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1.
Methods Enzymol ; 697: 269-291, 2024.
Article in English | MEDLINE | ID: mdl-38816126

ABSTRACT

The design of small peptides that assemble into catalytically active intermolecular structures has proven to be a successful strategy towards developing minimalistic catalysts that exhibit some of the unique functional features of enzymes. Among these, catalytic amyloids have emerged as a fruitful source to unravel many different activities. These assemblies can potentially have broad applications that range from biotechnology to prebiotic chemistry. Although many peptides that assemble into catalytic amyloids have been developed in recent years, the elucidation of convergent mechanistic aspects of the catalysis and the structure/function relationship is still a challenge. Novel catalytic activities are necessary to better address these issues and expand the current repertoire of applicability. In this chapter, we described a methodology to produce catalytic amyloids that are specifically active towards the hydrolysis of phosphoanhydride bonds of nucleotides. The design of potentially active amyloid-prone peptide sequences is explored using as template the active site of enzymes with nucleotidyltransferase activity. The procedures include an approach for sequence design, in vitro aggregation assays, morphological characterization of the amyloid state and a comprehensive methodology to measure activity in vitro using nucleoside and deoxynucleosides triphosphates as model substrates. The proposed strategy can also be implemented to explore different types of activities for the design of future catalytic amyloids.


Subject(s)
Amyloid , Nucleotides , Hydrolysis , Amyloid/chemistry , Amyloid/metabolism , Nucleotides/chemistry , Nucleotides/metabolism , Catalytic Domain , Amino Acid Sequence , Catalysis , Biocatalysis
2.
Langmuir ; 40(12): 6094-6106, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38470353

ABSTRACT

Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.


Subject(s)
Amyloid , Peptides , Amyloid/chemistry , Peptides/chemistry , Metals/chemistry , Amyloidogenic Proteins , Ions
3.
Ther Clin Risk Manag ; 19: 1005-1018, 2023.
Article in English | MEDLINE | ID: mdl-38050617

ABSTRACT

Purpose: Thiopurine S-methyltransferase (TPMT) is an enzyme that metabolizes purine analogs, agents used in the treatment of acute lymphoblastic leukemia. Improper drug metabolism leads to toxicity in chemotherapy patients and reduces treatment effectiveness. TPMT variants associated with reduced enzymatic activity vary across populations. Therefore, studying these variants in heterogeneous populations, such as Ecuadorians, can help identify molecular causes of deficiency for this enzyme. Methods: We sequenced the entire TPMT coding region in 550 Ecuadorian individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnicities. Moreover, we conducted an ancestry analysis using 46 informative ancestry markers. Results: We identified 8 single nucleotide variants in the coding region of TPMT. The most prevalent alleles were TPMT*3A, TPMT*3B, and TPMT*3C, with frequencies of 0.055, 0.012, and 0.015, respectively. Additionally, we found rare alleles TPMT*4 and TPMT*8 with frequencies of 0.005 and 0.003. Correlating the ancestry proportions with TPMT-deficient genotypes, we observed that the Native American ancestry proportion influenced the distribution of the TPMT*1/TPMT*3A genotype (OR = 5.977, p = 0.002), while the contribution of African ancestral populations was associated with the TPMT*1/TPMT*3C genotype (OR = 9.769, p = 0.003). The rates of TPMT-deficient genotypes observed in Mestizo (f = 0.121) and Indigenous (f = 0.273) groups provide evidence for the influence of Native American ancestry and the prevalence of the TPMT*3A allele. In contrast, although Afro-Ecuadorian groups demonstrate similar deficiency rates (f = 0.160), the genetic factors involved are associated with contributions from African ancestral populations, specifically the prevalent TPMT*3C allele. Conclusion: The distribution of TPMT-deficient variants offers valuable insights into the populations under study, underscoring the necessity for genetic screening strategies to prevent thiopurine toxicity events among Latin American minority groups.

