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1.
J Am Soc Mass Spectrom ; 35(7): 1394-1402, 2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38905538

RESUMO

Mass-spectrometry based assays in structural biology studies measure either intact or digested proteins. Typically, different mass spectrometers are dedicated for such measurements: those optimized for rapid analysis of peptides or those designed for high molecular weight analysis. A commercial trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) platform is widely utilized for proteomics and metabolomics, with ion mobility providing a separation dimension in addition to liquid chromatography. The ability to perform high-quality native mass spectrometry of protein complexes, however, remains largely uninvestigated. Here, we evaluate a commercial TIMS-Q-TOF platform for analyzing noncovalent protein complexes by utilizing the instrument's full range of ion mobility, MS, and MS/MS (both in-source activation and collision cell CID) capabilities. The TIMS analyzer is able to be tuned gently to yield collision cross sections of native-like complexes comparable to those previously reported on various instrument platforms. In-source activation and collision cell CID were robust for both small and large complexes. TIMS-CID was performed on protein complexes streptavidin (53 kDa), avidin (68 kDa), and cholera toxin B (CTB, 58 kDa). Complexes pyruvate kinase (237 kDa) and GroEL (801 kDa) were beyond the trapping capabilities of the commercial TIMS analyzer, but TOF mass spectra could be acquired. The presented results indicate that the commercial TIMS-Q-TOF platform can be used for both omics and native mass spectrometry applications; however, modifications to the commercial RF drivers for both the TIMS analyzer and quadrupole (currently limited to m/z 3000) are necessary to mobility analyze protein complexes greater than about 60 kDa.


Assuntos
Espectrometria de Mobilidade Iônica , Espectrometria de Mobilidade Iônica/métodos , Espectrometria de Massas em Tandem/métodos , Proteômica/métodos , Piruvato Quinase/química , Piruvato Quinase/análise , Estreptavidina/química , Estreptavidina/análise , Toxina da Cólera/análise , Toxina da Cólera/química , Avidina/química , Avidina/análise , Proteínas/análise , Proteínas/química
2.
Protein Sci ; 33(7): e5075, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38895978

RESUMO

Rheostat positions, which can be substituted with various amino acids to tune protein function across a range of outcomes, are a developing area for advancing personalized medicine and bioengineering. Current methods cannot accurately predict which proteins contain rheostat positions or their substitution outcomes. To compare the prevalence of rheostat positions in homologs, we previously investigated their occurrence in two pyruvate kinase (PYK) isozymes. Human liver PYK contained numerous rheostat positions that tuned the apparent affinity for the substrate phosphoenolpyruvate (Kapp-PEP) across a wide range. In contrast, no functional rheostat positions were identified in Zymomonas mobilis PYK (ZmPYK). Further, the set of ZmPYK substitutions included an unusually large number that lacked measurable activity. We hypothesized that the inactive substitution variants had reduced protein stability, precluding detection of Kapp-PEP tuning. Using modified buffers, robust enzymatic activity was obtained for 19 previously-inactive ZmPYK substitution variants at three positions. Surprisingly, both previously-inactive and previously-active substitution variants all had Kapp-PEP values close to wild-type. Thus, none of the three positions were functional rheostat positions, and, unlike human liver PYK, ZmPYK's Kapp-PEP remained poorly tunable by single substitutions. To directly assess effects on stability, we performed thermal denaturation experiments for all ZmPYK substitution variants. Many diminished stability, two enhanced stability, and the three positions showed different thermal sensitivity to substitution, with one position acting as a "stability rheostat." The differences between the two PYK homologs raises interesting questions about the underlying mechanism(s) that permit functional tuning by single substitutions in some proteins but not in others.


