.

scholarly journals In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at the peptide level

2016 ◽  
Author(s):  
Luitzen de Jong ◽  
Edward A. de Koning ◽  
Winfried Roseboom ◽  
Hansuk Buncherd ◽  
Martin J. Wanner ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Protein Interactions ◽  
Cross Linking ◽  
Bacterial Cells ◽  
Protein Protein Interactions ◽  
Genome Wide ◽  
Peptide Level ◽  
Complex Protein ◽  
Genome Wide Data ◽  
Cross Links

AbstractIdentification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacteriumBacillus subtilisas an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species,Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and β′ subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.

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