4.
Cell Death Discov ; 9(1): 438, 2023 Dec 02.
Article in English | MEDLINE | ID: mdl-38042807

ABSTRACT

Parkinson's disease (PD) is the second most common late-onset neurodegenerative disease and the predominant cause of movement problems. PD is characterized by motor control impairment by extensive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). This selective dopaminergic neuronal loss is in part triggered by intracellular protein inclusions called Lewy bodies, which are composed mainly of misfolded alpha-synuclein (α-syn) protein. We previously reported insulin-like growth factor 2 (IGF2) as a key protein downregulated in PD patients. Here we demonstrated that IGF2 treatment or IGF2 overexpression reduced the α-syn aggregates and their toxicity by IGF2 receptor (IGF2R) activation in cellular PD models. Also, we observed IGF2 and its interaction with IGF2R enhance the α-syn secretion. To determine the possible IGF2 neuroprotective effect in vivo we used a gene therapy approach in an idiopathic PD model based on α-syn preformed fibrils intracerebral injection. IGF2 gene therapy revealed a significantly preventing of motor impairment in idiopathic PD model. Moreover, IGF2 expression prevents dopaminergic neuronal loss in the SN together with a decrease in α-syn accumulation (phospho-α-syn levels) in the striatum and SN brain region. Furthermore, the IGF2 neuroprotective effect was associated with the prevention of synaptic spines loss in dopaminergic neurons in vivo. The possible mechanism of IGF2 in cell survival effect could be associated with the decrease of the intracellular accumulation of α-syn and the improvement of dopaminergic synaptic function. Our results identify to IGF2 as a relevant factor for the prevention of α-syn toxicity in both in vitro and preclinical PD models.

6.
Malar J ; 22(1): 283, 2023 Sep 26.
Article in English | MEDLINE | ID: mdl-37752491

ABSTRACT

BACKGROUND: Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is an X-linked disorder affecting over 400 million people worldwide. Individuals with molecular variants associated with reduced enzymatic activity are susceptible to oxidative stress in red blood cells, thereby increasing the risk of pathophysiological conditions and toxicity to anti-malarial treatments. Globally, the prevalence of G6PDd varies among populations. Accordingly, this study aims to characterize G6PDd distribution within the Ecuadorian population and to describe the spatial distribution of reported malaria cases. METHODS: Molecular variants associated with G6PDd were genotyped in 581 individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnic groups. Additionally, spatial analysis was conducted to identify significant malaria clusters with high incidence rates across Ecuador, using data collected from 2010 to 2021. RESULTS: The A- c.202G > A and A- c.968T > C variants underpin the genetic basis of G6PDd in the studied population. The overall prevalence of G6PDd was 4.6% in the entire population. However, this frequency increased to 19.2% among Afro-Ecuadorian people. Spatial analysis revealed 12 malaria clusters, primarily located in the north of the country and its Amazon region, with relative risks of infection of 2.02 to 87.88. CONCLUSIONS: The findings of this study hold significant implications for public health interventions, treatment strategies, and targeted efforts to mitigate the burden of malaria in Ecuador. The high prevalence of G6PDd among Afro-Ecuadorian groups in the northern endemic areas necessitates the development of comprehensive malaria eradication strategies tailored to this geographical region.


Subject(s)
Glucosephosphate Dehydrogenase Deficiency , Malaria , Humans , Ecuador/epidemiology , Erythrocytes , Ethnicity , Glucosephosphate Dehydrogenase Deficiency/epidemiology , Glucosephosphate Dehydrogenase Deficiency/genetics , Malaria/epidemiology
7.
Nanomaterials (Basel) ; 12(21)2022 Oct 28.
Article in English | MEDLINE | ID: mdl-36364578

ABSTRACT

Peptides and proteins can aggregate into highly ordered and structured conformations called amyloids. These supramolecular structures generally have convergent features, such as the formation of intermolecular beta sheets, that lead to fibrillary architectures. The resulting fibrils have unique mechanical properties that can be exploited to develop novel nanomaterials. In recent years, sequences of small peptides have been rationally designed to self-assemble into amyloids that catalyze several chemical reactions. These amyloids exhibit reactive surfaces that can mimic the active sites of enzymes. In this review, I provide a state-of-the-art summary of the development of catalytically active amyloids. I will focus especially on catalytic activities mediated by hydrolysis, which are the most studied examples to date, as well as novel types of recently reported activities that promise to expand the possible repertoires. The combination of mechanical properties with catalytic activity in an amyloid scaffold has great potential for the development of future bionanomaterials aimed at specific applications.