Assuntos
Piruvato Quinase , Zymomonas , Humanos , Zymomonas/enzimologia , Zymomonas/genética , Zymomonas/química , Zymomonas/metabolismo , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Piruvato Quinase/genética , Substituição de Aminoácidos , Estabilidade Proteica , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Estabilidade Enzimática , Fígado/enzimologia , Fígado/metabolismo , Fígado/química , Fosfoenolpiruvato/metabolismo , Fosfoenolpiruvato/química
3.
J Biosci Bioeng ; 138(1): 29-35, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38719683

RESUMO

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. Considering the onsite use of RPA reagents, lyophilized RPA reagents with long storage stability are highly desired. In this study, as one of the approaches to solve this problem, we attempted to use a thermostable pyruvate kinase (PK). PK gene was isolated from a thermophilic bacterium Thermotoga maritima (Tma-PK). Tma-PK was expressed in Escherichia coli and purified from the cells. Tma-PK exhibited higher thermostability than human PK. The purified Tma-PK preparation was applied to RPA as an ATP-regenerating enzyme. Liquid RPA reagent with Tma-PK exhibited the same performance as that with human PK. Lyophilized RPA reagent with Tma-PK exhibited higher performance than that with human PK. Combined with our previous results of RPA reagents of thermostable Pol from a thermophilic bacterium, Aeribacillus pallidus, the results in this study suggest that thermostable enzymes are preferable to mesophilic ones as a component in lyophilized RPA reagents.


Assuntos
Estabilidade Enzimática , Liofilização , Técnicas de Amplificação de Ácido Nucleico , Piruvato Quinase , Thermotoga maritima , Thermotoga maritima/enzimologia , Thermotoga maritima/genética , Piruvato Quinase/metabolismo , Piruvato Quinase/genética , Piruvato Quinase/química , Técnicas de Amplificação de Ácido Nucleico/métodos , Humanos , Recombinases/metabolismo , Recombinases/química , Recombinases/genética , Escherichia coli/genética , Escherichia coli/metabolismo , DNA Polimerase Dirigida por DNA/metabolismo , DNA Polimerase Dirigida por DNA/química , DNA Polimerase Dirigida por DNA/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química
4.
Cell Rep Methods ; 4(5): 100764, 2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38714198

RESUMO

Co-assembling enzymes with nanoparticles (NPs) into nanoclusters allows them to access channeling, a highly efficient form of multienzyme catalysis. Using pyruvate kinase (PykA) and lactate dehydrogenase (LDH) to convert phosphoenolpyruvic acid to lactic acid with semiconductor quantum dots (QDs) confirms how enzyme cluster formation dictates the rate of coupled catalytic flux (kflux) across a series of differentially sized/shaped QDs and 2D nanoplatelets (NPLs). Enzyme kinetics and coupled flux were used to demonstrate that by mixing different NP systems into clusters, a >10× improvement in kflux is observed relative to free enzymes, which is also ≥2× greater than enhancement on individual NPs. Cluster formation was characterized with gel electrophoresis and transmission electron microscopy (TEM) imaging. The generalizability of this mixed-NP approach to improving flux is confirmed by application to a seven-enzyme system. This represents a powerful approach for accessing channeling with almost any choice of enzymes constituting a multienzyme cascade.


Assuntos
L-Lactato Desidrogenase , Ácido Láctico , Nanopartículas , Fosfoenolpiruvato , Piruvato Quinase , L-Lactato Desidrogenase/metabolismo , L-Lactato Desidrogenase/química , Ácido Láctico/metabolismo , Ácido Láctico/química , Piruvato Quinase/metabolismo , Piruvato Quinase/química , Nanopartículas/química , Fosfoenolpiruvato/metabolismo , Pontos Quânticos/química , Cinética
5.
J Agric Food Chem ; 72(20): 11724-11732, 2024 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-38718268

