Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 47
Filtrar
1.
Protein Sci ; 33(6): e5020, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38747397

RESUMO

Wheat germ agglutinin (WGA) demonstrates potential as an oral delivery agent owing to its selective binding to carbohydrates and its capacity to traverse biological membranes. In this study, we employed differential scanning calorimetry and molecular dynamics simulations to comprehensively characterize the thermal unfolding process of both the complete lectin and its four isolated domains. Furthermore, we present the nuclear magnetic resonance structures of three domains that were previously lacking experimental structures in their isolated forms. Our results provide a collective understanding of the energetic and structural factors governing the intricate unfolding mechanism of the complete agglutinin, shedding light on the specific role played by each domain in this process. The analysis revealed negligible interdomain cooperativity, highlighting instead significant coupling between dimer dissociation and the unfolding of the more labile domains. By comparing the dominant interactions, we rationalized the stability differences among the domains. Understanding the structural stability of WGA opens avenues for enhanced drug delivery strategies, underscoring its potential as a promising carrier throughout the gastrointestinal environment.


Assuntos
Simulação de Dinâmica Molecular , Estabilidade Proteica , Aglutininas do Germe de Trigo , Aglutininas do Germe de Trigo/química , Aglutininas do Germe de Trigo/metabolismo , Ressonância Magnética Nuclear Biomolecular , Domínios Proteicos , Varredura Diferencial de Calorimetria
2.
Microb Cell Fact ; 23(1): 41, 2024 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-38321489

RESUMO

BACKGROUND: Developing effective vaccines against SARS-CoV-2 that consider manufacturing limitations, equitable access, and acceptance is necessary for developing platforms to produce antigens that can be efficiently presented for generating neutralizing antibodies and as a model for new vaccines. RESULTS: This work presents the development of an applicable technology through the oral administration of the SARS-CoV-2 RBD antigen fused with a peptide to improve its antigenic presentation. We focused on the development and production of the recombinant receptor binding domain (RBD) produced in E. coli modified with the addition of amino acids extension designed to improve antigen presentation. The production was carried out in shake flask and bioreactor cultures, obtaining around 200 mg/L of the antigen. The peptide-fused RBD and peptide-free RBD proteins were characterized and compared using SDS-PAGE gel, high-performance chromatography, and circular dichroism. The peptide-fused RBD was formulated in an oil-in-water emulsion for oral mice immunization. The peptide-fused RBD, compared to RBD, induced robust IgG production in mice, capable of recognizing the recombinant RBD in Enzyme-linked immunosorbent assays. In addition, the peptide-fused RBD generated neutralizing antibodies in the sera of the dosed mice. The formulation showed no reactive episodes and no changes in temperature or vomiting. CONCLUSIONS: Our study demonstrated the effectiveness of the designed peptide added to the RBD to improve antigen immunostimulation by oral administration.


Assuntos
COVID-19 , SARS-CoV-2 , Animais , Humanos , Camundongos , Adjuvantes Imunológicos , Vacinas contra COVID-19 , Escherichia coli , Administração Oral , Antígenos Virais , Anticorpos Neutralizantes , Peptídeos , Anticorpos Antivirais
3.
Biochim Biophys Acta Proteins Proteom ; 1871(4): 140906, 2023 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-36918120

RESUMO

Potassium channels play a key role in regulating many physiological processes, thus, alterations in their proper functioning can lead to the development of several diseases. Hence, the search for compounds capable of regulating the activity of these channels constitutes an intense field of investigation. Potassium scorpion toxins are grouped into six subfamilies (α, ß, γ, κ, δ, and λ). However, experimental structures and functional analyses of the long chain ß-KTx subfamily are lacking. In this study, we recombinantly produced the toxins TcoKIK and beta-KTx14.3 present in the venom of Tityus costatus and Lychas mucronatus scorpions, respectively. The 3D structures of these ß-KTx toxins were determined by nuclear magnetic resonance. In both toxins, the N-terminal region is unstructured, while the C-terminal possesses the classic CSα/ß motif. TcoKIK did not show any clear activity against frog Shaker and human KCNQ1 potassium channels; however, beta-KTx14.3 was able to block the KCNQ1 channel. The toxin-channel interaction mode was investigated using molecular dynamics simulations. The results showed that this toxin could form a stable network of polar-to-polar and hydrophobic interactions with KCNQ1, involving key conserved residues in both molecular partners. The discovery and characterization of a toxin capable of inhibiting KCNQ1 pave the way for the future development of novel drugs for the treatment of human diseases caused by the malfunction of this potassium channel. STATEMENT OF SIGNIFICANCE: Scorpion toxins have been shown to rarely block human KCNQ1 channels, which participate in the regulation of cardiac processes. In this study, we obtained recombinant beta-KTx14.3 and TcoKIK toxins and determined their 3D structures by nuclear magnetic resonance. Electrophysiological studies and molecular dynamics models were employed to examine the interactions between these two toxins and the human KCNQ1, which is the major driver channel of cardiac repolarization; beta-KTx14.3 was found to block effectively this channel. Our findings provide insights for the development of novel toxin-based drugs for the treatment of cardiac channelopathies involving KCNQ1-like channels.


