Protein radical labeling, like fast photochemical oxidation of proteins (FPOP), coupled to a top-down mass spectrometry (MS) analysis offers an alternative analytical method for probing protein structure or protein interaction with other biomolecules, for instance, proteins and DNA. However, with the increasing mass of studied analytes, the MS/MS spectra become complex and exhibit a low signal-to-noise ratio. Nevertheless, these difficulties may be overcome by protein isotope depletion. Thus, we aimed to use protein isotope depletion to analyze FPOP-oxidized samples by top-down MS analysis. For this purpose, we prepared isotopically natural (IN) and depleted (ID) forms of the FOXO4 DNA binding domain (FOXO4-DBD) and studied the protein-DNA interaction interface with double-stranded DNA, the insulin response element (IRE), after exposing the complex to hydroxyl radicals. As shown by comparing tandem mass spectra of natural and depleted proteins, the ID form increased the signal-to-noise ratio of useful fragment ions, thereby enhancing the sequence coverage by more than 19%. This improvement in the detection of fragment ions enabled us to detect 22 more oxidized residues in the ID samples than in the IN sample. Moreover, less common modifications were detected in the ID sample, including the formation of ketones and lysine carbonylation. Given the higher quality of ID top-down MSMS data set, these results provide more detailed information on the complex formation between transcription factors and DNA-response elements. Therefore, our study highlights the benefits of isotopic depletion for quantitative top-down proteomics. Data are available via ProteomeXchange with the identifier PXD044447.

• MeSH
• DNA MeSH
• ionty MeSH
• izotopy MeSH
• proteiny * analýza   MeSH
• tandemová hmotnostní spektrometrie * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• ionty MeSH
• izotopy MeSH
• proteiny * MeSH

Transcription factor p53 protects cells against tumorigenesis when subjected to various cellular stresses. Under these conditions, p53 interacts with transcription factor Forkhead box O (FOXO) 4, thereby inducing cellular senescence by upregulating the transcription of senescence-associated protein p21. However, the structural details of this interaction remain unclear. Here, we characterize the interaction between p53 and FOXO4 by NMR, chemical cross-linking, and analytical ultracentrifugation. Our results reveal that the interaction between p53 TAD and the FOXO4 Forkhead domain is essential for the overall stability of the p53:FOXO4 complex. Furthermore, contacts involving the N-terminal segment of FOXO4, the C-terminal negative regulatory domain of p53 and the DNA-binding domains of both proteins stabilize the complex, whose formation blocks p53 binding to DNA but without affecting the DNA-binding properties of FOXO4. Therefore, our structural findings may help to understand the intertwined functions of p53 and FOXO4 in cellular homeostasis, longevity, and stress response.

• Klíčová slova
• DNA binding, Forkhead box O 4, nuclear magnetic resonance, protein-protein interaction, senescence, transcription factor p53,
• MeSH
• DNA chemie   MeSH
• forkhead transkripční faktory * chemie   genetika   metabolismus   MeSH
• nádorový supresorový protein p53 * genetika   metabolismus   MeSH
• proteiny buněčného cyklu metabolismus   MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• forkhead transkripční faktory * MeSH
• nádorový supresorový protein p53 * MeSH
• proteiny buněčného cyklu MeSH

The limited information available on the structure of complexes involving transcription factors and cognate DNA response elements represents a major obstacle in the quest to understand their mechanism of action at the molecular level. We implemented a concerted structural proteomics approach, which combined hydrogen-deuterium exchange (HDX), quantitative protein-protein and protein-nucleic acid cross-linking (XL), and homology analysis, to model the structure of the complex between the full-length DNA binding domain (DBD) of Forkhead box protein O4 (FOXO4) and its DNA binding element (DBE). The results confirmed that FOXO4-DBD assumes the characteristic forkhead topology shared by these types of transcription factors, but its binding mode differs significantly from those of other members of the family. The results showed that the binding interaction stabilized regions that were rather flexible and disordered in the unbound form. Surprisingly, the conformational effects were not limited only to the interface between bound components, but extended also to distal regions that may be essential to recruiting additional factors to the transcription machinery. In addition to providing valuable new insights into the binding mechanism, this project provided an excellent evaluation of the merits of structural proteomics approaches in the investigation of systems that are not directly amenable to traditional high-resolution techniques.