RESUMO

Protein post-translational modifications (PTMs) play an essential role in meat quality development. However, the effect of specific PTM sites on meat proteins has not been investigated yet. The characteristics of pyruvate kinase M (PKM) were found to exhibit a close correlation with final meat quality, and thus, serine 99 (S99) and lysine 137 (K137) in PKM were mutated to study their effect on PKM function. The structural and functional properties of five lamb PKM variants, including wild-type PKM (wtPKM), PKM_S99D (S99 phosphorylation), PKM_S99A (PKM S99 dephosphorylation), PKM_K137Q (PKM K137 acetylation), and PKM_K137R (PKM K137 deacetylation), were evaluated. The results showed that the secondary structure, tertiary structure, and polymer formation were affected among different PKM variants. In addition, the glycolytic activity of PKM_K137Q was decreased because of its weakened binding with phosphoenolpyruvate. In the PKM_K137R variant, the actin phosphorylation level exhibited a decrease, suggesting a low kinase activity of PKM_K137R. The results of molecular simulation showed a 42% reduction in the interface area between PKM_K137R and actin, in contrast to wtPKM and actin. These findings are significant for revealing the mechanism of how PTMs regulate PKM function and provide a theoretical foundation for the development of precise meat quality preservation technology.


Assuntos
Glicólise , Piruvato Quinase , Piruvato Quinase/metabolismo , Piruvato Quinase/genética , Piruvato Quinase/química , Fosforilação , Animais , Acetilação , Ovinos , Processamento de Proteína Pós-Traducional , Proteínas Quinases/metabolismo , Proteínas Quinases/genética , Proteínas Quinases/química , Carne/análise
6.
J Physiol Biochem ; 80(2): 261-275, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38329688

RESUMO

Pyruvate kinase M2 (PKM2), a subtype of pyruvate kinase (PK), has been shown to play an important role in the development of cancer. It regulates the last step of glycolytic pathway. PKM2 has both pyruvate kinase and protein kinase activity, and the conversion of these two functions of PKM2 depends on the mutual change of dimer and tetramer. The dimerization of PKM2 can promote the proliferation and growth of tumor cells, so inhibiting the dimerization of PKM2 is essential to curing cancer. The aggregation of PKM2 is regulated by both endogenous and exogenous cofactors as well as post-translational modification (PTM). Although there are many studies on the different aggregation of PKM2 in the process of tumor development, there are few summaries in recent years. In this review, we first introduce the role of PKM2 in various biological processes of tumor growth. Then, we summarize the aggregation regulation mechanism of PKM2 by various endogenous cofactors such as Fructose-1, 6-diphosphate (FBP), various amino acids, and post-translational modification (PTMs). Finally, the related inhibitors and agonists of PKM2 are summarized to provide reference for regulating PKM2 aggregation in the treatment of cancer in the future.


Assuntos
Proteínas de Transporte , Proteínas de Membrana , Neoplasias , Processamento de Proteína Pós-Traducional , Proteínas de Ligação a Hormônio da Tireoide , Hormônios Tireóideos , Humanos , Neoplasias/metabolismo , Neoplasias/patologia , Neoplasias/genética , Neoplasias/enzimologia , Hormônios Tireóideos/metabolismo , Proteínas de Transporte/metabolismo , Proteínas de Transporte/genética , Proteínas de Membrana/metabolismo , Proteínas de Membrana/genética , Animais , Progressão da Doença , Proliferação de Células , Multimerização Proteica , Piruvato Quinase/metabolismo , Piruvato Quinase/genética , Piruvato Quinase/química
7.
J Virol ; 98(3): e0175123, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38319105