Assuntos
Canais de Potássio , Venenos de Escorpião , Humanos , Canais de Potássio/metabolismo , Venenos de Escorpião/farmacologia , Venenos de Escorpião/química , Sequência de Aminoácidos , Canal de Potássio KCNQ1/genética , Simulação de Dinâmica Molecular
4.
Front Pharmacol ; 13: 1012008, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36313289

RESUMO

In addition to playing a central role in the mitochondria as the main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions in the cell membrane. Its malfunction has been linked to a growing number of human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, and aging diseases. Furthermore, inhibition of this enzyme jeopardizes the survival of several bacterial pathogens of public health concern. Therefore, FOF1-ATP synthase has emerged as a novel drug target both to treat human diseases and to combat antibiotic resistance. In this work, we carried out a computational characterization of the binding sites of the fungal antibiotic aurovertin in the bovine F1 subcomplex, which shares a large identity with the human enzyme. Molecular dynamics simulations showed that although the binding sites can be described as preformed, the inhibitor hinders inter-subunit communications and exerts long-range effects on the dynamics of the catalytic site residues. End-point binding free energy calculations revealed hot spot residues for aurovertin recognition. These residues were also relevant to stabilize solvent sites determined from mixed-solvent molecular dynamics, which mimic the interaction between aurovertin and the enzyme, and could be used as pharmacophore constraints in virtual screening campaigns. To explore the possibility of finding species-specific inhibitors targeting the aurovertin binding site, we performed free energy calculations for two bacterial enzymes with experimentally solved 3D structures. Finally, an analysis of bacterial sequences was carried out to determine conservation of the aurovertin binding site. Taken together, our results constitute a first step in paving the way for structure-based development of new allosteric drugs targeting FOF1-ATP synthase sites of exogenous inhibitors.

5.
Antibiotics (Basel) ; 11(5)2022 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-35625201

RESUMO

With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, to develop drugs with novel modes of bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as an attractive antimicrobial target, validated by the pharmaceutical approval of an inhibitor to treat multidrug-resistant tuberculosis. In this work, we aimed to design, through two types of in silico strategies, new allosteric inhibitors of the ATP synthase, by targeting the catalytic ß subunit, a centerpiece in communication between rotor subunits and catalytic sites, to drive the rotary mechanism. As a model system, we used the F1 sector of Escherichia coli, a bacterium included in the priority list of multidrug-resistant pathogens. Drug-like molecules and an IF1-derived peptide, designed through molecular dynamics simulations and sequence mining approaches, respectively, exhibited in vitro micromolar inhibitor potency against F1. An analysis of bacterial and Mammalia sequences of the key structural helix-turn-turn motif of the C-terminal domain of the ß subunit revealed highly and moderately conserved positions that could be exploited for the development of new species-specific allosteric inhibitors. To our knowledge, these inhibitors are the first binders computationally designed against the catalytic subunit of FOF1-ATP synthase.