• Klíčová slova
• DNA, FOXO4, cross-linking, molecular modeling, protein, protein-nucleic acid cross-linking, trans-dichlorodiamineplatinum(II), hydrogen-deuterium exchange, transcription factor, transplatin,
• MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• DNA chemie   metabolismus   MeSH
• hmotnostní spektrometrie MeSH
• molekulární struktura MeSH
• responzivní elementy MeSH
• transkripční faktory chemie   metabolismus   MeSH
• vodík-deuteriová výměna MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• DNA MeSH
• transkripční faktory MeSH

Stimulator of interferon genes (STING) binds cyclic dinucleotides (CDNs), which induce a large conformational change of the protein. The structural basis of activation of STING by CDNs is rather well understood. Unliganded STING forms an open dimer that undergoes a large conformational change (∼10 Å) to a closed conformation upon the binding of a CDN molecule. This event activates downstream effectors of STING and subsequently leads to activation of the type 1 interferon response. However, a previously solved structure of STING with 3',3'-c-di-GMP shows Mg atoms mediating the interaction of STING with this CDN. Here, it is shown that no Mg atoms are needed for this interaction; in fact, magnesium can in some cases obstruct the binding of a CDN to STING.

• Klíčová slova
• 3′,3′-c-di-GMP, CDN, STING, cGAS, crystal structure,
• MeSH
• guanosinmonofosfát cyklický chemie   metabolismus   MeSH
• hořčík metabolismus   MeSH
• krystalografie rentgenová MeSH
• membránové proteiny chemie   genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• guanosinmonofosfát cyklický MeSH
• hořčík MeSH
• membránové proteiny MeSH
• STING1 protein, human MeSH Prohlížeč

FOXO transcription factors regulate cellular homeostasis, longevity and response to stress. FOXO1 (also known as FKHR) is a key regulator of hepatic glucose production and lipid metabolism, and its specific inhibition may have beneficial effects on diabetic hyperglycemia by reducing hepatic glucose production. Moreover, all FOXO proteins are considered potential drug targets for drug resistance prevention in cancer therapy. However, the development of specific FOXO inhibitors requires a detailed understanding of structural differences between individual FOXO DNA-binding domains. The high-resolution structure of the DNA-binding domain of FOXO1 reported in this study and its comparison with structures of other FOXO proteins revealed differences in both their conformation and flexibility. These differences are encoded by variations in protein sequences and account for the distinct functions of FOXO proteins. In particular, the positions of the helices H1, H2 and H3, whose interface form the hydrophobic core of the Forkhead domain, and the interactions between hydrophobic residues located on the interface between the N-terminal segment, the H2-H3 loop, and the recognition helix H3 differ among apo FOXO1, FOXO3 and FOXO4 proteins. Therefore, the availability of apo structures of DNA-binding domains of all three major FOXO proteins will support the development of FOXO-type-specific inhibitors.

• Klíčová slova
• DNA-binding domain, FOXO1, Forkhead domain, nuclear magnetic resonance, structure,
• MeSH
• forkhead box protein O1 chemie   genetika   metabolismus   MeSH
• forkhead transkripční faktory chemie   genetika   metabolismus   MeSH
• hydrofobní a hydrofilní interakce MeSH
• lidé MeSH
• magnetická rezonanční spektroskopie MeSH
• molekulární modely MeSH
• myši MeSH
• protein FOXO3 chemie   genetika   metabolismus   MeSH
• proteinové domény MeSH
• sekundární struktura proteinů MeSH
• sekvenční analýza proteinů MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• forkhead box protein O1 MeSH
• forkhead transkripční faktory MeSH
• protein FOXO3 MeSH

Phosphatidylinositol 4-kinase IIIβ (PI4KB) is a key enzyme of the Golgi system because it produces its lipid hallmark - the phosphatidylinositol 4-phosphate (PI4P). It is recruited to Golgi by the Golgi resident ACBD3 protein, regulated by 14-3-3 proteins and it also serves as an adaptor because it recruits the small GTPase Rab11. Here, we analyzed the protein complexes formed by PI4KB in vitro using small angle x-ray scattering (SAXS) and we discovered that these protein complexes are highly flexible. The 14-3-3:PI4KB:Rab11 protein complex has 2:1:1 stoichiometry and its different conformations are rather compact, however, the ACBD3:PI4KB protein complex has both, very compact and very extended conformations. Furthermore, in vitro reconstitution revealed that the membrane is necessary for the formation of ACBD3:PI4KB:Rab11 protein complex at physiological (nanomolar) concentrations.

