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1.
Trends Biochem Sci ; 49(8): 667-680, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38677921

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa , Bacterias Gramnegativas , Chaperonas Moleculares , Proteínas Periplasmáticas , Proteínas de la Membrana Bacteriana Externa/biosíntesis , Bacterias Gramnegativas/genética , Bacterias Gramnegativas/metabolismo , Bacterias Gramnegativas/patogenicidad , Pliegue de Proteína , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Proteínas Periplasmáticas/metabolismo , Conformación Proteica
2.
Proc Natl Acad Sci U S A ; 119(48): e2210536119, 2022 11 29.
Artículo en Inglés | MEDLINE | ID: mdl-36417429

RESUMEN

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.


Asunto(s)
Proteínas de Escherichia coli , Replegamiento Proteico , 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 ; 123(16): 2379-2391, 2024 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-38778541

RESUMEN

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.


Asunto(s)
Hidrodinámica , Polietilenglicoles , Polietilenglicoles/química , Humanos , Albúmina Sérica Humana/química , Simulación de Dinámica Molecular , Agua/química , Difusión
4.
Diabet Med ; 40(2): e14991, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36281547

RESUMEN

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.


Asunto(s)
Diabetes Mellitus Tipo 2 , Diabetes Gestacional , Estado Prediabético , Embarazo , Recién Nacido , Humanos , Femenino , Masculino , Diabetes Gestacional/diagnóstico , Peso al Nacer , Diabetes Mellitus Tipo 2/etiología , Diabetes Mellitus Tipo 2/complicaciones , Estudios Retrospectivos , Estado Prediabético/complicaciones , Ontario/epidemiología
5.
Diabet Med ; 40(8): e15128, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37143386

RESUMEN

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.


Asunto(s)
Diabetes Mellitus Tipo 2 , Diabetes Gestacional , Femenino , Humanos , Embarazo , Estudios de Cohortes , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/epidemiología , Diabetes Gestacional/diagnóstico , Diabetes Gestacional/epidemiología , Emigración e Inmigración , Ontario/epidemiología , Estudios Retrospectivos , Adolescente , Adulto Joven , Adulto , Persona de Mediana Edad
6.
Eur Biophys J ; 52(4-5): 215-224, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-36602579

RESUMEN

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.


Asunto(s)
Hidrodinámica , Agua , Sustancias Macromoleculares , Fenómenos Físicos , Viscosidad
7.
Eur Biophys J ; 52(4-5): 415-425, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-36899114

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa , Hidrodinámica , Proteínas de la Membrana Bacteriana Externa/química , Proteínas de la Membrana Bacteriana Externa/metabolismo , Chaperonas Moleculares/metabolismo , Periplasma/metabolismo , Membrana Celular/metabolismo , Conformación Proteica
8.
Proc Natl Acad Sci U S A ; 117(45): 28026-28035, 2020 11 10.
Artículo en Inglés | MEDLINE | ID: mdl-33093201

RESUMEN

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.


Asunto(s)
Proteínas Portadoras/metabolismo , Proteínas de Escherichia coli/metabolismo , Chaperonas Moleculares/metabolismo , Isomerasa de Peptidilprolil/metabolismo , Membrana Externa Bacteriana/metabolismo , Membrana Externa Bacteriana/fisiología , Proteínas de la Membrana Bacteriana Externa/metabolismo , Membrana Celular/metabolismo , Escherichia coli/enzimología , Escherichia coli/metabolismo , Modelos Biológicos , Periplasma/metabolismo , Pliegue de Proteína
9.
Diabetologia ; 64(4): 805-813, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33486538

RESUMEN

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.


Asunto(s)
Pueblo Asiatico , Índice de Masa Corporal , Diabetes Gestacional/etnología , Emigrantes e Inmigrantes , Ganancia de Peso Gestacional/etnología , Disparidades en el Estado de Salud , Obesidad/etnología , Adolescente , Adulto , China/etnología , Diabetes Gestacional/diagnóstico , Femenino , Humanos , Persona de Mediana Edad , Obesidad/diagnóstico , Ontario/epidemiología , Embarazo , Prevalencia , Estudios Retrospectivos , Medición de Riesgo , Factores de Riesgo , Adulto Joven
10.
J Am Chem Soc ; 143(2): 764-772, 2021 01 20.
Artículo en Inglés | MEDLINE | ID: mdl-33412852

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/química , Membrana Dobles de Lípidos/química , Proteínas de la Membrana/química , Fosfolipasas A1/química , Interacciones Hidrofóbicas e Hidrofílicas , Simulación de Dinámica Molecular , Estabilidad Proteica , Termodinámica
12.
Trends Biochem Sci ; 41(10): 872-882, 2016 10.
Artículo en Inglés | MEDLINE | ID: mdl-27450425

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Chaperonas Moleculares/química , Periplasma/metabolismo , Proteínas de la Membrana Bacteriana Externa/genética , Proteínas de la Membrana Bacteriana Externa/metabolismo , Sitios de Unión , Escherichia coli/genética , Escherichia coli/ultraestructura , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Expresión Génica , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Simulación de Dinámica Molecular , Periplasma/genética , Periplasma/ultraestructura , Unión Proteica , Conformación Proteica en Lámina beta , Pliegue de Proteína , Dominios y Motivos de Interacción de Proteínas , Transporte de Proteínas , Desplegamiento Proteico , Termodinámica
13.
Biophys J ; 118(8): 2042-2055, 2020 04 21.
Artículo en Inglés | MEDLINE | ID: mdl-32224301

RESUMEN

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.