RESUMO

Viruses exploit the host cell's energy metabolism system to support their replication. Mitochondria, known as the powerhouse of the cell, play a critical role in regulating cell survival and virus replication. Our prior research indicated that the classical swine fever virus (CSFV) alters mitochondrial dynamics and triggers glycolytic metabolic reprogramming. However, the role and mechanism of PKM2, a key regulatory enzyme of glycolytic metabolism, in CSFV replication remain unclear. In this study, we discovered that CSFV enhances PKM2 expression and utilizes PKM2 to inhibit pyruvate production. Using an affinity purification coupled mass spectrometry system, we successfully identified PKM as a novel interaction partner of the CSFV non-structural protein NS4A. Furthermore, we validated the interaction between PKM2 and both CSFV NS4A and NS5A through co-immunoprecipitation and confocal analysis. PKM2 was found to promote the expression of both NS4A and NS5A. Moreover, we observed that PKM2 induces mitophagy by activating the AMPK-mTOR signaling pathway, thereby facilitating CSFV proliferation. In summary, our data reveal a novel mechanism whereby PKM2, a metabolic enzyme, promotes CSFV proliferation by inducing mitophagy. These findings offer a new avenue for developing antiviral strategies. IMPORTANCE: Viruses rely on the host cell's material-energy metabolic system for replication, inducing host metabolic disorders and subsequent immunosuppression-a major contributor to persistent viral infections. Classical swine fever virus (CSFV) is no exception. Classical swine fever is a severe acute infectious disease caused by CSFV, resulting in significant economic losses to the global pig industry. While the role of the metabolic enzyme PKM2 (pyruvate dehydrogenase) in the glycolytic pathway of tumor cells has been extensively studied, its involvement in viral infection remains relatively unknown. Our data unveil a new mechanism by which the metabolic enzyme PKM2 mediates CSFV infection, offering novel avenues for the development of antiviral strategies.


Assuntos
Proteínas Quinases Ativadas por AMP , Vírus da Febre Suína Clássica , Mitofagia , Piruvato Quinase , Serina-Treonina Quinases TOR , Proteínas não Estruturais Virais , Replicação Viral , Animais , Proteínas Quinases Ativadas por AMP/metabolismo , Antivirais , Peste Suína Clássica/metabolismo , Peste Suína Clássica/virologia , Vírus da Febre Suína Clássica/crescimento & desenvolvimento , Vírus da Febre Suína Clássica/fisiologia , Desenho de Fármacos , Glicólise , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Piruvatos/metabolismo , Transdução de Sinais , Suínos/metabolismo , Suínos/virologia , Serina-Treonina Quinases TOR/metabolismo , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo
8.
Database (Oxford) ; 20232023 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-37171062

RESUMO

Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.


Assuntos
Isoenzimas , Piruvato Quinase , Humanos , Piruvato Quinase/genética , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Isoenzimas/metabolismo , Ligantes , Proteínas/química , Regulação Alostérica , Biologia Computacional
9.
PLoS One ; 18(3): e0282508, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36897854

RESUMO

PKM2 is a rate-limiting enzyme in the glycolytic process and is involved in regulating tumor proliferation. Several amino acids (AAs) such as Asn, Asp, Val, and Cys have been shown to bind to the AA binding pocket of PKM2 and modulate its oligomeric state, substrate binding affinity, and activity. Although previous studies have attributed that the main chain and side chain of bound AAs are responsible for initiating signal to regulate PKM2, the signal transduction pathway remains elusive. To identify the residues involved in signal transfer process, N70 and N75 located at two ends of a ß strand connecting the active site and AA binding pocket were altered. Biochemical studies of these variants with various AA ligands (Asn, Asp, Val, and Cys), illustrate that N70 and N75, along with ß1 connecting these residues are part of the signal transduction pathway between the AA binding pocket and the active site. The results demonstrate that mutation of N70 to D prevents the transfer of the inhibitory signal mediated by Val and Cys, whereas N75 to L alteration blocks the activating signal initiated by Asn and Asp. Taken together, this study confirms that N70 is one of the residues responsible for transmitting the inhibitory signal and N75 is involved in the activation signal flow.


Assuntos
Piruvato Quinase , Aminoácidos/metabolismo , Domínio Catalítico , Isoformas de Proteínas/metabolismo , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Humanos , Transdução de Sinais , Proteínas de Ligação a Hormônio da Tireoide
10.
Curr Drug Targets ; 24(6): 464-483, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36998144

RESUMO

Pyruvate kinase M2 (PKM2) has surfaced as a potential target for anti-cancer therapy. PKM2 is known to be overexpressed in the tumor cells and is a critical metabolic conduit in supplying the augmented bioenergetic demands of the recalcitrant cancer cells. The presence of PKM2 in structurally diverse tetrameric as well as dimeric forms has opened new avenues to design novel modulators. It is also a truism to state that drug discovery has advanced significantly from various computational techniques like molecular docking, virtual screening, molecular dynamics, and pharmacophore mapping. The present review focuses on the role of computational tools in exploring novel modulators of PKM2. The structural features of various isoforms of PKM2 have been discussed along with reported modulators. An extensive analysis of the structure-based and ligand- based in silico methods aimed at PKM2 modulation has been conducted with an in-depth review of the literature. The role of advanced tools like QSAR and quantum mechanics has been established with a brief discussion of future perspectives.


