The PXDLS linear motif regulates circadian rhythmicity through protein–protein interactions

Integrase (IN) enzymes are found in all retroviruses and are crucial in the retroviral integration process. Many studies have revealed how exogenous IN enzymes, such as the human immunodeficiency virus (HIV) IN, contribute to altered cellular function. However, the same consideration has not been given to viral IN originating from symbionts within our own DNA. Endogenous retrovirus-K (ERVK) is pathologically associated with neurological and inflammatory diseases along with several cancers. The ERVK IN interactome is unknown, and the question of how conserved the ERVK IN protein–protein interaction motifs are as compared to other retroviral integrases is addressed in this paper. The ERVK IN protein sequence was analyzed using the Eukaryotic Linear Motif (ELM) database, and the results are compared to ELMs of other betaretroviral INs and similar eukaryotic INs. A list of putative ERVK IN cellular protein interactors was curated from the ELM list and submitted for STRING analysis to generate an ERVK IN interactome. KEGG analysis was used to identify key pathways potentially influenced by ERVK IN. It was determined that the ERVK IN potentially interacts with cellular proteins involved in the DNA damage response (DDR), cell cycle, immunity, inflammation, cell signaling, selective autophagy, and intracellular trafficking. The most prominent pathway identified was viral carcinogenesis, in addition to select cancers, neurological diseases, and diabetic complications. This potentiates the role of ERVK IN in these pathologies via protein–protein interactions facilitating alterations in key disease pathways.

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

10.1101/2021.04.13.439572 ◽

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.

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Structural properties and peptide ligand binding of the capsid homology domains of human Arc

10.1101/2020.12.17.423319 ◽

2020 ◽

Author(s):

Erik I. Hallin ◽

Clive R. Bramham ◽

Petri Kursula

Keyword(s):

Protein Interactions ◽

Peptide Binding ◽

Normal Function ◽

Peptide Ligand ◽

Sequence Specificity ◽

Protein Protein Interactions ◽

Linear Motif ◽

X Ray Crystallography ◽

Peptide Binding Site ◽

Binding Cavity

AbstractThe activity-regulated cytoskeleton-associated protein (Arc) is important for synaptic scaling and the normal function of the brain. Arc interacts with many neuronal postsynaptic proteins, but the mechanistic details of its function have not been fully established. The C-terminal domain of Arc consists of tandem domains, termed the N- and C-lobe. The N-lobe harbours a peptide binding site, able to bind to multiple targets. By measuring the affinity of various peptides towards human Arc, we have refined the specificity determinants of this site. We found two sites in the GKAP repeat region that may bind to Arc and confirmed these interactions by X-ray crystallography. Comparison of the crystal structures of three human Arc-peptide complexes identifies 3 conserved C-H...π interactions at the binding cavity, which explain the sequence specificity of short linear motif binding by Arc. By analysing the structures, we further characterise central residues of the Arc lobe fold, show the effects of peptide binding on protein dynamics, and identify acyl carrier proteins as structures similar to the Arc lobes. We hypothesise that Arc may affect protein-protein interactions and phase separation at the postsynaptic density, affecting protein turnover and re-modelling of the synapse.

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Rewiring of RSK-PDZ interactions by linear motif phosphorylation

10.1101/419721 ◽

2018 ◽

Author(s):

Gergo Gogl ◽

Beata Biri-Kovacs ◽

Fabien Durbesson ◽

Pau Jane ◽

Yves Nomine ◽

...

Keyword(s):

Protein Interactions ◽

Pdz Domain ◽

Pdz Domains ◽

Protein Protein Interactions ◽

Linear Motif ◽

Large Numbers ◽

Phosphorylation Event ◽

Protein Change

ABSTRACTProtein phosphorylation is a key regulator of protein-protein interactions. How does the interactome of a protein change during extracellular stimulations? While many individual examples of phosphorylation-regulated interactions were described previously, studies addressing the interactome changes induced by a particular phosphorylation event remain scarce. Here, we try to answer this question, by focusing on interactions between a phosphorylable PDZ-binding linear motif and the entire complement of human PDZ domains. Using a combination ofin vitroquantitative techniques and cell-based approaches, we demonstrate that the activation of the mitotic effector kinase RSK1 causes dramatic changes in its connectivity with PDZ domain containing proteins. These changes consist of modulations of the binding affinity of numerous interactions, rather than on/off switching of a few interactions. Our results highlight the previously unappreciated role of phosphorylation in the complex and subtle rewiring of large numbers of protein-protein interactions.

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Spot protein-protein interactions... fast

PSI Structural Genomics Knowledgebase ◽

10.1038/th_psisgkb.2010.08 ◽

2010 ◽

Author(s):

Maria Hodges

Keyword(s):

Protein Interactions ◽

Protein Protein Interactions

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Combination of chemical cross-linking and pull-down assay to study transient protein-protein interactions

Protocol Exchange ◽

10.1038/nprot.2006.297 ◽

2006 ◽

Cited By ~ 1

Author(s):

Feng Gong ◽

Deirdre Fahy ◽

Michael J. Smerdon

Keyword(s):

Protein Interactions ◽

Cross Linking ◽

Protein Protein Interactions ◽

Chemical Cross Linking

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

Zeitschrift für Gastroenterologie ◽

10.1055/s-0031-1285581 ◽

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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Partial Purification of a Specific Plasminogen Activator from Porcine Parotid Glands

Thrombosis and Haemostasis ◽

10.1055/s-0038-1649179 ◽

1974 ◽

Vol 31 (03) ◽

pp. 403-414 ◽

Cited By ~ 3

Author(s):

Terence Cartwright

Keyword(s):

Nucleic Acid ◽

Salivary Glands ◽

Plasminogen Activator ◽

Protein Interactions ◽

Partial Purification ◽

Protein Protein Interactions ◽

Parotid Glands ◽

Two Stage ◽

Preliminary Characterization ◽

Specific Inhibitors

SummaryA method is described for the extraction with buffers of near physiological pH of a plasminogen activator from porcine salivary glands. Substantial purification of the activator was achieved although this was to some extent complicated by concomitant extraction of nucleic acid from the glands. Preliminary characterization experiments using specific inhibitors suggested that the activator functioned by a similar mechanism to that proposed for urokinase, but with some important kinetic differences in two-stage assay systems. The lack of reactivity of the pig gland enzyme in these systems might be related to the tendency to protein-protein interactions observed with this material.

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Target-Templated de novo Design of Macrocyclic D-/L-Peptides: Inhibitors of the PD-1/PD-L1 Interaction

10.26434/chemrxiv.11663337.v3 ◽

2020 ◽

Author(s):

Salvador Guardiola ◽

Monica Varese ◽

Xavier Roig ◽

Jesús Garcia ◽

Ernest Giralt

Keyword(s):

Protein Interactions ◽

Cyclic Peptides ◽

General Framework ◽

Large Scale ◽

De Novo ◽

Inhibitory Effect ◽

Original Text ◽

Protein Protein Interactions ◽

Retraction Notice ◽

Pharmaceutical Properties

NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above. ------------------------------------------------------------------------ Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our de novo design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.

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