• MeSH
• adaptorové proteiny signální transdukční metabolismus   MeSH
• fosfotransferasy s alkoholovou skupinou jako akceptorem metabolismus   MeSH
• intracelulární membrány metabolismus   MeSH
• maloúhlový rozptyl MeSH
• membránové proteiny metabolismus   MeSH
• multimerizace proteinu * MeSH
• proteiny 14-3-3 metabolismus   MeSH
• Rab proteiny vázající GTP metabolismus   MeSH
• rekombinantní proteiny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ACBD3 protein, human MeSH Prohlížeč
• adaptorové proteiny signální transdukční MeSH
• fosfotransferasy s alkoholovou skupinou jako akceptorem MeSH
• membránové proteiny MeSH
• phosphatidylinositol 4-kinase IIIbeta, human MeSH Prohlížeč
• proteiny 14-3-3 MeSH
• Rab proteiny vázající GTP MeSH
• rab11 protein MeSH Prohlížeč
• rekombinantní proteiny MeSH

NExo is an enzyme from Neisseria meningitidis that is specialized in the removal of the 3'-phosphate and other 3'-lesions, which are potential blocks for DNA repair. NExo is a highly active DNA 3'-phosphatase, and although it is from the class II AP family it lacks AP endonuclease activity. In contrast, the NExo homologue NApe, lacks 3'-phosphatase activity but is an efficient AP endonuclease. These enzymes act together to protect the meningococcus from DNA damage arising mainly from oxidative stress and spontaneous base loss. In this work, we present crystal structures of the specialized 3'-phosphatase NExo bound to DNA in the presence and absence of a 3'-phosphate lesion. We have outlined the reaction mechanism of NExo, and using point mutations we bring mechanistic insights into the specificity of the 3'-phosphatase activity of NExo. Our data provide further insight into the molecular origins of plasticity in substrate recognition for this class of enzymes. From this we hypothesize that these specialized enzymes lead to enhanced efficiency and accuracy of DNA repair and that this is important for the biological niche occupied by this bacterium.

• MeSH
• bakteriální proteiny chemie   MeSH
• DNA vazebné proteiny chemie   MeSH
• DNA-lyasa (apurinová nebo apyrimidinová) chemie   MeSH
• DNA chemie   MeSH
• endonukleasy metabolismus   MeSH
• exodeoxyribonukleasy chemie   MeSH
• katalytická doména MeSH
• konformace proteinů MeSH
• krystalografie rentgenová MeSH
• mutace MeSH
• mutageneze cílená MeSH
• Neisseria meningitidis enzymologie   genetika   MeSH
• oprava DNA * MeSH
• oxidační stres MeSH
• poškození DNA MeSH
• substrátová specifita MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• DNA vazebné proteiny MeSH
• DNA-lyasa (apurinová nebo apyrimidinová) MeSH
• DNA MeSH
• endonukleasy MeSH
• exodeoxyribonukleasy MeSH

14-3-3 proteins bind phosphorylated binding partners to regulate several of their properties, including enzymatic activity, stability and subcellular localization. Here, two crystal structures are presented: the crystal structures of the 14-3-3 protein (also known as Bmh1) from the yeast Lachancea thermotolerans in the unliganded form and bound to a phosphopeptide derived from human PI4KB (phosphatidylinositol 4-kinase B). The structures demonstrate the high evolutionary conservation of ligand recognition by 14-3-3 proteins. The structural analysis suggests that ligand recognition by 14-3-3 proteins evolved very early in the evolution of eukaryotes and remained conserved, underlying the importance of 14-3-3 proteins in physiology.