Assuntos
Simulação de Dinâmica Molecular , Piruvato Quinase , Humanos , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Simulação de Acoplamento Molecular , Descoberta de Drogas/métodos , Metabolismo Energético
11.
Chembiochem ; 24(1): e202200339, 2023 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-36250581

RESUMO

Enzymes are effective biological catalysts that accelerate almost all metabolic reactions in living organisms. Synthetic modulators of enzymes are useful tools for the study of enzymatic reactions and can provide starting points for the design of new drugs. Here, we report on the discovery of a class of biologically active compounds that covalently modifies lysine residues in human liver pyruvate kinase (PKL), leading to allosteric activation of the enzyme (EC50 =0.29 µM). Surprisingly, the allosteric activation control point resides on the lysine residue K282 present in the catalytic site of PKL. These findings were confirmed by structural data, MS/MS experiments, and molecular modelling studies. Altogether, our study provides a molecular basis for the activation mechanism and establishes a framework for further development of human liver pyruvate kinase covalent activators.


Assuntos
Lisina , Piruvato Quinase , Humanos , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Espectrometria de Massas em Tandem , Fígado , Domínio Catalítico , Regulação Alostérica
12.
Molecules ; 27(20)2022 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-36296707

RESUMO

The reliance of tumor cells on aerobic glycolysis is one of the emerging hallmarks of cancer. Pyruvate kinase M2 (PKM2), an important enzyme of glycolytic pathway, is highly expressed in a number of cancer cells. Tumor cells heavily depend on PKM2 to fulfill their divergent energetic and biosynthetic requirements, suggesting it as novel drug target for cancer therapies. Based on this context, we performed enzymatic-assay-based screening of the in-house phenolic compounds library for the identification of PKM2 inhibitors. This screening identified silibinin, curcumin, resveratrol, and ellagic acid as potential inhibitors of PKM2 with IC50 values of 0.91 µM, 1.12 µM, 3.07 µM, and 4.20 µM respectively. For the determination of Ki constants and the inhibition type of hit compounds, Lineweaver-Burk graphs were plotted. Silibinin and ellagic acid performed the competitive inhibition of PKM2 with Ki constants of 0.61 µM and 5.06 µM, while curcumin and resveratrol were identified as non-competitive inhibitors of PKM2 with Ki constants of 1.20 µM and 7.34 µM. The in silico screening of phenolic compounds against three binding sites of PKM2 provided insight into the binding pattern and functionally important amino residues of PKM2. Further, the evaluation of cytotoxicity via MTT assay demonstrated ellagic acid as potent inhibitor of cancer cell growth (IC50 = 20 µM). These results present ellagic acid, silibinin, curcumin, and resveratrol as inhibitors of PKM2 to interrogate metabolic reprogramming in cancer cells. This study has also provided the foundation for further research to validate the potential of identified bioactive entities for PKM2 targeted-cancer therapies.


Assuntos
Curcumina , Leucemia Mieloide Aguda , Humanos , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Curcumina/farmacologia , Resveratrol/farmacologia , Ácido Elágico , Silibina , Glicólise , Linhagem Celular Tumoral
13.
Protein Sci ; 31(7): e4336, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35762709