8.
Methods Mol Biol ; 2538: 207-216, 2022.
Article in English | MEDLINE | ID: mdl-35951302

ABSTRACT

The amyloid fold is nowadays recognized as an alternative conformation accessible to different proteins and peptides. The highly stable and ordered structural organization of amyloid fibrils can be exploited for the design of novel nanomaterials with emergent properties. Recent works have demonstrated that the functional features of the active site of enzymes can be partially recreated using this fold as a scaffold to develop catalytically active amyloids. We describe in this chapter a protocol to design functionally active amyloids that emerge from the self-assembly in vitro of synthetic peptides with sequences based on the active site of enzymes. Using this protocol, we show the development of amyloids that catalyze the metal-dependent hydrolysis of the phosphoanhydride bonds of nucleoside triphosphates.


Subject(s)
Amyloid , Amyloidogenic Proteins , Amyloid/chemistry , Amyloidogenic Proteins/chemistry , Catalysis , Catalytic Domain , Peptides/chemistry
9.
Multimed (Granma) ; 26(4): e2501, jul.-ago. 2022. graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1406113

ABSTRACT

RESUMEN La enfermedad por coronavirus del 2019es una preocupación a nivel mundial, su propagación está relacionada a características propias del virus y a la toma de acciones gubernamentales, de salud pública y hábitos sociales. Utilizar herramientas matemáticas y computacionales ayuda a tener un panorama de la situación actual y a futuro de esta problemática. Con el objetivo de reflejar el comportamiento de esta enfermedad mediante simulación con dinámica de sistemas y evaluar la cantidad de contagios activos, muertes y recuperados en Paraguay en el mes de febrero del 2021 se utilizó el software Vensim aplicando una modificación del modelo básico de epidemiología de Kermack y McKendrick que considera a la población de susceptibles, infectados y recuperados. La simulación de esta dinámica ha presentado diferencias de 758 casos activos, 216 muertes y 37009 recuperados respecto a lo reportado, siendo los casos activos la aproximación más importante del estudio.


ABSTRACT The 2019 coronavirus disease is a worldwide concern, its spread is related to the characteristics of the virus and the taking of government, public health and social habits. Using mathematical and computational tools help to have an overview of the current situation and a future of this problem. In order to reflect behavior of this disease through simulation with system dynamics and evaluating the number of active infections, deaths and recoveries in Paraguay in the month of February 2021, the Vensim software was released by applying a modification of the basic model of epidemiology of Kermack and McKendrick who consider the population of susceptible, processed and recovered. The simulation of this dynamic has presented differences of 758 active cases, 216 deaths and 37009 recovered with respect to what was reported, with active cases being the most important approximation of the study.


RESUMO A doença do coronavírus 2019 é uma preocupação mundial, sua disseminação está relacionada às características do vírus e à toma de ações governamentais, de saúde pública e hábitos sociais. O uso de ferramentas matemáticas e computacionais ajudam a ter uma visão geral da situação atual e futura deste problema. Para refletir o comportamento desta doença através de simulação com dinâmica de sistemas e avaliar o número de infecções ativas, óbitos e recuperações no Paraguai no mês de fevereiro de 2021, foi utilizado o software Vensim, aplicando uma modificação do modelo básico de epidemiologia de Kermack e McKendrick que considera a população de suscetíveis, infectados e recuperados. A simulação dessa dinâmica apresentou diferenças de 758 casos ativos, 216 óbitos e 37.009 recuperados em relação ao informado, sendo os casos ativos a aproximação mais importante do estudo.