Asunto(s)
Membrana Dobles de Lípidos , Proteínas de la Membrana , Aminoácidos , Interacciones Hidrofóbicas e Hidrofílicas , Programas Informáticos
14.
J Am Chem Soc ; 142(13): 6227-6235, 2020 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-32134659

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Escherichia coli/química , Agua/química , Enlace de Hidrógeno , Modelos Moleculares , Estabilidad Proteica , Termodinámica
15.
Nat Methods ; 14(4): 427-434, 2017 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-28288122

RESUMEN

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.


Asunto(s)
Técnicas Biosensibles/métodos , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Membrana Celular/metabolismo , Proteínas Quinasas Dependientes de AMP Cíclico/análisis , Escherichia coli/genética , Transferencia Resonante de Energía de Fluorescencia/métodos , Colorantes Fluorescentes , Proteínas Fluorescentes Verdes/metabolismo , Células HeLa , Humanos , Microscopía/instrumentación , Microscopía/métodos , Imagen Molecular/métodos , Mutagénesis Sitio-Dirigida , Mapeo de Interacción de Proteínas/métodos , Procesos Estocásticos
16.
Angew Chem Int Ed Engl ; 59(27): 11108-11114, 2020 06 26.
Artículo en Inglés | MEDLINE | ID: mdl-32277554

RESUMEN

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.


Asunto(s)
Entropía , Proteínas de la Membrana/química , Cristalografía por Rayos X , Conformación Molecular , Resonancia Magnética Nuclear Biomolecular
17.
Proc Natl Acad Sci U S A ; 113(33): E4794-800, 2016 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-27482090

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/biosíntesis , Chaperonas Moleculares/fisiología , Periplasma/metabolismo , Proteínas de la Membrana Bacteriana Externa/química , Proteínas Portadoras/fisiología , Proteínas de Escherichia coli/fisiología , Proteínas de Choque Térmico/fisiología , Isomerasa de Peptidilprolil/fisiología , Proteínas Periplasmáticas/fisiología , Agregado de Proteínas , Pliegue de Proteína , Serina Endopeptidasas/fisiología , Procesos Estocásticos
18.
Biophys J ; 114(4): 856-869, 2018 02 27.
Artículo en Inglés | MEDLINE | ID: mdl-29490246

RESUMEN

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.


Asunto(s)
Proteínas Intrínsecamente Desordenadas/química , Ácidos Nucleicos/química , Pliegue de Proteína , Programas Informáticos , Animales , Humanos , Hidrodinámica , Modelos Moleculares , Conformación Proteica
19.
Mol Microbiol ; 106(5): 777-792, 2017 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-28941249

RESUMEN

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.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/genética , Proteínas de Escherichia coli/genética , Fosfolipasas A1/genética , Serina Endopeptidasas/genética , Proteínas de la Membrana Bacteriana Externa/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas de Choque Térmico/metabolismo , Periplasma/metabolismo , Proteínas Periplasmáticas/metabolismo , Fosfolipasas A1/metabolismo , Dominios Proteicos/genética , Pliegue de Proteína , Estructura Terciaria de Proteína/genética , Serina Endopeptidasas/metabolismo
20.
J Obstet Gynaecol Can ; 40(11): 1528-1537, 2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-30297272