RESUMO

Various protein properties are often illuminated using sequence comparisons of protein homologs. For example, in analyses of the pyruvate kinase multiple sequence alignment, the set of positions that changed during speciation ("phylogenetic" positions) were enriched for "rheostat" positions in human liver pyruvate kinase (hLPYK). (Rheostat positions are those which, when substituted with various amino acids, yield a range of functional outcomes). However, the correlation was moderate, which could result from multiple biophysical constraints acting on the same position during evolution and/or various sources of noise. To further examine this correlation, we here tested Zymomonas mobilis PYK (ZmPYK), which has <65% sequence identity to any other PYK sequence. Twenty-six ZmPYK positions were selected based on their phylogenetic scores, substituted with multiple amino acids, and assessed for changes in Kapp-PEP . Although we expected to identify multiple, strong rheostat positions, only one moderate rheostat position was detected. Instead, nearly half of the 271 ZmPYK variants were inactive and most others showed near wild-type function. Indeed, for the active ZmPYK variants, the total range of Kapp,PEP values ("tunability") was 40-fold less than that observed for hLPYK variants. The combined functional studies and sequence comparisons suggest that ZmPYK has evolved functional and/or structural attributes that differ from the rest of the family. We hypothesize that including such "orphan" sequences in MSA analyses obscures the correlations used to predict rheostat positions. Finally, results raise the intriguing biophysical question as to how the same protein fold can support rheostat positions in one homolog but not another.


Assuntos
Piruvato Quinase , Zymomonas , Aminoácidos , Humanos , Proteínas/química , Piruvato Quinase/química , Zymomonas/genética , Zymomonas/metabolismo
14.
Org Biomol Chem ; 20(9): 1869-1873, 2022 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-35156979

RESUMO

A biocatalytic cascade based on concerted operation of pyruvate kinase and luciferase with a bioluminescent output was switched reversibly between low and high activity by applying an external magnetic field at different positions or removing it. The enzymes participating in the reaction cascade were bound to magnetic nanoparticles to allow their translocation or aggregation/dispersion to be controlled by the magnetic field. The reaction intensity, measured as the bioluminescent output, was dependent on the effective distances between the enzymes transported on the magnetic nanoparticles controlled by the magnets.


Assuntos
Fluorescência , Luciferases/metabolismo , Nanopartículas de Magnetita/química , Piruvato Quinase/metabolismo , Aliivibrio fischeri/enzimologia , Animais , Biocatálise , Luciferases/química , Medições Luminescentes , Campos Magnéticos , Piruvato Quinase/química , Coelhos
15.
Nat Cell Biol ; 23(10): 1085-1094, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34616026

RESUMO

Cells respond to stress by blocking translation, rewiring metabolism and forming transient messenger ribonucleoprotein assemblies called stress granules (SGs). After stress release, re-establishing homeostasis and disassembling SGs requires ATP-consuming processes. However, the molecular mechanisms whereby cells restore ATP production and disassemble SGs after stress remain poorly understood. Here we show that upon stress, the ATP-producing enzyme Cdc19 forms inactive amyloids, and that their rapid re-solubilization is essential to restore ATP production and disassemble SGs in glucose-containing media. Cdc19 re-solubilization is initiated by the glycolytic metabolite fructose-1,6-bisphosphate, which directly binds Cdc19 amyloids, allowing Hsp104 and Ssa2 chaperone recruitment and aggregate re-solubilization. Fructose-1,6-bisphosphate then promotes Cdc19 tetramerization, which boosts its activity to further enhance ATP production and SG disassembly. Together, these results describe a molecular mechanism that is critical for stress recovery and directly couples cellular metabolism with SG dynamics via the regulation of reversible Cdc19 amyloids.


Assuntos
Amiloide/química , Proteínas de Ciclo Celular/química , Grânulos Citoplasmáticos/química , Piruvato Quinase/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Estresse Fisiológico , Trifosfato de Adenosina/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Frutosedifosfatos/metabolismo , Proteínas de Choque Térmico HSP70/genética , Proteínas de Choque Térmico HSP70/metabolismo , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/metabolismo , Piruvato Quinase/química , Piruvato Quinase/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética
16.
Appl Biochem Biotechnol ; 193(11): 3651-3671, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34347252