• Klíčová slova
• 14-3-3 proteins, Bmh1, Bmh2, Lachancea thermotolerans, PI4KB, crystal structure, phosphopeptide,
• MeSH
• 1-fosfatidylinositol-4-kinasa chemie   genetika   metabolismus   MeSH
• Escherichia coli genetika   metabolismus   MeSH
• exprese genu MeSH
• fosfoproteiny chemie   genetika   metabolismus   MeSH
• fungální proteiny chemie   genetika   metabolismus   MeSH
• klonování DNA MeSH
• konformace proteinů, alfa-helix MeSH
• konzervovaná sekvence MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• ligandy MeSH
• molekulární evoluce MeSH
• molekulární modely MeSH
• plazmidy chemie   metabolismus   MeSH
• protein - isoformy chemie   genetika   metabolismus   MeSH
• proteiny 14-3-3 chemie   genetika   metabolismus   MeSH
• rekombinantní proteiny chemie   genetika   metabolismus   MeSH
• Saccharomycetales chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• strukturní homologie proteinů MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 1-fosfatidylinositol-4-kinasa MeSH
• fosfoproteiny MeSH
• fungální proteiny MeSH
• ligandy MeSH
• protein - isoformy MeSH
• proteiny 14-3-3 MeSH
• rekombinantní proteiny MeSH

Phosphatidylinositol 4-kinase beta (PI4KB) is one of four human PI4K enzymes that generate phosphatidylinositol 4-phosphate (PI4P), a minor but essential regulatory lipid found in all eukaryotic cells. To convert their lipid substrates, PI4Ks must be recruited to the correct membrane compartment. PI4KB is critical for the maintenance of the Golgi and trans Golgi network (TGN) PI4P pools, however, the actual targeting mechanism of PI4KB to the Golgi and TGN membranes is unknown. Here, we present an NMR structure of the complex of PI4KB and its interacting partner, Golgi adaptor protein acyl-coenzyme A binding domain containing protein 3 (ACBD3). We show that ACBD3 is capable of recruiting PI4KB to membranes both in vitro and in vivo, and that membrane recruitment of PI4KB by ACBD3 increases its enzymatic activity and that the ACBD3:PI4KB complex formation is essential for proper function of the Golgi.

• MeSH
• adaptorové proteiny signální transdukční chemie   metabolismus   MeSH
• buněčná membrána metabolismus   MeSH
• Cercopithecus aethiops MeSH
• COS buňky MeSH
• fosfatidylinositolfosfáty metabolismus   MeSH
• fosfotransferasy s alkoholovou skupinou jako akceptorem chemie   metabolismus   MeSH
• Golgiho aparát metabolismus   MeSH
• lidé MeSH
• membránové proteiny chemie   metabolismus   MeSH
• molekulární modely MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• sekundární struktura proteinů MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Intramural MeSH
• Názvy látek
• ACBD3 protein, human MeSH Prohlížeč
• adaptorové proteiny signální transdukční MeSH
• fosfatidylinositolfosfáty MeSH
• fosfotransferasy s alkoholovou skupinou jako akceptorem MeSH
• membránové proteiny MeSH
• phosphatidylinositol 4-kinase IIIbeta, human MeSH Prohlížeč
• phosphatidylinositol 4-phosphate MeSH Prohlížeč

Phosphoinositides are a class of phospholipids generated by the action of phosphoinositide kinases with key regulatory functions in eukaryotic cells. Here, we present the atomic structure of phosphatidylinositol 4-kinase type IIα (PI4K IIα), in complex with ATP solved by X-ray crystallography at 2.8 Å resolution. The structure revealed a non-typical kinase fold that could be divided into N- and C-lobes with the ATP binding groove located in between. Surprisingly, a second ATP was found in a lateral hydrophobic pocket of the C-lobe. Molecular simulations and mutagenesis analysis revealed the membrane binding mode and the putative function of the hydrophobic pocket. Taken together, our results suggest a mechanism of PI4K IIα recruitment, regulation, and function at the membrane.

• Klíčová slova
• Monte Carlo simulations, crystal structure, kinase, membrane, phosphatidyl inositol,
• MeSH
• fosfatidylinositoly chemie   metabolismus   MeSH
• fosfotransferasy s alkoholovou skupinou jako akceptorem chemie   metabolismus   ultrastruktura   MeSH
• inositol chemie   MeSH
• konformace proteinů * MeSH
• krystalografie rentgenová * MeSH
• lidé MeSH
• membrány chemie   MeSH
• metoda Monte Carlo MeSH
• signální transdukce MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vedlejší histokompatibilní antigeny MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fosfatidylinositoly MeSH
• fosfotransferasy s alkoholovou skupinou jako akceptorem MeSH
• inositol MeSH
• phosphatidylinositol phosphate 4-kinase MeSH Prohlížeč
• vedlejší histokompatibilní antigeny MeSH