6.
Appl Microbiol Biotechnol ; 106(8): 2883-2902, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35412129

RESUMO

The overproduction of recombinant proteins in Escherichia coli leads to insoluble aggregates of proteins called inclusion bodies (IBs). IBs are considered dynamic entities that harbor high percentages of the recombinant protein, which can be found in different conformational states. The production conditions influence the properties of IBs and recombinant protein recovery and solubilization. The E. coli growth in thermoinduced systems is generally carried out at 30 °C and then recombinant protein production at 42 °C. Since the heat shock response in E. coli is triggered above 34 °C, the synthesis of heat shock proteins can modify the yields of the recombinant protein and the structural quality of IBs. The objective of this work was to evaluate the effect of different pre-induction temperatures (30 and 34 °C) on the growth of E. coli W3110 producing the human granulocyte-macrophage colony-stimulating factor (rHuGM-CSF) and on the IBs structure in a λpL/pR-cI857 thermoinducible system. The recombinant E. coli cultures growing at 34 °C showed a ~ 69% increase in the specific growth rate compared to cultures grown at 30 °C. The amount of rHuGM-CSF in IBs was significantly higher in cultures grown at 34 °C. Main folding chaperones (DnaK and GroEL) were associated with IBs and their co-chaperones (DnaJ and GroES) with the soluble protein fraction. Finally, IBs from cultures that grew at 34 °C had a lower content of amyloid-like structure and were more sensitive to proteolytic degradation than IBs obtained from cultures at 30 °C. Our study presents evidence that increasing the pre-induction temperature in a thermoinduced system allows obtaining higher recombinant protein and reducing amyloid contents of the IBs. KEY POINTS: • Pre-induction temperature determines inclusion bodies architecture • In pre-induction (above 34 °C), the heat shock response increases recombinant protein production • Inclusion bodies at higher pre-induction temperature show a lower amyloid content.


Assuntos
Corpos de Inclusão , Proteínas Recombinantes , Humanos , Escherichia coli/metabolismo , Fator Estimulador de Colônias de Granulócitos e Macrófagos/metabolismo , Proteínas Recombinantes/biossíntese , Temperatura
7.
Microb Cell Fact ; 20(1): 88, 2021 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-33888152

RESUMO

SARS-CoV-2 is a novel ß-coronavirus that caused the COVID-19 pandemic disease, which spread rapidly, infecting more than 134 million people, and killing almost 2.9 million thus far. Based on the urgent need for therapeutic and prophylactic strategies, the identification and characterization of antibodies has been accelerated, since they have been fundamental in treating other viral diseases. Here, we summarized in an integrative manner the present understanding of the immune response and physiopathology caused by SARS-CoV-2, including the activation of the humoral immune response in SARS-CoV-2 infection and therefore, the synthesis of antibodies. Furthermore, we also discussed about the antibodies that can be generated in COVID-19 convalescent sera and their associated clinical studies, including a detailed characterization of a variety of human antibodies and identification of antibodies from other sources, which have powerful neutralizing capacities. Accordingly, the development of effective treatments to mitigate COVID-19 is expected. Finally, we reviewed the challenges faced in producing potential therapeutic antibodies and nanobodies by cell factories at an industrial level while ensuring their quality, efficacy, and safety.


Assuntos
Anticorpos Antivirais/uso terapêutico , Tratamento Farmacológico da COVID-19 , Anticorpos Monoclonais/biossíntese , Anticorpos Monoclonais/química , Anticorpos Monoclonais/uso terapêutico , Anticorpos Neutralizantes/química , Anticorpos Neutralizantes/uso terapêutico , Anticorpos Antivirais/sangue , COVID-19/imunologia , COVID-19/virologia , Humanos , Imunidade Humoral , Imunidade Inata , Imunoglobulinas/química , Imunoglobulinas/uso terapêutico , SARS-CoV-2/imunologia , SARS-CoV-2/isolamento & purificação , Anticorpos de Cadeia Única/química , Anticorpos de Cadeia Única/uso terapêutico
8.
Arch Biochem Biophys ; 699: 108750, 2021 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-33421379

RESUMO

Bovine ß-lactoglobulin, an abundant protein in whey, is a promising nanocarrier for peroral administration of drug-like hydrophobic molecules, a process that involves transit through the different acidic conditions of the human digestive tract. Among the several pH-induced conformational rearrangements that this lipocalin undergoes, the Tanford transition is particularly relevant. This transition, which occurs with a midpoint around neutral pH, involves a conformational change of the E-F loop that regulates accessibility to the primary binding site. The effect of this transition on the ligand binding properties of this protein has scarcely been explored. In this study, we carried out an energetic and structural characterization of ß-lactoglobulin molecular recognition at pH values above and below the zone in which the Tanford transition occurs. The combined analysis of crystallographic, calorimetric, and molecular dynamics data sheds new light on the interplay between self-association, ligand binding, and the Tanford pre- and post-transition conformational states, revealing novel aspects underlying the molecular recognition mechanism of this enigmatic lipocalin.


