scholarly journals In Sulfolobus solfataricus, the Poly(ADP-Ribose) Polymerase-Like Thermoprotein Is a Multifunctional Enzyme

2020 ◽  
Vol 8 (10) ◽  
pp. 1523
Author(s):  
Anna De Maio ◽  
Elena Porzio ◽  
Sergio Rotondo ◽  
Anna Rita Bianchi ◽  
Maria Rosaria Faraone-Mennella
Keyword(s):  
Atpase Activity ◽  
Protein Interactions ◽  
Sulfolobus Solfataricus ◽  
Ability To Work ◽  
Target Proteins ◽  
Multifunctional Enzyme ◽  
Adp Ribosylation ◽  
Reciprocal Influence ◽  
Set Up

In Sulfolobus solfataricus, Sso, the ADP-ribosylating thermozyme is known to carry both auto- and heteromodification of target proteins via short chains of ADP-ribose. Here, we provide evidence that this thermoprotein is a multifunctional enzyme, also showing ATPase activity. Electrophoretic and kinetic analyses were performed using NAD+ and ATP as substrates. The results showed that ATP is acting as a negative effector on the NAD+-dependent reaction, and is also responsible for inducing the dimerization of the thermozyme. These findings enabled us to further investigate the kinetic of ADP-ribosylation activity in the presence of ATP, and to also assay its ability to work as a substrate. Moreover, since the heteroacceptor of ADP-ribose is the sulfolobal Sso7 protein, known as an ATPase, some reconstitution experiments were set up to study the reciprocal influence of the ADP-ribosylating thermozyme and the Sso7 protein on their activities, considering also the possibility of direct enzyme/Sso7 protein interactions. This study provides new insights into the ATP-ase activity of the ADP-ribosylating thermozyme, which is able to establish stable complexes with Sso7 protein.

scholarly journals Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chun-Song Yang ◽  
Kasey Jividen ◽  
Teddy Kamata ◽  
Natalia Dworak ◽  
Luke Oostdyk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Prostate Cancer Cells ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Complex Assembly ◽  
Adp Ribosylation ◽  
Signaling Axis ◽  
Regulate Protein ◽  
Protein Complex Assembly

AbstractAndrogen signaling through the androgen receptor (AR) directs gene expression in both normal and prostate cancer cells. Androgen regulates multiple aspects of the AR life cycle, including its localization and post-translational modification, but understanding how modifications are read and integrated with AR activity has been difficult. Here, we show that ADP-ribosylation regulates AR through a nuclear pathway mediated by Parp7. We show that Parp7 mono-ADP-ribosylates agonist-bound AR, and that ADP-ribosyl-cysteines within the N-terminal domain mediate recruitment of the E3 ligase Dtx3L/Parp9. Molecular recognition of ADP-ribosyl-cysteine is provided by tandem macrodomains in Parp9, and Dtx3L/Parp9 modulates expression of a subset of AR-regulated genes. Parp7, ADP-ribosylation of AR, and AR-Dtx3L/Parp9 complex assembly are inhibited by Olaparib, a compound used clinically to inhibit poly-ADP-ribosyltransferases Parp1/2. Our study reveals the components of an androgen signaling axis that uses a writer and reader of ADP-ribosylation to regulate protein-protein interactions and AR activity.

A crosslinked and ribosylated actin trimer does not interact productively with myosin

2019 ◽  
Vol 97 (2) ◽  
pp. 140-147 ◽  
Author(s):  
Navneet Sidhu ◽  
John F. Dawson
Keyword(s):  
Binding Site ◽  
Protein Interactions ◽  
Binding Proteins ◽  
Binding Protein ◽  
Dnase I ◽  
Protein Protein Interactions ◽  
Adp Ribosylation ◽  
Myosin Binding ◽  
Pointed End

A purified F-actin-derived actin trimer that interacts with end-binding proteins did not activate or bind the side-binding protein myosin under rigor conditions. Remodeling of the actin trimer by the binding of gelsolin did not rescue myosin binding, nor did the use of different means of inhibiting the polymerization of the trimer. Our results demonstrate that ADP-ribosylation on all actin subunits of an F-actin-derived trimer inhibits myosin binding and that the binding of DNase-I to the pointed end subunits of a crosslinked trimer also remodels the myosin binding site. Taken together, this work highlights the need for a careful balance between modification of actin subunits and maintaining protein–protein interactions to produce a physiologically relevant short F-actin complex.

