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1.
Trends Biochem Sci ; 2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38677921

RESUMO

The survival and virulence of Gram-negative bacteria require proper biogenesis and maintenance of the outer membrane (OM), which is densely packed with ß-barrel OM proteins (OMPs). Before reaching the OM, precursor unfolded OMPs (uOMPs) must cross the whole cell envelope. A network of periplasmic chaperones and proteases maintains unfolded but folding-competent conformations of these membrane proteins in the aqueous periplasm while simultaneously preventing off-pathway aggregation. These periplasmic proteins utilize different strategies, including conformational heterogeneity, oligomerization, multivalency, and kinetic partitioning, to perform and regulate their functions. Redundant and unique characteristics of the individual periplasmic players synergize to create a protein quality control team capable responding to changing environmental stresses.

2.
Proc Natl Acad Sci U S A ; 119(48): e2210536119, 2022 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-36417429

RESUMO

The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chain's intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting many proteins safe passage to their native states; however, it is challenging to interrogate the folding process for large numbers of proteins in a complex background with most biophysical techniques. Hence, most chaperone-assisted protein refolding studies are conducted in defined buffers on single purified clients. Here, we develop a limited proteolysis-mass spectrometry approach paired with an isotope-labeling strategy to globally monitor the structures of refolding Escherichia coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data and is particularly important for restoring acidic proteins and proteins with high molecular weight, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. We suggest that these proteins may fold most efficiently cotranslationally, and then remain kinetically trapped in their native conformations.


Assuntos
Proteínas de Escherichia coli , Redobramento de Proteína , Proteoma , Citosol/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Proteínas de Choque Térmico/metabolismo , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Proteoma/metabolismo
3.
Biophys J ; 2024 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-38778541

RESUMO

Polyethylene glycol (PEG) conjugation provides a protective modification that enhances the pharmacokinetics and solubility of proteins for therapeutic use. A knowledge of the structural ensemble of these PEGylated proteins is necessary to understand the molecular details that contribute to their hydrodynamic and colligative properties. Because of the large size and dynamic flexibility of pharmaceutically important PEGylated proteins, the determination of structure is challenging. In addition, the hydration of these conjugates that contain large polymers is difficult to determine with traditional methods that identify only first shell hydration water, which does not account for the complete hydrodynamic volume of a macromolecule. Here, we demonstrate that structural ensembles, generated by coarse-grained simulations, can be analyzed with HullRad and used to predict sedimentation coefficients and concentration-dependent hydrodynamic and diffusion nonideality coefficients of PEGylated proteins. A knowledge of these concentration-dependent properties enhances the ability to design and analyze new modified protein therapeutics. HullRad accomplishes this analysis by effectively accounting for the complete hydration of a macromolecule, including that of flexible polymers.

4.
Diabet Med ; 40(2): e14991, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36281547

RESUMO

AIMS: As an indicator of maternal cardiometabolic health, newborn birthweight may be an important predictor of maternal type 2 diabetes mellitus (diabetes). We evaluated the relation between offspring birthweight and onset of maternal diabetes after pregnancy. METHODS: This retrospective cohort study used linked population-based health databases from Ontario, Canada. We included women aged 16-50 years without pre-pregnancy diabetes, and who had a live birth between 2006 and 2014. We used Cox proportional hazard regression to evaluate the association between age- and sex-standardized offspring birthweight percentile categories and incident maternal diabetes, while adjusting for maternal age, parity, year, ethnicity, gestational diabetes (GDM) and hypertensive disorders of pregnancy (HDP). Results were further stratified by the presence of GDM in the index pregnancy. RESULTS: Of 893,777 eligible participants, 14,329 (1.6%) women were diagnosed with diabetes over a median (IQR) of 4.4 (1.5-7.4) years of follow-up. There was a continuous positive relation between newborn birthweight above the 75th percentile and maternal diabetes. Relative to a birthweight between the 50th and 74.9th percentiles, women whose newborn had a birthweight between the 97th and 100th percentiles had an adjusted hazards ratio (aHR) of diabetes of 2.30 (95% CI 2.16-2.46), including an aHR of 2.01 (95% CI 1.83-2.21) among those with GDM, and 2.59 (2.36-2.84) in those without GDM. CONCLUSIONS: A higher offspring birthweight signals an increased risk of maternal diabetes, offering another potentially useful way to identify women especially predisposed to diabetes.