Assuntos
Lactoglobulinas/metabolismo , Dodecilsulfato de Sódio/metabolismo , Animais , Sítios de Ligação , Bovinos , Cristalografia por Raios X , Concentração de Íons de Hidrogênio , Lactoglobulinas/química , Ligantes , Simulação de Dinâmica Molecular , Transição de Fase , Ligação Proteica , Conformação Proteica , Dodecilsulfato de Sódio/química , Termodinâmica
9.
FEBS Lett ; 595(2): 183-194, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33151544

RESUMO

Enzyme subunit interfaces have remarkable potential in drug design as both target and scaffold for their own inhibitors. We show an evolution-driven strategy for the de novo design of peptide inhibitors targeting interfaces of the Escherichia coli FoF1-ATP synthase as a case study. The evolutionary algorithm ROSE was applied to generate diversity-oriented peptide libraries by engineering peptide fragments from ATP synthase interfaces. The resulting peptides were scored with PPI-Detect, a sequence-based predictor of protein-protein interactions. Two selected peptides were confirmed by in vitro inhibition and binding tests. The proposed methodology can be widely applied to design peptides targeting relevant interfaces of enzymatic complexes.


Assuntos
Biologia Computacional/métodos , Inibidores Enzimáticos/farmacologia , Escherichia coli/enzimologia , Fragmentos de Peptídeos/farmacologia , ATPases Translocadoras de Prótons/metabolismo , Algoritmos , Simulação por Computador , Desenho de Fármacos , Inibidores Enzimáticos/química , Escherichia coli/efeitos dos fármacos , Proteínas de Escherichia coli/antagonistas & inibidores , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Modelos Moleculares , Fragmentos de Peptídeos/química , Biblioteca de Peptídeos , Ligação Proteica/efeitos dos fármacos , ATPases Translocadoras de Prótons/antagonistas & inibidores , ATPases Translocadoras de Prótons/química , ATPases Translocadoras de Prótons/genética , Alinhamento de Sequência , Relação Estrutura-Atividade
10.
Biophys Chem ; 257: 106315, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31841862

RESUMO

Lipocalins are a widely distributed family of extracellular proteins typically involved in the transport of small hydrophobic molecules. To gain new insights into the molecular basis that governs ligand recognition by this ancient protein family, the binding properties of the domain-swapped dimer bovine odorant binding protein (bOBP) and its monomeric mutant bOBP121G+ were characterized using calorimetric techniques and molecular dynamics simulations. Thermal unfolding profiles revealed that the isolated bOBP subunits behave as a cooperative folding unit. In addition, bOBP and bOBP121G+ exhibited similar ligand binding properties, characterized by a non-classical hydrophobic effect signature. The energetic differences in the binding of bOBP to 1-hexen-3-ol and the physiological ligand 1-octen-3-ol were strikingly larger than those observed for the interaction of other lipocalins with congeneric ligands. MD simulations revealed that the recurrent opening of transient pores in the submicrosecond timescale allows a profuse exchange of water molecules between the protein interior and the surrounding solvent. This picture contrasts with other lipocalins whose ligand-free binding cavities are devoid of solvent molecules. Furthermore, the simulations indicated that internal water molecules solvate the protein cavity suboptimally, forming fewer hydrogen bonds and having lower density and higher potential energy than bulk water molecules. Upon ligand occupation, water molecules were displaced from the binding cavity in an amount that depended on the ligand size. Taken together, calorimetric and MD-simulation results are consistent with a significant contribution of cavity desolvation to the enthalpically-driven interaction of bOBP with its hydrophobic ligands.