ADP-ribosylation reactions in Sulfolobus solfataricus, a thermoacidophilic archaeon

1995 ◽  
Vol 1246 (2) ◽  
pp. 151-159 ◽  
Author(s):  
M.Rosaria Faraone-Mennella ◽  
Filomena De Lucia ◽  
Anna De Maio ◽  
Agata Gambacorta ◽  
Piera Quesada ◽  
...  
Keyword(s):  
Sulfolobus Solfataricus ◽  
Adp Ribosylation

Divalent cation and lipid-protein interactions of biomembranes

1993 ◽  
Vol 13 (3) ◽  
pp. 143-157 ◽  
Author(s):  
F. Y. Yang ◽  
Y. G. Huang ◽  
Y. P. Tu
Keyword(s):  
Adenylate Cyclase ◽  
Atpase Activity ◽  
Enzymatic Activity ◽  
Divalent Cation ◽  
Protein Interactions ◽  
Physical State ◽  
Divalent Cations ◽  
Activity Change ◽  
Lipid Protein Interactions

Divalent cations play an important role in the functions of biomembranes. This review deals with three topics: (1) Mg2+-mediated change in physical state of phospholipid induces conformation and activity change of reconstituted mitochondrial H+-ATPase, (2) a proper transmembrane Ca2+ gradient is essential for the higher enzymatic activity of adenylate cyclase, and (3) role of transmembrane Ca2+ gradient in the modulation of reconstituted sarcoplasmic reticulm Ca2+-ATPase activity.

scholarly journals SET7/9-dependent methylation of ARTD1 at K508 stimulates poly-ADP-ribose formation after oxidative stress

Open Biology ◽  
2013 ◽  
Vol 3 (10) ◽  
pp. 120173 ◽  
Author(s):  
Ingrid Kassner ◽  
Anneli Andersson ◽  
Monika Fey ◽  
Martin Tomas ◽  
Elisa Ferrando-May ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Protein Interactions ◽  
Protein Function ◽  
Dependent Manner ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Target Proteins ◽  
Protein Methyltransferase

ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1, formerly PARP1) is localized in the nucleus, where it ADP-ribosylates specific target proteins. The post-translational modification (PTM) with a single ADP-ribose unit or with polymeric ADP-ribose (PAR) chains regulates protein function as well as protein–protein interactions and is implicated in many biological processes and diseases. SET7/9 (Setd7, KMT7) is a protein methyltransferase that catalyses lysine monomethylation of histones, but also methylates many non-histone target proteins such as p53 or DNMT1. Here, we identify ARTD1 as a new SET7/9 target protein that is methylated at K508 in vitro and in vivo . ARTD1 auto-modification inhibits its methylation by SET7/9, while auto-poly-ADP-ribosylation is not impaired by prior methylation of ARTD1. Moreover, ARTD1 methylation by SET7/9 enhances the synthesis of PAR upon oxidative stress in vivo . Furthermore, laser irradiation-induced PAR formation and ARTD1 recruitment to sites of DNA damage in a SET7/9-dependent manner. Together, these results reveal a novel mechanism for the regulation of cellular ARTD1 activity by SET7/9 to assure efficient PAR formation upon cellular stress.

scholarly journals A universal entropy-driven mechanism for thioredoxin–target recognition

2015 ◽  
Vol 112 (26) ◽  
pp. 7960-7965 ◽  
Author(s):  
Prakash B. Palde ◽  
Kate S. Carroll
Keyword(s):  
Protein Interactions ◽  
Redox Regulation ◽  
Noncovalent Interactions ◽  
Target Recognition ◽  
Redox Homeostasis ◽  
Titration Calorimetry ◽  
Conformational Restriction ◽  
Target Proteins ◽  
Thiol Oxidoreductase ◽  
Insight Into