Assuntos
Diabetes Mellitus Tipo 2 , Diabetes Gestacional , Estado Pré-Diabético , Gravidez , Recém-Nascido , Humanos , Feminino , Masculino , Diabetes Gestacional/diagnóstico , Peso ao Nascer , Diabetes Mellitus Tipo 2/etiologia , Diabetes Mellitus Tipo 2/complicações , Estudos Retrospectivos , Estado Pré-Diabético/complicações , Ontário/epidemiologia
5.
Diabet Med ; 40(8): e15128, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37143386

RESUMO

AIMS: The aim of this study was to examine the influence of immigration status and region of origin on the risk of type 2 diabetes in women with prior gestational diabetes (GDM). METHODS: This retrospective population-based cohort study included women with gestational diabetes (GDM) aged 16 to 50 years in Ontario, Canada, who gave birth between 2006 and 2014. We compared the incidence of type 2 diabetes after delivery between long-term residents and immigrants-overall, by time since immigration and by region of-using Cox regression adjusted for age, year, neighbourhood income, rurality, infant birth weight and presence of hypertensive disorders of pregnancy (HDP). RESULTS: Among 38,515 women with prior GDM (42% immigrants), immigrants had a significantly higher risk of type 2 diabetes compared with long-term residents (adjusted hazard ratio [HR] 1.19, 95% confidence interval [CI] 1.13-1.26), with no meaningful difference based on time since immigration. The highest adjusted relative risks of type 2 diabetes compared with long-term residents were found for immigrants from Sub-Saharan Africa (HR 1.63, 95% CI 1.40-1.90), Latin America/Caribbean (HR 1.44, 95% CI 1.28-1.62) and South Asia (HR 1.34, 95% CI 1.25-1.44). CONCLUSIONS: Immigration is associated with a significantly higher risk of type 2 diabetes after GDM, particularly for women from certain low- and middle-income countries. Diabetes prevention strategies will need to consider the unique needs of immigrants from these regions.


Assuntos
Diabetes Mellitus Tipo 2 , Diabetes Gestacional , Feminino , Humanos , Gravidez , Estudos de Coortes , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/epidemiologia , Diabetes Gestacional/diagnóstico , Diabetes Gestacional/epidemiologia , Emigração e Imigração , Ontário/epidemiologia , Estudos Retrospectivos , Adolescente , Adulto Jovem , Adulto , Pessoa de Meia-Idade
6.
Eur Biophys J ; 52(4-5): 215-224, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-36602579

RESUMO

Hydration of biological macromolecules is important for their stability and function. Historically, attempts have been made to describe the degree of macromolecular hydration using a single parameter over a narrow range of values. Here, we describe a method to calculate two types of hydration: surface shell water and entrained water. A consideration of these two types of hydration helps to explain the "hydration problem" in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and related macromolecular properties such as sedimentation and diffusion coefficients, intrinsic viscosities, and the concentration-dependent non-ideality identified with sedimentation velocity experiments.


Assuntos
Hidrodinâmica , Água , Substâncias Macromoleculares , Fenômenos Físicos , Viscosidade
7.
Eur Biophys J ; 52(4-5): 415-425, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-36899114

RESUMO

Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative bacteria. Here, we developed a method to model unfolded OMP (uOMP) conformational ensembles using the experimental properties of two well-studied OMPs. The overall sizes and shapes of the unfolded ensembles in the absence of a denaturant were experimentally defined by measuring the sedimentation coefficient as a function of urea concentration. We used these data to model a full range of unfolded conformations by parameterizing a targeted coarse-grained simulation protocol. The ensemble members were further refined by short molecular dynamics simulations to reflect proper torsion angles. The final conformational ensembles have polymer properties different from unfolded soluble and intrinsically disordered proteins and reveal inherent differences in the unfolded states that necessitate further investigation. Building these uOMP ensembles advances the understanding of OMP biogenesis and provides essential information for interpreting structures of uOMP-chaperone complexes.