RESUMEN

OBJECTIVE: The objective is to provide guidance for pregnant women, and obstetric care and exercise professionals, on prenatal physical activity. OUTCOMES: The outcomes evaluated were maternal, fetal, or neonatal morbidity or fetal mortality during and following pregnancy. EVIDENCE: Literature was retrieved through searches of Medline, EMBASE, PsycINFO, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Scopus and Web of Science Core Collection, CINAHL Plus with Full-text, Child Development & Adolescent Studies, ERIC, Sport Discus, ClinicalTrials.gov, and the Trip Database from database inception up to January 6, 2017. Primary studies of any design were eligible, except case studies. Results were limited to English, Spanish, or French language materials. Articles related to maternal physical activity during pregnancy reporting on maternal, fetal, or neonatal morbidity or fetal mortality were eligible for inclusion. The quality of evidence was rated using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) methodology. VALUES: The Guidelines Consensus Panel solicited feedback from end-users (obstetric care providers, exercise professionals, researchers, policy organizations, and pregnant and postpartum women). The development of this guideline followed the Appraisal of Guidelines for Research Evaluation (AGREE) II instrument. BENEFITS, HARMS, AND COSTS: The benefits of prenatal physical activity are moderate, and no harms were identified; therefore, the difference between desirable and undesirable consequences (net benefit) is expected to be moderate. The majority of stakeholders and end-users indicated that following these recommendations would be feasible, acceptable, and equitable. Following these recommendations is likely to require minimal resources from both individual and health systems perspectives. PREAMBLE: This guideline provide evidence-based recommendations regarding physical activity throughout pregnancy in the promotion of maternal, fetal, and neonatal health. In the absence of contraindications (see later for a detailed list), following this guideline is associated with: (1) fewer newborn complications (i.e., large for gestational age); and (2) maternal health benefits (i.e., decreased risk of preeclampsia, gestational hypertension, gestational diabetes, Caesarean section, instrumental delivery, urinary incontinence, excessive gestational weight gain, and depression; improved blood glucose; decreased total gestational weight gain; and decreased severity of depressive symptoms and lumbopelvic pain). Physical activity is not associated with miscarriage, stillbirth, neonatal death, preterm birth, preterm/prelabour rupture of membranes, neonatal hypoglycemia, low birth weight, birth defects, induction of labour, or birth complications. In general, more physical activity (frequency, duration, and/or volume) is associated with greater benefits. However, evidence was not identified regarding the safety or additional benefit of exercising at levels significantly above the recommendations. Prenatal physical activity should be considered a front-line therapy for reducing the risk of pregnancy complications and enhancing maternal physical and mental health. For pregnant women not currently meeting this guideline, a progressive adjustment toward them is recommended. Previously active women may continue physical activity throughout pregnancy. Women may need to modify physical activity as pregnancy progresses. There may be periods when following the guideline is not possible due to fatigue and/or discomforts of pregnancy; women are encouraged to do what they can and to return to following the recommendations when they are able. This guideline were informed by an extensive systematic review of the literature, expert opinion, end-user consultation and considerations of feasibility, acceptability, costs, and equity. RECOMMENDATIONS: The specific recommendations in this 2019 Canadian Guideline for Physical Activity Throughout Pregnancy are provided below with corresponding statements indicating the quality of the evidence informing the recommendations and the strength of the recommendations (explanations follow). CONTRAINDICATIONS: All pregnant women can participate in physical activity throughout pregnancy with the exception of those who have contraindications (listed below). Women with absolute contraindications may continue their usual activities of daily living but should not participate in more strenuous activities. Women with relative contraindications should discuss the advantages and disadvantages of moderate-to-vigorous intensity physical activity with their obstetric care provider prior to participation. Absolute contraindications to exercise are the following: Relative contraindications to exercise are the following: STRENGTH OF THE RECOMMENDATIONS: The GRADE system was utilized to grade the strength of the recommendations. Recommendations are rated as strong or weak based on the: (1) balance between benefits and harms; (2) overall quality of the evidence; (3) importance of outcomes (i.e., values and preferences of pregnant women); (4) use of resources (i.e., cost); (5) impact on health equity; (6) feasibility, and (7) acceptability. Strong recommendation: Most or all pregnant women will be best served by the recommended course of action. Weak recommendation: Not all pregnant women will be best served by the recommended course of action; there is a need to consider other factors such as the individual's circumstances, preferences, values, resources available, or setting. Consultation with an obstetric care provider may assist in decision-making. QUALITY OF THE EVIDENCE: The quality of the evidence refers to the level of confidence in the evidence and ranges from very low to high. High quality: The Guideline Consensus Panel is very confident that the estimated effect of physical activity on the health outcome is close to the true effect. Moderate quality: The Guideline Consensus Panel is moderately confident in the estimated effect of physical activity on the health outcome; the estimate of the effect is likely to be close to the true effect, but there is a possibility that it is substantially different. Low quality: The Guideline Consensus Panel's confidence in the estimated effect of physical activity on the health outcome is limited; the estimate of the effect may be substantially different from the true effect. Very low quality: The Guideline Consensus Panel has very little confidence in the estimated effect of physical activity on the health outcome; the estimate of the effect is likely to be substantially different from the true effect. aThis was a weak recommendation because the quality of evidence was low, and the net benefit between women who were physically active and those who were not was small. bThis was a strong recommendation because, despite low quality evidence supporting physical activity during pregnancy for women categorized as overweight or obese, there was evidence from randomized controlled trials demonstrating an improvement in gestational weight gain and blood glucose. cModerate-intensity physical activity is intense enough to noticeably increase heart rate; a person can talk but not sing during activities of this intensity. Examples of moderate-intensity physical activity include brisk walking, water aerobics, stationary cycling (moderate effort), resistance training, carrying moderate loads, and household chores (e.g., gardening, washing windows). dThis was a weak recommendation because urinary incontinence was was not rated as a "critical" outcome and the evidence was low quality. eThis was a weak recommendation because: (1) the quality of evidence was very low; and (2) although harms were investigated there was limited available information to inform the balance of benefits and harms. This recommendation was primarily based on expert opinion.


Asunto(s)
Ejercicio Físico/fisiología , Embarazo/fisiología , Atención Prenatal/métodos , Canadá , Femenino , Humanos , Complicaciones del Embarazo/prevención & control , Resultado del Embarazo
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