Cysteine residues in cytosolic proteins are maintained in their reduced state, but can undergo oxidation owing to posttranslational modification during redox signaling or under conditions of oxidative stress. In large part, the reduction of oxidized protein cysteines is mediated by a small 12-kDa thiol oxidoreductase, thioredoxin (Trx). Trx provides reducing equivalents for central metabolic enzymes and is implicated in redox regulation of a wide number of target proteins, including transcription factors. Despite its importance in cellular redox homeostasis, the precise mechanism by which Trx recognizes target proteins, especially in the absence of any apparent signature binding sequence or motif, remains unknown. Knowledge of the forces associated with the molecular recognition that governs Trx–protein interactions is fundamental to our understanding of target specificity. To gain insight into Trx–target recognition, we have thermodynamically characterized the noncovalent interactions between Trx and target proteins before S-S reduction using isothermal titration calorimetry (ITC). Our findings indicate that Trx recognizes the oxidized form of its target proteins with exquisite selectivity, compared with their reduced counterparts. Furthermore, we show that recognition is dependent on the conformational restriction inherent to oxidized targets. Significantly, the thermodynamic signatures for multiple Trx targets reveal favorable entropic contributions as the major recognition force dictating these protein–protein interactions. Taken together, our data afford significant new insight into the molecular forces responsible for Trx–target recognition and should aid the design of new strategies for thiol oxidoreductase inhibition.

scholarly journals A novel cochaperonin that modulates the ATPase activity of cytoplasmic chaperonin.

1994 ◽  
Vol 125 (5) ◽  
pp. 989-996 ◽  
Author(s):  
Y Gao ◽  
R Melki ◽  
P D Walden ◽  
S A Lewis ◽  
C Ampe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Atpase Activity ◽  
Beta Tubulin ◽  
Folding Process ◽  
Target Proteins ◽  
Chaperonin Groel ◽  
Significant Homology ◽  
Additional Protein ◽  
Cloned Cdna

The folding of alpha- and beta-tubulin requires three proteins: the heteromeric TCP-1-containing cytoplasmic chaperonin and two additional protein cofactors (A and B). We show that these cofactors participate in the folding process and do not merely trigger release, since in the presence of Mg-ATP alone, alpha- and beta-tubulin target proteins are discharged from cytoplasmic chaperonin in a nonnative form. Like the prokaryotic cochaperonin GroES, which interacts with the prototypical Escherichia coli chaperonin GroEL and regulates its ATPase activity, cofactor A modulates the ATPase activity of its cognate chaperonin. However, the sequence of cofactor A derived from a cloned cDNA defines a 13-kD polypeptide with no significant homology to other known proteins. Moreover, while GroES functions as a heptameric ring, cofactor A behaves as a dimer. Thus, cofactor A is a novel cochaperonin that is structurally unrelated to GroES.

scholarly journals The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division

2017 ◽  
Vol 199 (14) ◽  
Author(s):  
Atsushi Yahashiri ◽  
Matthew A. Jorgenson ◽  
David S. Weiss
Keyword(s):  
Cell Wall ◽  
Cell Division ◽  
Protein Interactions ◽  
Cell Separation ◽  
Protein Protein Interactions ◽  
Target Proteins ◽  
Bacterial Proteins ◽  
Binding Domains ◽  
Division Site ◽  
Daughter Cell Separation

ABSTRACT Sporulation-related repeat (SPOR) domains are small peptidoglycan (PG) binding domains found in thousands of bacterial proteins. The name “SPOR domain” stems from the fact that several early examples came from proteins involved in sporulation, but SPOR domain proteins are quite diverse and contribute to a variety of processes that involve remodeling of the PG sacculus, especially with respect to cell division. SPOR domains target proteins to the division site by binding to regions of PG devoid of stem peptides (“denuded” glycans), which in turn are enriched in septal PG by the intense, localized activity of cell wall amidases involved in daughter cell separation. This targeting mechanism sets SPOR domain proteins apart from most other septal ring proteins, which localize via protein-protein interactions. In addition to SPOR domains, bacteria contain several other PG-binding domains that can exploit features of the cell wall to target proteins to specific subcellular sites.