Assuntos
Proteínas da Membrana Bacteriana Externa , Hidrodinâmica , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Chaperonas Moleculares/metabolismo , Periplasma/metabolismo , Membrana Celular/metabolismo , Conformação Proteica
8.
Proc Natl Acad Sci U S A ; 117(45): 28026-28035, 2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-33093201

RESUMO

The periplasmic chaperone network ensures the biogenesis of bacterial outer membrane proteins (OMPs) and has recently been identified as a promising target for antibiotics. SurA is the most important member of this network, both due to its genetic interaction with the ß-barrel assembly machinery complex as well as its ability to prevent unfolded OMP (uOMP) aggregation. Using only binding energy, the mechanism by which SurA carries out these two functions is not well-understood. Here, we use a combination of photo-crosslinking, mass spectrometry, solution scattering, and molecular modeling techniques to elucidate the key structural features that define how SurA solubilizes uOMPs. Our experimental data support a model in which SurA binds uOMPs in a groove formed between the core and P1 domains. This binding event results in a drastic expansion of the rest of the uOMP, which has many biological implications. Using these experimental data as restraints, we adopted an integrative modeling approach to create a sparse ensemble of models of a SurA•uOMP complex. We validated key structural features of the SurA•uOMP ensemble using independent scattering and chemical crosslinking data. Our data suggest that SurA utilizes three distinct binding modes to interact with uOMPs and that more than one SurA can bind a uOMP at a time. This work demonstrates that SurA operates in a distinct fashion compared to other chaperones in the OMP biogenesis network.


Assuntos
Proteínas de Transporte/metabolismo , Proteínas de Escherichia coli/metabolismo , Chaperonas Moleculares/metabolismo , Peptidilprolil Isomerase/metabolismo , Membrana Externa Bacteriana/metabolismo , Membrana Externa Bacteriana/fisiologia , Proteínas da Membrana Bacteriana Externa/metabolismo , Membrana Celular/metabolismo , Escherichia coli/enzimologia , Escherichia coli/metabolismo , Modelos Biológicos , Periplasma/metabolismo , Dobramento de Proteína
9.
Diabetologia ; 64(4): 805-813, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33486538

RESUMO

AIMS/HYPOTHESIS: The aim of this study was to examine how BMI influences the association between Asian ethnicity and risk of gestational diabetes (GDM). METHODS: This population-based cohort study included pregnant women without pre-existing diabetes mellitus in Ontario, Canada between 2012 and 2014. Women of Chinese and South Asian ethnicity were identified using a validated surname algorithm. GDM was ascertained using hospitalisation codes. The relationship between ethnicity and GDM was modelled using modified Poisson regression, adjusted for maternal age, pre-pregnancy BMI, parity, previous GDM, long-term residency status, income quintile and smoking status. An interaction term between ethnicity and pre-pregnancy BMI was tested. RESULTS: Of 231,618 pregnant women, 9289 (4.0%) were of South Asian ethnicity and 12,240 (5.3%) were of Chinese ethnicity. Relative to women from the general population, in whom prevalence of GDM was 4.3%, the adjusted RR of GDM was higher among those of South Asian ethnicity (1.81 [95% CI 1.64, 1.99]) and Chinese ethnicity (1.66 [95% CI 1.53, 1.80]). The association between GDM and Asian ethnicity remained significant across BMI categories but differed according to BMI. The prevalence of GDM exceeded 5% at an estimated BMI of 21.5 kg/m2 among South Asian women, 23.0 kg/m2 among Chinese women and 29.5 kg/m2 among the general population. CONCLUSIONS/INTERPRETATION: The risk of GDM is significantly higher in South Asian and Chinese women, whose BMI is lower than that of women in the general population. Accordingly, targeted GDM prevention strategies may need to consider lower BMI cut-points for Asian populations.