RESUMO

Finding reliable cheap sources for producing chemicals and materials is always challenging. During recent decades, photosynthetic organisms such as cyanobacteria, which used CO2 as a carbon source for making products, have attracted a great deal of attention. Among cyanobacteria, Synechocystis sp. PCC 6803 has been considered as a model strain and has some desirable features that make it suitable for use as an industrial strain. Pyruvate kinase (PK) catalyzes the transformation of phosphoenolpyruvate (PEP) to pyruvate in the last step of glycolysis that is an essential enzyme to produce adenosine triphosphate (ATP) in all organisms. Therefore, it plays a critical role in regulating cell metabolism. However, active and allosteric sites of PK and allosteric mechanisms governing PK activity are poorly understood in many bacteria. This study was aimed to provide more insight into PKs of Synechocystis sp. PCC 6803, using in silico methods. The results indicated that predicted structures of PKs from Synechocystis sp. PCC 6803 are reliable and can be considered for further studies. Molecular docking studies suggested that for predicted structures of sll0587 and sll1275, respectively, there are three and two possible active or allosteric sites. Furthermore, molecular interaction analysis of modeled structures proposes that sll0587 is strongly inhibited by ATP and when ATP concentration is low, this isoenzyme is active.


Assuntos
Trifosfato de Adenosina/química , Proteínas de Bactérias/química , Simulação por Computador , Piruvato Quinase/química , Synechocystis/enzimologia , Especificidade por Substrato
17.
Protein Sci ; 30(9): 1833-1853, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34076313

RESUMO

When amino acids vary during evolution, the outcome can be functionally neutral or biologically-important. We previously found that substituting a subset of nonconserved positions, "rheostat" positions, can have surprising effects on protein function. Since changes at rheostat positions can facilitate functional evolution or cause disease, more examples are needed to understand their unique biophysical characteristics. Here, we explored whether "phylogenetic" patterns of change in multiple sequence alignments (such as positions with subfamily specific conservation) predict the locations of functional rheostat positions. To that end, we experimentally tested eight phylogenetic positions in human liver pyruvate kinase (hLPYK), using 10-15 substitutions per position and biochemical assays that yielded five functional parameters. Five positions were strongly rheostatic and three were non-neutral. To test the corollary that positions with low phylogenetic scores were not rheostat positions, we combined these phylogenetic positions with previously-identified hLPYK rheostat, "toggle" (most substitution abolished function), and "neutral" (all substitutions were like wild-type) positions. Despite representing 428 variants, this set of 33 positions was poorly statistically powered. Thus, we turned to the in vivo phenotypic dataset for E. coli lactose repressor protein (LacI), which comprised 12-13 substitutions at 329 positions and could be used to identify rheostat, toggle, and neutral positions. Combined hLPYK and LacI results show that positions with strong phylogenetic patterns of change are more likely to exhibit rheostat substitution outcomes than neutral or toggle outcomes. Furthermore, phylogenetic patterns were more successful at identifying rheostat positions than were co-evolutionary or eigenvector centrality measures of evolutionary change.


Assuntos
Substituição de Aminoácidos , DNA/química , Proteínas de Escherichia coli/química , Evolução Molecular , Repressores Lac/química , Piruvato Quinase/química , Difosfato de Adenosina/química , Difosfato de Adenosina/metabolismo , Sítios de Ligação , Clonagem Molecular , Biologia Computacional/métodos , DNA/genética , DNA/metabolismo , Escherichia coli/classificação , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Humanos , Cinética , Repressores Lac/genética , Repressores Lac/metabolismo , Modelos Moleculares , Mutação , Fosfoenolpiruvato/química , Fosfoenolpiruvato/metabolismo , Filogenia , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Piruvato Quinase/genética , Piruvato Quinase/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Relação Estrutura-Atividade , Termodinâmica
19.
Med Chem ; 17(7): 699-706, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-32310051