scholarly journals Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases

2021 ◽  
Vol 17 (11) ◽  
pp. e1009171
Author(s):  
Tunca Doğan ◽  
Ece Akhan Güzelcan ◽  
Marcus Baumann ◽  
Altay Koyas ◽  
Heval Atas ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Domain ◽  
Training Data ◽  
Drug Candidate ◽  
Domain Pair ◽  
Lim Kinase ◽  
Target Proteins ◽  
Data Points ◽  
Drug Compound ◽  
Compound Target

Predictive approaches such as virtual screening have been used in drug discovery with the objective of reducing developmental time and costs. Current machine learning and network-based approaches have issues related to generalization, usability, or model interpretability, especially due to the complexity of target proteins’ structure/function, and bias in system training datasets. Here, we propose a new method “DRUIDom” (DRUg Interacting Domain prediction) to identify bio-interactions between drug candidate compounds and targets by utilizing the domain modularity of proteins, to overcome problems associated with current approaches. DRUIDom is composed of two methodological steps. First, ligands/compounds are statistically mapped to structural domains of their target proteins, with the aim of identifying their interactions. As such, other proteins containing the same mapped domain or domain pair become new candidate targets for the corresponding compounds. Next, a million-scale dataset of small molecule compounds, including those mapped to domains in the previous step, are clustered based on their molecular similarities, and their domain associations are propagated to other compounds within the same clusters. Experimentally verified bioactivity data points, obtained from public databases, are meticulously filtered to construct datasets of active/interacting and inactive/non-interacting drug/compound–target pairs (~2.9M data points), and used as training data for calculating parameters of compound–domain mappings, which led to 27,032 high-confidence associations between 250 domains and 8,165 compounds, and a finalized output of ~5 million new compound–protein interactions. DRUIDom is experimentally validated by syntheses and bioactivity analyses of compounds predicted to target LIM-kinase proteins, which play critical roles in the regulation of cell motility, cell cycle progression, and differentiation through actin filament dynamics. We showed that LIMK-inhibitor-2 and its derivatives significantly block the cancer cell migration through inhibition of LIMK phosphorylation and the downstream protein cofilin. One of the derivative compounds (LIMKi-2d) was identified as a promising candidate due to its action on resistant Mahlavu liver cancer cells. The results demonstrated that DRUIDom can be exploited to identify drug candidate compounds for intended targets and to predict new target proteins based on the defined compound–domain relationships. Datasets, results, and the source code of DRUIDom are fully-available at: https://github.com/cansyl/DRUIDom.

scholarly journals Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces

2020 ◽  
Author(s):  
Chantal Prévost ◽  
Sophie Sacquin-Mora
Keyword(s):  
Protein Interactions ◽  
Protein Interface ◽  
Protein Interfaces ◽  
Reference Protein ◽  
Dynamic Perspective ◽  
Set Up ◽  
The Stability ◽  
Dynamics Simulations ◽  
Dynamic Quality

The modeling of protein assemblies on the atomic level remains a central issue in structural biology, as protein interactions play a key role in numerous cellular processes. This problem is traditionally addressed using docking tools, where the quality of the models that are produced is based on their similarity to a single reference experimental structure. However, this approach using a static reference does not take into account the dynamic quality of the protein interface. Here, we used all-atom classical Molecular Dynamics simulations to investigate the stability of the interface for three complexes that previously served as targets in the CAPRI competition, and for each one of these targets, ten models distributed over the High, Medium and Acceptable categories. To assess the quality of these models from a dynamic perspective, we set up new criteria which take into account the stability of the reference protein interface. We show that, when the protein interfaces are allowed to evolve along time, the original ranking based on the static CAPRI criteria no longer holds as over 50% of the docking models undergo a category change (either toward a better or a lower group) when reassessing their quality using dynamic information.

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