Assuntos
Povo Asiático , Índice de Massa Corporal , Diabetes Gestacional/etnologia , Emigrantes e Imigrantes , Ganho de Peso na Gestação/etnologia , Disparidades nos Níveis de Saúde , Obesidade/etnologia , Adolescente , Adulto , China/etnologia , Diabetes Gestacional/diagnóstico , Feminino , Humanos , Pessoa de Meia-Idade , Obesidade/diagnóstico , Ontário/epidemiologia , Gravidez , Prevalência , Estudos Retrospectivos , Medição de Risco , Fatores de Risco , Adulto Jovem
10.
J Am Chem Soc ; 143(2): 764-772, 2021 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-33412852

RESUMO

Through the insertion of nonpolar side chains into the bilayer, the hydrophobic effect has long been accepted as a driving force for membrane protein folding. However, how the changing chemical composition of the bilayer affects the magnitude of the side-chain transfer free energies (ΔGsc°) has historically not been well understood. A particularly challenging region for experimental interrogation is the bilayer interfacial region that is characterized by a steep polarity gradient. In this study, we have determined the ΔGsc° for nonpolar side chains as a function of bilayer position using a combination of experiment and simulation. We discovered an empirical correlation between the surface area of the nonpolar side chain, the transfer free energies, and the local water concentration in the membrane that allows for ΔGsc° to be accurately estimated at any location in the bilayer. Using these water-to-bilayer ΔGsc° values, we calculated the interface-to-bilayer transfer free energy (ΔGi,b°). We find that the ΔGi,b° are similar to the "biological", translocon-based transfer free energies, indicating that the translocon energetically mimics the bilayer interface. Together these findings can be applied to increase the accuracy of computational workflows used to identify and design membrane proteins as well as bring greater insight into our understanding of how disease-causing mutations affect membrane protein folding and function.


Assuntos
Proteínas da Membrana Bacteriana Externa/química , Bicamadas Lipídicas/química , Proteínas de Membrana/química , Fosfolipases A1/química , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Estabilidade Proteica , Termodinâmica
12.
Trends Biochem Sci ; 41(10): 872-882, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27450425

RESUMO

Outer membrane proteins (OMPs) play a central role in the integrity of the outer membrane of Gram-negative bacteria. Unfolded OMPs (uOMPs) transit across the periplasm, and subsequent folding and assembly are crucial for biogenesis. Chaperones and the essential ß-barrel assembly machinery (BAM) complex facilitate these processes. In vitro studies suggest that some chaperones sequester uOMPs in internal cavities during their periplasmic transit to prevent deleterious aggregation. Upon reaching the outer membrane, the BAM complex acts catalytically to accelerate uOMP folding. Complementary in vivo experiments have revealed the localization and activity of the BAM complex in living cells. Completing an understanding of OMP biogenesis will require a holistic view of the interplay among the individual components discussed here.


Assuntos
Proteínas da Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Chaperonas Moleculares/química , Periplasma/metabolismo , Proteínas da Membrana Bacteriana Externa/genética , Proteínas da Membrana Bacteriana Externa/metabolismo , Sítios de Ligação , Escherichia coli/genética , Escherichia coli/ultraestrutura , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Simulação de Dinâmica Molecular , Periplasma/genética , Periplasma/ultraestrutura , Ligação Proteica , Conformação Proteica em Folha beta , Dobramento de Proteína , Domínios e Motivos de Interação entre Proteínas , Transporte Proteico , Desdobramento de Proteína , Termodinâmica
13.
Biophys J ; 118(8): 2042-2055, 2020 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-32224301

RESUMO

Protein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. Although soluble protein design has advanced, membrane protein design remains challenging because of difficulties in modeling the lipid bilayer. In this work, we developed an implicit approach that captures the anisotropic structure, shape of water-filled pores, and nanoscale dimensions of membranes with different lipid compositions. The model improves performance in computational benchmarks against experimental targets, including prediction of protein orientations in the bilayer, ΔΔG calculations, native structure discrimination, and native sequence recovery. When applied to de novo protein design, this approach designs sequences with an amino acid distribution near the native amino acid distribution in membrane proteins, overcoming a critical flaw in previous membrane models that were prone to generating leucine-rich designs. Furthermore, the proteins designed in the new membrane model exhibit native-like features including interfacial aromatic side chains, hydrophobic lengths compatible with bilayer thickness, and polar pores. Our method advances high-resolution membrane protein structure prediction and design toward tackling key biological questions and engineering challenges.