10.
J Pers Med ; 12(6)2022 Jun 10.
Article in English | MEDLINE | ID: mdl-35743735

ABSTRACT

Dihydropyrimidine dehydrogenase is one of the main pharmacological metabolizers of fluoropyrimidines, a group of drugs widely used in clinical oncology. Around 20 to 30% of patients treated with fluoropyrimidines experience severe toxicity caused by a partial or total decrease in enzymatic activity. This decrease is due to molecular variants in the DPYD gene. Their prevalence and allelic frequencies vary considerably worldwide, so their description in heterogeneous groups such as the Ecuadorian population will allow for the description of pharmacogenetic variants and proper characterization of this population. Thus, we genotyped all the molecular variants with a predictive value for DPYD in a total of 410 Ecuadorian individuals belonging to Mestizo, Afro-Ecuadorian, and Indigenous ethnic groups. Moreover, we developed a genetic ancestry analysis using 46 autosomal ancestry informative markers. We determined 20 genetic variations in 5 amplified regions, including 3 novel single nucleotide variants. The allele frequencies for DPYD variants c.1627G>A (*5, rs1801159), c.1129-15T>C (rs56293913), c.1218G>A (rs61622928), rs1337752, rs141050810, rs2786783, rs2811178, and g.97450142G>A (chr1, GRCh38.p13) are significantly related to Native American and African ancestry proportions. In addition, the FST calculated from these variants demonstrates the closeness between Indigenous and Mestizo populations, and evidences genetic divergence between Afro-Ecuadorian groups when compared with Mestizo and Indigenous ethnic groups. In conclusion, the genetic variability in the DPYD gene is related to the genetic component of ancestral populations in different Ecuadorian ethnic groups. The absence and low frequency of variants with predictive value for fluoropyrimidine toxicity such as DPYD *2A, HapB3, and c.2846A>T (prevalent in populations with European ancestry) is consistent with the genetic background found.

11.
MULTIMED ; 26(4)2022. graf
Article in Spanish | CUMED | ID: cum-78887

ABSTRACT

La enfermedad por coronavirus del 2019 es una preocupación a nivel mundial, su propagación está relacionada a características propias del virus y a la toma de acciones gubernamentales, de salud pública y hábitos sociales. Utilizar herramientas matemáticas y computacionales ayuda a tener un panorama de la situación actual y al futuro de esta problemática. Con el objetivo de reflejar el comportamiento de esta enfermedad mediante simulación con dinámica de sistemas y evaluar la cantidad de contagios activos, muertes y recuperados en Paraguay en el mes de febrero del 2021 se utilizó el software Vensim aplicando una modificación del modelo básico de epidemiología de Kermack y McKendrick que considera a la población de susceptibles, infectados y recuperados. La simulación de esta dinámica ha presentado diferencias de 758 casos activos, 216 muertes y 37009 recuperados respecto a lo reportado, siendo los casos activos la aproximación más importante del estudio(AU)


The 2019 coronavirus disease is a worldwide concern, its spread is related to the characteristics of the virus and the taking of government, public health and social habits. Using mathematical and computational tools help to have an overview of the current situation and a future of this problem. In order to reflect behavior of this disease through simulation with system dynamics and evaluating the number of active infections, deaths and recoveries in Paraguay in the month of February 2021, the Vensim software was released by applying a modification of the basic model of epidemiology of Kermack and McKendrick who consider the population of susceptible, processed and recovered. The simulation of this dynamic has presented differences of 758 active cases, 216 deaths and 37009 recovered with respect to what was reported, with active cases being the most important approximation of the study(EU)


Subject(s)
Humans , Simulation Exercise/methods , Coronavirus Infections/prevention & control , Software , Severe acute respiratory syndrome-related coronavirus , Coronavirus Infections/complications , Coronavirus Infections/epidemiology
12.
Front Aging Neurosci ; 13: 782617, 2021.
Article in English | MEDLINE | ID: mdl-34867305

ABSTRACT

Amyloids are highly ordered aggregates composed of proteins or peptides. They are involved in several pathologies, including hallmark neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD). Individuals affected by these diseases accumulate in their brains amyloids inclusions composed of misfolded forms of a peptide (Aß) and a protein (Tau) in AD and α-synuclein protein (α-Sn) in PD. Tau and α-Sn aggregates are also present in other neurodegenerative diseases. The insoluble nature and heterogeneity of amyloids have hampered their study at the molecular level. However, the use of solid state NMR and Cryogenic-electron microscopy along with fine-tuned modulation of the aggregation in vitro and improved isolation methods of brain-derived amyloids has allowed the elucidation of these elusive conformations at high resolution. In this work, we review the latest progress on the recent amyloid structures reported for Aß, Tau, and α-Sn. The two-fold symmetry emerges as a convergent feature in the tridimensional arrangement of the protofilaments in the fibrillary structure of these pathological amyloids, with many of them exhibiting a Greek-key topology as part of their overall architecture. These specific features can serve as novel guides to seek potential molecular targets in drug design efforts.

