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1.
Methods Mol Biol ; 2750: 143-163, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38108975

RESUMEN

Overexpression of recombinant protein in mammalian cells is widely used for producing biologics, as protein maturation and post-translational modifications are similar to human cells. Some therapeutics, such as mRNA vaccines, target nonnative cells that may contain inefficient secretory machinery. For example, gene replacement therapies for alpha-1 antitrypsin (AAT), a glycoprotein normally produced in hepatocytes, are often targeted to muscle cells due to ease of delivery. In this chapter, we define methods for expressing AAT in representative cell types such as Huh-7; hepatocytes; Chinese hamster ovarian cells (CHO), a common host to produce biologics; and C2C12, a muscle progenitor cell line. Methods for metabolically labeling AAT to monitor secretion in these cell lines are described along with the use of proteostasis activators to increase the amount of AAT secreted in both C2C12 myoblasts and differentiated myotubes. Assays to assess the activity and glycan composition of overexpressed AAT are also presented. The usage of the proteostasis activator SAHA provided a 40% improvement in expression of active AAT in muscle-like cells and may be an advantageous adjuvant for recombinant production of proteins delivered by mRNA vaccines.


Asunto(s)
Productos Biológicos , Vacunas de ARNm , Animales , Cricetinae , Humanos , Hepatocitos , Fibras Musculares Esqueléticas , Células CHO , Mamíferos
2.
Mol Cell ; 83(24): 4524-4537.e5, 2023 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-38052210

RESUMEN

N-glycans act as quality control tags by recruiting lectin chaperones to assist protein maturation in the endoplasmic reticulum. The location and composition of N-glycans (glyco-code) are key to the chaperone-selection process. Serpins, a class of serine protease inhibitors, fold non-sequentially to achieve metastable active states. Here, the role of the glyco-code in assuring successful maturation and quality control of two human serpins, alpha-1 antitrypsin (AAT) and antithrombin III (ATIII), is described. We find that AAT, which has glycans near its N terminus, is assisted by early lectin chaperone binding. In contrast, ATIII, which has more C-terminal glycans, is initially helped by BiP and then later by lectin chaperones mediated by UGGT reglucosylation. UGGT action is increased for misfolding-prone disease variants, and these clients are preferentially glucosylated on their most C-terminal glycan. Our study illustrates how serpins utilize N-glycan presence, position, and composition to direct their proper folding, quality control, and trafficking.


Asunto(s)
Chaperonas Moleculares , Pliegue de Proteína , Humanos , Chaperonas Moleculares/metabolismo , Lectinas/metabolismo , Polisacáridos/química , Control de Calidad
3.
Environ Sci Nano ; 10(9): 2551-2565, 2023 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-37868332

RESUMEN

Biofilms are abundantly present in both natural and engineered environmental systems and will likely influence broader particle fate and transport phenomena. While some developed models describe the interactions between nanoparticles and biofilms, studies are only beginning to uncover the complexity of nanoparticle diffusion patterns. With the knowledge of the nanoparticle potential to influence bacterial processes, more systematic studies are needed to uncover the dynamics of bacteria-nanoparticle interactions. This study explored specific microbial responses to nanoparticles and the heterogeneity of nanoparticle diffusion. Pseudomonas aeruginosa biofilms (cultivated for 48 and 96 hours, representing early and late stages of development) were exposed to charged (aminated and carboxylated) polystyrene nanoparticles. With a combination of advanced fluorescence microscopy and real time quantitative PCR, we characterized the diffusion of polystyrene nanoparticles in P. aeruginosa biofilms and evaluated how biofilms respond to the presence of nanoparticles in terms of the expression of key EPS production-associated genes (pelA and rpsL) and quorum-sensing associated (lasR) genes. Our findings show that nanoparticle diffusion coefficients are independent of the particle surface charge only in mature biofilms and that the presence of nanoparticles influences bacterial gene expression. Independent of the particle's charge polystyrene nanoparticles down-regulated pelA in mature biofilms. By contrast, charge-specific responses were identified in lasR and rpsL gene expression. The targeted genes expression analysis and heterogeneous diffusion models demonstrate that particle charge influences nanoparticle mobility and provides significant insight into the intrinsic structural heterogeneity of P. aeruginosa biofilms. These findings suggest that biofilm maturity and particle charge are essential factors to consider when evaluating the transport of nanoparticles within a biofilm matrix.