Assuntos
Bicamadas Lipídicas , Proteínas de Membrana , Aminoácidos , Interações Hidrofóbicas e Hidrofílicas , Software
14.
J Am Chem Soc ; 142(13): 6227-6235, 2020 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-32134659

RESUMO

A hallmark feature of biological lipid bilayer structure is a depth-dependent polarity gradient largely resulting from the change in water concentration over the angstrom length scale. This gradient is particularly steep as it crosses the membrane interfacial regions where the water concentration drops at least a million-fold along the direction of the bilayer normal. Although local water content is often assumed to be a major determinant of membrane protein stability, the effect of the water-induced polarity gradient upon backbone hydrogen bond strength has not been systematically investigated. We addressed this question by measuring the free energy change for a number of backbone hydrogen bonds in the transmembrane protein OmpW. These values were obtained at 33 backbone amides from hydrogen/deuterium fractionation factors by nuclear magnetic resonance spectroscopy. We surprisingly found that OmpW backbone hydrogen bond energies do not vary over a wide range of water concentrations that are characteristic of the solvation environment in the bilayer interfacial region. We validated the interpretation of our results by determining the hydrodynamic and solvation properties of our OmpW-micelle complex using analytical ultracentrifugation and molecular dynamics simulations. The magnitudes of the backbone hydrogen bond free energy changes in our study are comparable to those observed in water-soluble proteins, the H-segment of the leader peptidase helix used in the von Heijne and White biological scale experiments, and several interfacial peptides. Our results agree with those reported for the transmembrane α-helical portion of the amyloid precursor protein after the latter values were adjusted for kinetic isotope effects. Overall, our work suggests that backbone hydrogen bonds provide modest thermodynamic stability to membrane protein structures and that many amides are unaffected by dehydration within the bilayer.


Assuntos
Proteínas da Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Escherichia coli/química , Água/química , Ligação de Hidrogênio , Modelos Moleculares , Estabilidade Proteica , Termodinâmica
15.
Nat Methods ; 14(4): 427-434, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28288122

RESUMO

Compartmentalized biochemical activities are essential to all cellular processes, but there is no generalizable method to visualize dynamic protein activities in living cells at a resolution commensurate with cellular compartmentalization. Here, we introduce a new class of fluorescent biosensors that detect biochemical activities in living cells at a resolution up to threefold better than the diffraction limit. These 'FLINC' biosensors use binding-induced changes in protein fluorescence dynamics to translate kinase activities or protein-protein interactions into changes in fluorescence fluctuations, which are quantifiable through stochastic optical fluctuation imaging. A protein kinase A (PKA) biosensor allowed us to resolve minute PKA activity microdomains on the plasma membranes of living cells and to uncover the role of clustered anchoring proteins in organizing these activity microdomains. Together, these findings suggest that biochemical activities of the cell are spatially organized into an activity architecture whose structural and functional characteristics can be revealed by these new biosensors.


Assuntos
Técnicas Biossensoriais/métodos , Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Membrana Celular/metabolismo , Proteínas Quinases Dependentes de AMP Cíclico/análise , Escherichia coli/genética , Transferência Ressonante de Energia de Fluorescência/métodos , Corantes Fluorescentes , Proteínas de Fluorescência Verde/metabolismo , Células HeLa , Humanos , Microscopia/instrumentação , Microscopia/métodos , Imagem Molecular/métodos , Mutagênese Sítio-Dirigida , Mapeamento de Interação de Proteínas/métodos , Processos Estocásticos
16.
Angew Chem Int Ed Engl ; 59(27): 11108-11114, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32277554

RESUMO

The internal motions of integral membrane proteins have largely eluded comprehensive experimental characterization. Here the fast side-chain dynamics of the α-helical sensory rhodopsin II and the ß-barrel outer membrane protein W have been investigated in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Despite their differing topologies, both proteins have a similar distribution of methyl-bearing side-chain motion that is largely independent of membrane mimetic. The methyl-bearing side chains of both proteins are, on average, more dynamic in the ps-ns timescale than any soluble protein characterized to date. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect. Furthermore, the high conformational entropy could greatly influence the thermodynamics underlying membrane-protein functions, including ligand binding, allostery, and signaling.