Assuntos
Ligantes , Receptores Odorantes/química , Solventes/química , Animais , Sítios de Ligação , Bovinos , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Estabilidade Proteica , Receptores Odorantes/genética , Receptores Odorantes/metabolismo , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Termodinâmica , Água/química
11.
Biophys Chem ; 247: 13-24, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30780079

RESUMO

One of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (human EFL1, yeast Efl1) GTPase and the Shwachman-Diamond syndrome protein (human SBDS, yeast Sdo1) to release the eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes. However, the nature of such conformational changes or the mechanism by which they are prompted are still largely unknown. In previous studies, it has been established that this GTPase interacts with its cofactor in solution in an inverted orientation with respect to the binding mode derived from 60S ribosome subunit cryo-EM data. To shed new light on this conundrum, we characterized calorimetrically the energetic basis describing the recognition of Efl1 to GT(D)P, Sdo1 and their intercommunication in solution. A structural-based analysis of the binding signatures indicates that Efl1 has a large structural flexibility. The mutual effects of Sdo1 and nucleotides on Efl1 modulate in a very specific and robust way the complex conformational landscape of Efl1, resembling the behavior observed with other GTPases and their cofactors.


Assuntos
GTP Fosfo-Hidrolases/metabolismo , Nucleotídeos de Guanina/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/química , Nucleotídeos de Guanina/química , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química
12.
Biopolymers ; 110(1): e23242, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30485415

RESUMO

Wheat germ agglutinin (WGA), a chitin binding lectin, has attracted increasing interest because of its unique characteristics such as conformational stability, binding specificity and transcytosis capacity. To pave the way for the study of the molecular basis of WGA's structural stability and binding capacity, as well as to facilitate its use in biomedical and biotechnological developments, we produced recombinant WGA and its 4 isolated hevein-like domains in a bacterial system. All the proteins were expressed as fusion constructs linked to a thioredoxin domain, which was enzymatically or chemically released. The structural and ligand-binding properties of recombinant WGA were similar to the wild lectin. The 4 isolated domains folded and were ligand-binding competent, indicating that each domain constitutes an independent folding unity. The biophysical characterization of the recombinant domains sheds new light on the intricate folding and binding behavior of this emblematic lectin.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Fenômenos Biofísicos , Lectinas de Plantas/química , Triticum/química , Aglutininas do Germe de Trigo/química , Peptídeos Catiônicos Antimicrobianos/genética , Células Germinativas/química , Lectinas de Plantas/genética , Triticum/genética , Aglutininas do Germe de Trigo/genética
13.
FEBS J ; 286(5): 882-900, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30589511

RESUMO

Function, structure, and stability are strongly coupled in obligated oligomers, such as triosephosphate isomerase (TIM). However, little is known about how this coupling evolved. To address this question, five ancestral TIMs (ancTIMs) in the opisthokont lineage were inferred. The encoded proteins were purified and characterized, and spectroscopic and hydrodynamic analysis indicated that all are folded dimers. The catalytic efficiency of ancTIMs is very high and all dissociate into inactive and partially unfolded monomers. The placement of catalytic residues in the three-dimensional structure, as well as the enthalpy-driven binding signature of the oldest ancestor (TIM63) resemble extant TIMs. Although TIM63 dimers dissociate more readily than do extant TIMs, calorimetric data show that the free ancestral subunits are folded to a greater extent than their extant counterparts are, suggesting that full catalytic proficiency was established in the dimer before the stability of the isolated monomer eroded. Notably, the low association energy in ancTIMs is compensated for by a high activation barrier, and by a significant shift in the dimer-monomer equilibrium induced by ligand binding. Our results indicate that before the animal and fungi lineages diverged, TIM was an obligated oligomer with substrate binding properties and catalytic efficiency that resemble that of extant TIMs. Therefore, TIM function and association have been strongly coupled at least for the last third of biological evolution on earth. DATABASES: PDB Entry: 6NEE. ENZYMES: Triosephosphate isomerase 5.3.1.1, Glycerol-3-phosphate dehydrogenase 1.1.1.8.


Assuntos
Biocatálise , Evolução Biológica , Termodinâmica , Triose-Fosfato Isomerase/química , Triose-Fosfato Isomerase/metabolismo , Animais , Cristalografia por Raios X , Fungos/enzimologia , Ligação Proteica , Conformação Proteica , Estabilidade Proteica , Análise Espectral/métodos
14.
Peptides ; 94: 49-55, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28687455

RESUMO

Chemokines are important mediators of immunological responses during inflammation and under steady-state conditions. In addition to regulating cell migration, some chemotactic cytokines have direct effects on bacteria. Here, we characterized the antibacterial ability of the synthetic oligopeptide CCL1357-75, which corresponds to the carboxyl-terminal region of the human chemokine CCL13. In vitro measurements indicated that CCL1357-75 disrupts the cell membrane of Pseudomonas aeruginosa through a mechanism coupled to an unordered-helicoidal conformational transition. In a murine pneumonic model, CCL1357-75 improved mouse survival and bacterial clearance and decreased neutrophil recruitment, proinflammatory cytokines and lung pathology compared with that observed in untreated infected animals. Overall, our study supports the ability of chemokines and/or chemokine-derived oligopeptides to act as direct defense agents against pathogenic bacteria and suggests their potential use as alternative antibiotics.