13.
Int J Mol Sci ; 22(17)2021 Aug 25.
Article in English | MEDLINE | ID: mdl-34502074

ABSTRACT

Amyloids are supramolecular assemblies composed of polypeptides stabilized by an intermolecular beta-sheet core. These misfolded conformations have been traditionally associated with pathological conditions such as Alzheimer's and Parkinson´s diseases. However, this classical paradigm has changed in the last decade since the discovery that the amyloid state represents a universal alternative fold accessible to virtually any polypeptide chain. Moreover, recent findings have demonstrated that the amyloid fold can serve as catalytic scaffolds, creating new opportunities for the design of novel active bionanomaterials. Here, we review the latest advances in this area, with particular emphasis on the design and development of catalytic amyloids that exhibit hydrolytic activities. To date, three different types of activities have been demonstrated: esterase, phosphoesterase and di-phosphohydrolase. These artificial hydrolases emerge upon the self-assembly of small peptides into amyloids, giving rise to catalytically active surfaces. The highly stable nature of the amyloid fold can provide an attractive alternative for the design of future synthetic hydrolases with diverse applications in the industry, such as the in situ decontamination of xenobiotics.


Subject(s)
Amyloid/chemistry , Hydrolases/chemistry , Amyloid/chemical synthesis , Amyloid/metabolism , Animals , Catalytic Domain , Humans , Hydrolases/chemical synthesis , Hydrolases/metabolism
14.
Am J Phys Anthropol ; 176(1): 109-119, 2021 09.
Article in English | MEDLINE | ID: mdl-34169504

ABSTRACT

OBJECTIVES: According to demographic history, Ecuador has experienced shifts in its Native American populations caused by European colonization and the African slave trade. The continuous admixture events among Europeans, Native Americans, and Africans occurred differently in each region of the country, producing a stratified population. Thus, the aim of this study was to investigate the level of genetic substructure in the Ecuadorian Mestizo population. MATERIALS AND METHODS: A total of 377 male and 209 female samples were genotyped for two sets of X-chromosomal markers (32 X-Indels and 12 X-STRs). Population analyses performed included Hardy-Weinberg equilibrium tests, LD analysis, PCA, pairwise FST s, and AMOVA. RESULTS: Significant levels of LD were observed between markers separated by distances of less than 1 cM, as well as between markers separated by distances varying from 10.891 to 163.53 cM. Among Ecuadorian regions, Amazonia showed the highest average R2 value. DISCUSSION: When X-chromosomal and autosomal differentiation values were compared, a sex-biased admixture between European men and Native American and African women was revealed, as well as between African men and Native American women. Moreover, a distinct Native American ancestry was discernible in the Amazonian population, in addition to sex-biased gene flow between Amazonia and the Andes and Pacific coast regions. Overall, these results underline the importance of integrating X chromosome information to achieve a more comprehensive view of the genetic and demographic histories of South American admixed populations.


Subject(s)
Genetic Variation/genetics , Genetics, Population/methods , Indians, South American/genetics , Anthropology, Physical , Chromosomes, Human, X/genetics , Ecuador , Female , Humans , INDEL Mutation/genetics , Linkage Disequilibrium/genetics , Male , Microsatellite Repeats/genetics
15.
Biochim Biophys Acta Gen Subj ; 1865(1): 129729, 2021 01.
Article in English | MEDLINE | ID: mdl-32916204