Assuntos
Entropia , Proteínas de Membrana/química , Cristalografia por Raios X , Conformação Molecular , Ressonância Magnética Nuclear Biomolecular
17.
Proc Natl Acad Sci U S A ; 113(33): E4794-800, 2016 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-27482090

RESUMO

Outer membrane protein (OMP) biogenesis is critical to bacterial physiology because the cellular envelope is vital to bacterial pathogenesis and antibiotic resistance. The process of OMP biogenesis has been studied in vivo, and each of its components has been studied in isolation in vitro. This work integrates parameters and observations from both in vivo and in vitro experiments into a holistic computational model termed "Outer Membrane Protein Biogenesis Model" (OMPBioM). We use OMPBioM to assess OMP biogenesis mathematically in a global manner. Using deterministic and stochastic methods, we are able to simulate OMP biogenesis under varying genetic conditions, each of which successfully replicates experimental observations. We observe that OMPs have a prolonged lifetime in the periplasm where an unfolded OMP makes, on average, hundreds of short-lived interactions with chaperones before folding into its native state. We find that some periplasmic chaperones function primarily as quality-control factors; this function complements the folding catalysis function of other chaperones. Additionally, the effective rate for the ß-barrel assembly machinery complex necessary for physiological folding was found to be higher than has currently been observed in vitro. Overall, we find a finely tuned balance between thermodynamic and kinetic parameters maximizes OMP folding flux and minimizes aggregation and unnecessary degradation. In sum, OMPBioM provides a global view of OMP biogenesis that yields unique insights into this essential pathway.


Assuntos
Proteínas da Membrana Bacteriana Externa/biossíntese , Chaperonas Moleculares/fisiologia , Periplasma/metabolismo , Proteínas da Membrana Bacteriana Externa/química , Proteínas de Transporte/fisiologia , Proteínas de Escherichia coli/fisiologia , Proteínas de Choque Térmico/fisiologia , Peptidilprolil Isomerase/fisiologia , Proteínas Periplásmicas/fisiologia , Agregados Proteicos , Dobramento de Proteína , Serina Endopeptidases/fisiologia , Processos Estocásticos
18.
Biophys J ; 114(4): 856-869, 2018 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-29490246

RESUMO

Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.


Assuntos
Proteínas Intrinsicamente Desordenadas/química , Ácidos Nucleicos/química , Dobramento de Proteína , Software , Animais , Humanos , Hidrodinâmica , Modelos Moleculares , Conformação Proteica
19.
Mol Microbiol ; 106(5): 777-792, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28941249

RESUMO

Almost all bacterial outer membrane proteins (OMPs) contain a ß barrel domain that serves as a membrane anchor, but the assembly and quality control of these proteins are poorly understood. Here, we show that the introduction of a single lipid-facing arginine residue near the middle of the ß barrel of the Escherichia coli OMPs OmpLA and EspP creates an energy barrier that impedes membrane insertion. Although several unintegrated OmpLA mutants remained insertion-competent, they were slowly degraded by the periplasmic protease DegP. Two EspP mutants were also gradually degraded by DegP but were toxic because they first bound to the Bam complex, an essential heteroligomer that catalyzes the membrane insertion of OMPs. Interestingly, another EspP mutant likewise formed a prolonged, deleterious interaction with the Bam complex but was protected from degradation and eventually inserted into the membrane in a native conformation. The different types of interactions between the EspP mutants and the Bam complex that we observed may correspond to distinct stages in OMP assembly. Our results show that sequences that significantly delay assembly are disfavored not only because unintegrated OMPs are subjected to degradation, but also because OMPs that assemble slowly can form dominant-negative interactions with the Bam complex.


Assuntos
Proteínas da Membrana Bacteriana Externa/genética , Proteínas de Escherichia coli/genética , Fosfolipases A1/genética , Serina Endopeptidases/genética , Proteínas da Membrana Bacteriana Externa/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas de Choque Térmico/metabolismo , Periplasma/metabolismo , Proteínas Periplásmicas/metabolismo , Fosfolipases A1/metabolismo , Domínios Proteicos/genética , Dobramento de Proteína , Estrutura Terciária de Proteína/genética , Serina Endopeptidases/metabolismo
20.
J Obstet Gynaecol Can ; 40(11): 1538-1548, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30343980