RESUMO

BACKGROUND: Finding efficient therapy against hospital-acquired MRSA infections has become rather important in the last decade. To this end, inhibition of the enzyme pyruvate kinase (PK) is being investigated for antibacterial activity, since this enzyme controls energy generation and metabolic flux distribution. Our main scaffold consists of benzimidazole and indole rings fused together. Both rings are famous for antibacterial properties and promising anti-MRSA compounds including indole ring. METHODS: Several 1-substituted-2-(1H-indol-3-yl)-N-substituted-1H-benzimidazole-5-carboxamidine analogues were developed, synthesized and their antibacterial activities were evaluated against Staphylococcus aureus (ATCC 25923), Methicillin resistant Staphylococcus aureus (MRSA) (ATCC 43300), and Staphylococcus epidermidis (ATCC 12228) by using tube dilution method. Molecular docking analysis with a characteristic protein called MRSA- Pyruvate Kinase has been conducted for the assessment of the activities of our compounds against Methicillinresistant S. aureus (MRSA). RESULTS: Among all the tested compounds, the most potent compound 36 had MIC values as 3.12, 3.12 and 6.25 µg/mL against S. aureus, Methicillin-resistant S. aureus (MRSA), and S. epidermidis, respectively. This compound had much better docking energy value than standard ampicillin and also created the link between two residues in different monomers of PK. DISCUSSION: This approach of using indol-amidine conjugate systems as anti-MRSA agents may include MRSA-PK as potential target. To further increase the affinity, some other H-bonding parts may be added. By doing so, another bridge with Ile361 residues on both sides can be created. Our compounds tend to violate log P limit of Lipinski, therefore some optimizations with formulation can be made. CONCLUSION: This study mainly includes the design, synthesis and optimization of indolebenzimidazole- amidine derivatives. Docking studies confirmed our results, since our most potent hit compound 36 created the necessary interactions between two chains of MRSA-PK. Further optimization can be considered to increase drug ability.


Assuntos
Antibacterianos/síntese química , Antibacterianos/farmacologia , Benzimidazóis/síntese química , Benzimidazóis/farmacologia , Simulação de Acoplamento Molecular , Antibacterianos/química , Antibacterianos/metabolismo , Benzimidazóis/química , Benzimidazóis/metabolismo , Técnicas de Química Sintética , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Conformação Proteica , Piruvato Quinase/química , Piruvato Quinase/metabolismo
20.
Insect Mol Biol ; 30(2): 176-187, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33280175

RESUMO

Larvae of the goldenrod gall fly, Eurosta solidaginis, rely on a freeze tolerance strategy to survive the sub-zero temperatures of Canadian winter. Critical to their survival is the accumulation of polyol cryoprotectants and global metabolic rate depression, both of which require the regulation of glycolysis and reorganization of carbohydrate metabolism. This study explored the role that pyruvate kinase (PK) regulation plays in this metabolic reorganization. PK was purified from control (5 °C-acclimated) and frozen (-15 °C-acclimated) larvae and enzyme kinetic properties, structural stability, and post-translational modifications were examined in both enzyme forms. The Km phosphoenolpyruvate (PEP) of frozen PK was 20% higher than that of control PK, whereas the Vmax of frozen PK was up to 50% lower than that of control PK at the lowest assay temperature, suggesting inhibition of the enzyme during the winter. Additionally, the activity and substrate affinity of both forms of PK decreased significantly at low assay temperatures, and both forms were regulated allosterically by a number of metabolites. Pro-Q™ Diamond phosphoprotein staining and immunoblotting experiments demonstrated significantly higher threonine phosphorylation of PK from frozen animals while acetylation and methylation levels remained constant. Together, these results indicate that PK exists in two structurally distinct forms in E. solidaginis. In response to conditions mimicking the transition to winter, PK appears to be regulated to support metabolic rate depression, the accumulation of polyol cryoprotectants, and the need for extended periods of anaerobic carbohydrate metabolism to allow the animal to survive whole-body freezing.


Assuntos
Piruvato Quinase/química , Piruvato Quinase/metabolismo , Tephritidae/enzimologia , Aclimatação , Animais , Temperatura Baixa , Congelamento , Larva/enzimologia , Fosforilação/fisiologia , Tephritidae/crescimento & desenvolvimento , Tephritidae/metabolismo
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