ABSTRACT

BACKGROUND: Amyloids are highly ordered polypeptide aggregates stabilized by a beta-sheet structural core. Though classically associated to pathology, reports on novel functional roles of these proteins have increasingly emerged in the past decade. Moreover, the recent discovery that amyloids formed with rationally designed small peptides can exhibit catalytic reactivity has opened up new opportunities in both biology and biotechnology. The observed activities typically require the binding of divalent metals, giving rise to active metal-amyloid complexes. METHODS: Peptide (SDIDVFI) was aggregated in vitro. The structure of the self-assembled species was analyzed using fluorescence, transmission electron microscopy, circular dichroism and computational modeling. A kinetic characterization of the emerging catalytic activity was performed. RESULTS: The peptide self-assembled into canonical amyloids that exhibited catalytic activity towards hydrolysis of the phosphoanhydride bonds of adenosine triphosphate (ATP), partially mimicking an ATPase-like enzyme. Both amyloid formation and activity are shown to depend on manganese (Mn2+) binding. The activity was not restricted to ATP but also affected all other ribonucleotides (GTP, CTP and UTP). Peptides carrying a single aspartate exhibited a similar activity. CONCLUSIONS: The phosphoanhydride bonds appear as the main specificity target of the Mn2+-amyloid complex. A single aspartate per peptide is sufficient to enable the hydrolytic activity. GENERAL SIGNIFICANCE: Catalytic amyloids are shown for the first time to catalyze the hydrolysis of all four ribonucleotides. Our results should contribute towards understanding the biological implications of amyloid-mediated reactivity as well as in the design of future catalytic amyloids for biotechnological applications.


Subject(s)
Adenosine Triphosphatases/metabolism , Adenosine Triphosphate/metabolism , Amyloid/metabolism , Peptides/metabolism , Adenosine Triphosphatases/chemistry , Amino Acid Sequence , Amyloid/chemistry , Amyloid/ultrastructure , Hydrolysis , Models, Molecular , Peptides/chemistry , Substrate Specificity
17.
Sci Rep ; 7: 45720, 2017 03 31.
Article in English | MEDLINE | ID: mdl-28361921

ABSTRACT

Microcin E492 (Mcc) is a pore-forming bacteriotoxin. Mcc activity is inhibited at the stationary phase by formation of amyloid-like aggregates in the culture. Here we report that, in a similar manner as prions, Mcc naturally exists as two conformers: a ß-sheet-rich, protease-resistant, aggregated, inactive form (Mccia), and a soluble, protease-sensitive, active form (Mcca). The exogenous addition of culture medium containing Mccia or purified in vitro-generated Mccia into the culture induces the rapid and efficient conversion of Mcca into Mccia, which is maintained indefinitely after passaging, changing the bacterial phenotype. Mccia prion-like activity is conformation-dependent and could be reduced by immunodepleting Mccia. Interestingly, an internal region of Mcc shares sequence similarity with the central domain of the prion protein, which is key to the formation of mammalian prions. A synthetic peptide spanning this sequence forms amyloid-like fibrils in vitro and is capable of inducing the conversion of Mcca into Mccia in vivo, suggesting that this region corresponds to the prion domain of Mcc. Our findings suggest that Mcc is the first prokaryotic protein with prion properties which harnesses prion-like transmission to regulate protein function, suggesting that propagation of biological information using a prion-based conformational switch is an evolutionary conserved mechanism.


Subject(s)
Bacteriocins/metabolism , Prions/metabolism , Bacteriocins/chemistry , Cells, Cultured , Escherichia coli , Prions/chemistry , Protein Aggregates , Protein Conformation
18.
Arch Biochem Biophys ; 621: 46-53, 2017 05 01.
Article in English | MEDLINE | ID: mdl-28288797

ABSTRACT

Amyloids are polypeptide aggregates involved in many pathologies including Alzheimer's disease. Amyloid assembly is a complex process affected by different interactions including hydrogen bonding, van der Waals forces and electrostatic interactions. The highly regular amyloid structure allows for an arrangement of residues that forces side chains to be closely positioned, giving rise to potentially unfavorable interactions such as electrostatic repulsions. In these cases, amyloid assembly will depend on a balance between stabilizing versus unfavorable interactions. In this study, we rationally designed several amyloid-prone model peptides that had two acidic groups and tested their assembly into amyloids under different conditions. We found that at low pH (pH 4.0), most peptides spontaneously formed amyloids whereas no or little aggregation was observed at higher pHs (pH 8.0). When divalent metals with affinity for carboxylate groups were added at millimolar concentrations, most peptides exhibited a metal-dependent switch to the amyloid state at pH 8.0. Our results show that electrostatic repulsion between amyloid-prone sequences can be overcome in conditions that affect protonation of residue side chains. Moreover, the presence of divalent metals can contribute to electrostatic shielding through specific coordination with acidic groups and thus promote amyloid assembly.