RESUMO

OBJECTIF: L'objectif est de guider les femmes enceintes et les professionnels de l'obstétrique et de l'exercice en ce qui concerne l'activité physique prénatale. RéSULTATS: Les issues évaluées étaient la morbidité maternelle, fœtale ou néonatale et la mortalité fœtale pendant et après la grossesse. DONNéES: Nous avons interrogé MEDLINE, Embase, PsycINFO, la Cochrane Database of Systematic Reviews, le Cochrane Central Register of Controlled Trials, Scopus et la Web of Science Core Collection, CINAHL Plus with Full Text, Child Development & Adolescent Studies, ERIC, SPORTDiscus, ClinicalTrials.gov de leur création jusqu'au 6 janvier 2017. Les études primaires de tous types étaient admissibles, à l'exception des études de cas. Seules les publications en anglais, en espagnol et en français ont été retenues. Les articles liés à l'activité physique durant la grossesse qui abordaient la morbidité maternelle, fœtale ou néonatale ou la mortalité fœtale étaient admissibles. La qualité des données probantes a été évaluée au moyen de l'approche GRADE (Grading of Recommendations Assessment, Development and Evaluation). VALEURS: Le groupe d'experts responsable des lignes directrices a recueilli les commentaires d'utilisateurs finaux (fournisseurs de soins obstétricaux, professionnels de l'exercice, chercheurs, organismes responsables de politiques, et femmes enceintes et en période postpartum). La directive clinique a été élaborée au moyen de l'outil Appraisal of Guidelines for Research Evaluation (AGREE) II. AVANTAGES, INCONVéNIENTS, ET COûTS: Les avantages de l'activité physique prénatale sont modérés, et aucun inconvénient n'a été relevé; la différence entre les conséquences désirables et indésirables (avantage net) devrait donc être modérée. La majorité des intervenants et des utilisateurs finaux ont indiqué qu'il serait faisable, acceptable et équitable de suivre ces recommandations, qui nécessitent généralement des ressources minimes de la part des personnes et des systèmes de santé. PRÉAMBULE: Les présentes lignes directrices contiennent des recommandations fondées sur des données probantes au sujet de l'activité physique durant la grossesse visant à favoriser la santé maternelle, fœtale et néonatale. En l'absence de contre-indications (voir la liste détaillée plus loin), le fait de suivre ces lignes directrices est associé à : 1) moins de complications pour le nouveau-né (p. ex., gros par rapport à l'âge gestationnel); et 2) des bienfaits pour la santé maternelle (p. ex., diminution du risque de prééclampsie, d'hypertension gravidique, de diabète gestationnel, de césarienne, d'accouchement opératoire, d'incontinence urinaire, de gain de poids excessif durant la grossesse et de dépression; amélioration de la glycémie; diminution du gain de poids total durant la grossesse; et diminution de la gravité des symptômes dépressifs et de la douleur lombo-pelvienne). L'activité physique n'est pas associée à la fausse couche, à la mortinaissance, au décès néonatal, à l'accouchement prématuré, à la rupture prématurée préterme des membranes, à l'hypoglycémie néonatale, au poids insuffisant à la naissance, aux anomalies congénitales, au déclenchement du travail, ou aux complications à la naissance. En général, une augmentation de l'activité physique (fréquence, durée ou volume) est liée à une augmentation des bienfaits. Cependant, nous n'avons pas trouvé de données probantes concernant l'innocuité ou l'avantage accru de l'exercice à des niveaux considérablement supérieurs aux recommandations. L'activité physique prénatale devrait être vue comme un traitement de première ligne pour réduire le risque de complications de la grossesse et améliorer la santé physique et mentale de la mère. Pour les femmes enceintes qui n'atteignent actuellement pas le niveau recommandé, nous recommandons une augmentation progressive pour l'atteindre. Les femmes déjà actives peuvent continuer de l'être tout au long de la grossesse. Elles pourraient devoir modifier le type d'activité à mesure que leur grossesse avance. Il peut devenir impossible de suivre les lignes directrices pendant certaines périodes en raison de la fatigue ou des inconforts de la grossesse; nous encourageons les femmes à faire ce qu'elles peuvent et à revenir aux recommandations lorsqu'elles en sont capables. Les recommandations qui suivent reposent sur une revue systématique approfondie de la littérature, l'opinion d'experts, la consultation d'utilisateurs finaux et des