Assuntos
Antibacterianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/farmacologia , Pneumonia Bacteriana/tratamento farmacológico , Infecções por Pseudomonas/tratamento farmacológico , Pseudomonas aeruginosa/efeitos dos fármacos , Animais , Antibacterianos/uso terapêutico , Peptídeos Catiônicos Antimicrobianos/uso terapêutico , Modelos Animais de Doenças , Humanos , Camundongos , Proteínas Quimioatraentes de Monócitos/química , Proteínas Quimioatraentes de Monócitos/metabolismo , Proteínas Quimioatraentes de Monócitos/farmacologia , Oligopeptídeos/farmacologia , Oligopeptídeos/uso terapêutico , Fragmentos de Peptídeos , Domínios Proteicos
16.
Amino Acids ; 49(2): 317-325, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-27896447

RESUMO

N-Glycosylation is a common post-translational modification that plays an important role in the proper folding and function of many proteins. This modification is largely dependent on the presence of a sequence motif called a "sequon" defined as Asn-Xxx-Ser/Thr. However, evidence has shown that the presence of such a "sequon" is insufficient to determine the occurrence of N-glycosylation with high precision. This study aims to elucidate patterns that can more accurately predict N-glycosylation sites in human proteins. The novel motifs are evaluated using benchmarking data from 188 organisms. Performance is largely sustained compared to the human data, which validates the robustness of the novel extracted "extended sequons". We, therefore, introduce new knowledge about sequence-related factors that control N-glycosylation.


Assuntos
Algoritmos , Proteínas/metabolismo , Bases de Dados de Proteínas , Glicosilação , Humanos , Processamento de Proteína Pós-Traducional , Proteínas/química , Software
17.
Biochim Biophys Acta ; 1857(9): 1392-1402, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27137408

RESUMO

The core of F1-ATPase consists of three catalytic (ß) and three noncatalytic (α) subunits, forming a hexameric ring in alternating positions. A wealth of experimental and theoretical data has provided a detailed picture of the complex role played by catalytic subunits. Although major conformational changes have only been seen in ß-subunits, it is clear that α-subunits have to respond to these changes in order to be able to transmit information during the rotary mechanism. However, the conformational behavior of α-subunits has not been explored in detail. Here, we have combined unbiased molecular dynamics (MD) simulations and calorimetrically measured thermodynamic signatures to investigate the conformational flexibility of isolated α-subunits, as a step toward deepening our understanding of its function inside the α3ß3 ring. The simulations indicate that the open-to-closed conformational transition of the α-subunit is essentially barrierless, which is ideal to accompany and transmit the movement of the catalytic subunits. Calorimetric measurements of the recombinant α-subunit from Geobacillus kaustophilus indicate that the isolated subunit undergoes no significant conformational changes upon nucleotide binding. Simulations confirm that the nucleotide-free and nucleotide-bound subunits show average conformations similar to that observed in the F1 crystal structure, but they reveal an increased conformational flexibility of the isolated α-subunit upon MgATP binding, which might explain the evolutionary conserved capacity of α-subunits to recognize nucleotides with considerable strength. Furthermore, we elucidate the different dependencies that α- and ß-subunits show on Mg(II) for recognizing ATP.