Subject(s)
Amyloid/chemical synthesis , Amyloid/ultrastructure , Manganese/chemistry , Models, Chemical , Models, Molecular , Peptides/chemistry , Binding Sites , Computer Simulation , Hydrogen-Ion Concentration , Protein Binding , Static Electricity
19.
Biol Res ; 50(1): 5, 2017 Feb 15.
Article in English | MEDLINE | ID: mdl-28202086

ABSTRACT

BACKGROUND: Salmonella pathogenicity island (SPI)-13 is conserved in many serovars of S. enterica, including S. Enteritidis, S. Typhimurium and S. Gallinarum. However, it is absent in typhoid serovars such as S. Typhi and Paratyphi A, which carry SPI-8 at the same genomic location. Because the interaction with macrophages is a critical step in Salmonella pathogenicity, in this study we investigated the role played by SPI-13 and SPI-8 in the interaction of S. Enteritidis and S. Typhi with cultured murine (RAW264.7) and human (THP-1) macrophages. RESULTS: Our results showed that SPI-13 was required for internalization of S. Enteritidis in murine but not human macrophages. On the other hand, SPI-8 was not required for the interaction of S. Typhi with human or murine macrophages. Of note, the presence of an intact copy of SPI-13 in a S. Typhi mutant carrying a deletion of SPI-8 did not improve its ability to be internalized by, or survive in human or murine macrophages. CONCLUSIONS: Altogether, our results point out to different roles for SPI-13 and SPI-8 during Salmonella infection. While SPI-13 contributes to the interaction of S. Enteritidis with murine macrophages, SPI-8 is not required in the interaction of S. Typhi with murine or human macrophages. We hypothesized that typhoid serovars have lost SPI-13 and maintained SPI-8 to improve their fitness during another phase of human infection.


Subject(s)
Genomic Islands/physiology , Macrophages/microbiology , Salmonella Infections/microbiology , Salmonella enteritidis/genetics , Salmonella typhi/genetics , Analysis of Variance , Animals , Bacterial Physiological Phenomena , Cell Survival , Cells, Cultured , Genome, Bacterial , Genomic Islands/genetics , Humans , Mice , Microbial Interactions/genetics , Muridae , Polymerase Chain Reaction , RAW 264.7 Cells , Serogroup , Species Specificity
20.
Biochem Biophys Res Commun ; 482(4): 1194-1200, 2017 Jan 22.
Article in English | MEDLINE | ID: mdl-27923655

ABSTRACT

Amyloids are protein aggregates of highly regular structure that are involved in diverse pathologies such as Alzheimer's and Parkinson's disease. Recent evidence has shown that under certain conditions, small peptides can self-assemble into amyloids that exhibit catalytic reactivity towards certain compounds. Here we report a novel peptide with a sequence derived from the active site of RNA polymerase that displays hydrolytic activity towards ATP. The catalytic reaction proceeds in the presence of the divalent metal manganese and the products are ADP and AMP. The kinetic data shows a substrate-dependent saturation of the activity with a maximum rate achieved at around 1 mM ATP. At higher ATP concentrations, we also observed substrate inhibition of the activity. The self-assembly of the peptide into amyloids is strictly metal-dependent and required for the catalysis. Our results show that aspartate-containing amyloids can also be catalysts under conditions that include interactions with metals. Moreover, we show for the first time an amyloid that exerts reactivity towards a biologically essential molecule.


Subject(s)
Adenosine Triphosphatases/chemistry , Amyloid/chemistry , Adenosine Diphosphate/chemistry , Adenosine Monophosphate/chemistry , Adenosine Triphosphate/chemistry , Amyloidogenic Proteins , Benzothiazoles , Catalysis , Catalytic Domain , Computer Simulation , Humans , Hydrogen-Ion Concentration , Hydrolysis , Ions , Magnesium/chemistry , Manganese/chemistry , Metals/chemistry , Peptides/chemistry , Thiazoles/chemistry
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