considérations de faisabilité, d'acceptabilité, de coût et d'équité. RECOMMANDATIONS: Les recommandations des Lignes directrices canadiennes sur l'activité physique durant la grossesse 2019 sont fournies ci-dessous avec des énoncés indiquant la qualité des données probantes utilisées et la force des recommandations (des explications suivent). CONTRE-INDICATIONS: Toutes les femmes enceintes peuvent faire de l'activité physique durant la grossesse, sauf celles qui présentent des contre-indications (voir ci-dessous). Celles présentant des contre-indications absolues peuvent poursuivre leurs activités quotidiennes habituelles, mais ne devraient pas faire d'activités plus vigoureuses. Celles présentant des contre-indications relatives devraient discuter des avantages et des inconvénients de l'activité physique d'intensité modérée à vigoureuse avec leur fournisseur de soins obstétricaux avant d'y prendre part. CONTRE-INDICATIONS ABSOLUES: Contre-indications relatives FORCE DES RECOMMANDATIONS: Nous avons utilisé le système GRADE pour évaluer la force des recommandations. Les recommandations sont jugées fortes ou faibles en fonction de : 1) l'équilibre entre les avantages et les inconvénients; 2) la qualité globale des données probantes; 3) l'importance des issues (valeurs et préférences des femmes enceintes); 4) l'utilisation de ressources (coût); 5) l'incidence sur l'équité en matière de santé; 6) la faisabilité et 7) l'acceptabilité. Recommandation forte : La majorité ou la totalité des femmes enceintes auraient avantage à suivre la recommandation. Recommandation faible : Les femmes enceintes n'auraient pas toutes avantage à suivre la recommandation; il faut tenir compte d'autres facteurs comme la situation, les préférences, les valeurs, les ressources et le milieu de chaque personne. La consultation d'un fournisseur de soins obstétricaux peut faciliter la prise de décisions. QUALITé DES DONNéES PROBANTES: La qualité des données probantes fait référence au degré de confiance dans les données et va de très faible à élevée. Qualité élevée : Le groupe d'experts responsable des lignes directrices est très convaincu que l'effet estimé de l'activité physique sur l'issue de santé est près de l'effet réel. Qualité moyenne : Le groupe d'experts responsable des lignes directrices a moyennement confiance en l'effet estimé de l'activité physique sur l'issue de santé; l'effet estimé est probablement près de l'effet réel, mais il est possible qu'il soit très différent. Qualité faible : Le groupe d'experts responsable des lignes directrices a peu confiance en l'effet estimé de l'activité physique sur l'issue de santé; l'effet estimé pourrait être très différent de l'effet réel. Qualité très faible : Le groupe d'experts responsable des lignes directrices a très peu confiance en l'effet estimé de l'activité physique sur l'issue de santé; l'effet estimé est probablement très différent de l'effet réel. a Il s'agit d'une recommandation faible parce que la qualité des données probantes était faible et que l'avantage net entre les femmes qui étaient physiquement actives et celles qui ne l'étaient pas était petit. b Il s'agit d'une recommandation forte parce que, malgré le fait que les données probantes appuyant l'activité physique durant la grossesse pour les femmes en surpoids ou obèses étaient de qualité faible, des données tirées d'essais cliniques randomisés démontraient une diminution du gain de poids durant la grossesse et une amélioration de la glycémie. c On parle d'intensité modérée lorsque l'activité est assez intense pour augmenter la fréquence cardiaque de façon perceptible; une personne peut parler, mais pas chanter durant les activités de cette intensité. Pensons par exemple à la marche rapide, à la gymnastique aquatique, au vélo stationnaire (effort modéré), à l'entraînement musculaire, au port de charges modérées et aux travaux ménagers (p. ex., jardinage, lavage de fenêtres). d Il s'agit d'une recommandation faible parce que l'incontinence urinaire n'était pas jugée comme étant une issue « critique ¼ et que les données étaient de qualité faible. e Il s'agit d'une recommandation faible parce que : 1) la qualité des données probantes était très faible; et 2) bien que nous ayons étudié les inconvénients, il y avait peu de renseignements disponibles sur l'équilibre entre les avantages et les inconvénients. Cette recommandation était principalement fondée sur l'opinion d'experts.

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