Assuntos
ATPases Translocadoras de Prótons/química , Calorimetria , Simulação de Dinâmica Molecular , Conformação Proteica , Subunidades Proteicas/química , Termodinâmica
18.
Rev Med Inst Mex Seguro Soc ; 53(2): 232-8, 2015.
Artigo em Espanhol | MEDLINE | ID: mdl-25760753

RESUMO

The non-Hodgkin lymphoma is a neoplastic entity that presents in extranodal form in 20 % of cases, usually occurs as solitary or generalized lymphadenopathy. There may be misdiagnosis if it manifests as primary extranodal disease because the primary infiltration may occur with different organs, despite the difficulty of diagnosis of primary extranodal location of non-Hodgkin lymphoma, histological and immunohistochemical studies are effective in preventing misdiagnosis. The presentation of this case is to describe this condition in its extranodal variety with cardiac infiltration in a 23 year-old woman with progressive dyspnea. Tumor mass was detected in right-atrial, venous catheterization biopsy was performed, this enabled the histopathological diagnosis and establish treatment. We present experiences from the attention of the case and review of the literature with special reference to diagnosis and treatment.


El linfoma no Hodgkin es una entidad neoplásica que puede presentarse extraganglionarmente en el 20 % de los casos, habitualmente se presenta como linfadenopatía solitaria o generalizada. Se puede presentar error en el diagnóstico si se manifiesta enfermedad primaria extraganglionar ya que pueden presentarse con infiltración primaria a diferentes órganos, a pesar de la dificultad del diagnóstico de linfoma no Hodgkin de localización primaria extraganglionar, los estudios histológicos e inmunohistoquímicos son efectivos a la hora de evitar un diagnóstico erróneo. La presentación de este caso tiene como objetivo describir este padecimiento en su variedad extraganglionar con infiltración cardiaca en una paciente de 23 años que debutó con disnea progresiva. Se detectó una masa tumoral intraauricular derecha, por lo que se realizó biopsia por cateterismo venoso, que permitió hacer el diagnóstico histopatológico y establecer el tratamiento. Se presentan las experiencias derivadas de la atención del caso y revisión de la literatura médica con especial referencia al diagnóstico y tratamiento.


Assuntos
Linfoma Difuso de Grandes Células B/diagnóstico , Diagnóstico Diferencial , Dispneia/etiologia , Feminino , Humanos , Linfoma Difuso de Grandes Células B/complicações , Adulto Jovem
19.
J Mol Recognit ; 28(2): 108-16, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25604964

RESUMO

The rational designing of binding abilities in proteins requires an understanding of the relationship between structure and thermodynamics. However, our knowledge of the molecular origin of high-affinity binding of ligands to proteins is still limited; such is the case for l-lysine-l-arginine-l-ornithine periplasmic binding protein (LAOBP), a periplasmic binding protein from Salmonella typhimurium that binds to l-arginine, l-lysine, and l-ornithine with nanomolar affinity and to l-histidine with micromolar affinity. Structural studies indicate that ligand binding induces a large conformational change in LAOBP. In this work, we studied the thermodynamics of l-histidine and l-arginine binding to LAOBP by isothermal titration calorimetry. For both ligands, the affinity is enthalpically driven, with a binding ΔCp of ~-300 cal mol(-1) K(-1) , most of which arises from the burial of protein nonpolar surfaces that accompanies the conformational change. Osmotic stress measurements revealed that several water molecules become sequestered upon complex formation. In addition, LAOBP prefers positively charged ligands in their side chain. An energetic analysis shows that the protein acquires a thermodynamically equivalent state with both ligands. The 1000-fold higher affinity of LAOBP for l-arginine as compared with l-histidine is mainly of enthalpic origin and can be ascribed to the formation of an extra pair of hydrogen bonds. Periplasmic binding proteins have evolved diverse energetic strategies for ligand recognition. STM4351, another arginine binding protein from Salmonella, shows an entropy-driven micromolar affinity toward l-arginine. In contrast, our data show that LAOBP achieves nanomolar affinity for the same ligand through enthalpy optimization.


Assuntos
Arginina/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Histidina/metabolismo , Salmonella typhimurium/metabolismo , Calorimetria , Cristalografia por Raios X , Ligação de Hidrogênio , Modelos Moleculares , Termodinâmica
20.
J Biol Chem ; 289(46): 31995-32009, 2014 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-25271167

RESUMO

Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association.


Assuntos
Phaseolus/química , Proteínas de Plantas/química , Sequência de Aminoácidos , Calorimetria , Cromatografia em Gel , Dicroísmo Circular , Reagentes de Ligações Cruzadas/química , Fluorometria , Espectroscopia de Ressonância Magnética , Espectrometria de Massas , Dados de Sequência Molecular , Concentração Osmolar , Ligação Proteica , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Homologia de Sequência de Aminoácidos , Água/química
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...