4.
bioRxiv ; 2023 Apr 26.
Artículo en Inglés | MEDLINE | ID: mdl-37163105

RESUMEN

Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α1-antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More ß-rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone ß-strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.

5.
J Biol Chem ; 298(12): 102652, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36444882

RESUMEN

The serpin plasminogen activator inhibitor 1 (PAI-1) spontaneously undergoes a massive structural change from a metastable and active conformation, with a solvent-accessible reactive center loop (RCL), to a stable, inactive, or latent conformation, with the RCL inserted into the central ß-sheet. Physiologically, conversion to the latent state is regulated by the binding of vitronectin, which hinders the latency transition rate approximately twofold. The molecular mechanisms leading to this rate change are unclear. Here, we investigated the effects of vitronectin on the PAI-1 latency transition using all-atom path sampling simulations in explicit solvent. In simulated latency transitions of free PAI-1, the RCL is quite mobile as is the gate, the region that impedes RCL access to the central ß-sheet. This mobility allows the formation of a transient salt bridge that facilitates the transition; this finding rationalizes existing mutagenesis results. Vitronectin binding reduces RCL and gate mobility by allosterically rigidifying structural elements over 40 Å away from the binding site, thus blocking transition to the latent conformation. The effects of vitronectin are propagated by a network of dynamically correlated residues including a number of conserved sites that were previously identified as important for PAI-1 stability. Simulations also revealed a transient pocket populated only in the vitronectin-bound state, corresponding to a cryptic drug-binding site identified by crystallography. Overall, these results shed new light on PAI-1 latency transition regulation by vitronectin and illustrate the potential of path sampling simulations for understanding functional protein conformational changes and for facilitating drug discovery.


Asunto(s)
Inhibidor 1 de Activador Plasminogénico , Vitronectina , Inhibidor 1 de Activador Plasminogénico/metabolismo , Vitronectina/química , Modelos Moleculares , Conformación Proteica , Solventes
6.
Molecules ; 27(19)2022 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-36234717

RESUMEN

Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes are a virulence factor in many Gram-positive organisms. The specific activity of the Bacillus thuringiensis PI-PLC is significantly increased by adding phosphatidylcholine (PC) to vesicles composed of the substrate phosphatidylinositol, in part because the inclusion of PC reduces the apparent Kd for the vesicle binding by as much as 1000-fold when comparing PC-rich vesicles to PI vesicles. This review summarizes (i) the experimental work that localized a site on BtPI-PLC where PC is bound as a PC choline cation-Tyr-π complex and (ii) the computational work (including all-atom molecular dynamics simulations) that refined the original complex and found a second persistent PC cation-Tyr-π complex. Both complexes are critical for vesicle binding. These results have led to a model for PC functioning as an allosteric effector of the enzyme by altering the protein dynamics and stabilizing an 'open' active site conformation.


Asunto(s)
Fosfolipasas de Tipo C , Tirosina , Cationes , Colina , Lecitinas , Fosfatidilinositoles/metabolismo , Fosfoinositido Fosfolipasa C/química , Fosfoinositido Fosfolipasa C/metabolismo , Fosfolipasas de Tipo C/metabolismo , Factores de Virulencia
7.
Proc Natl Acad Sci U S A ; 119(31): e2206103119, 2022 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-35901208

RESUMEN

Heterologous expression of proteins is used widely for the biosynthesis of biologics, many of which are secreted from cells. In addition, gene therapy and messenger RNA (mRNA) vaccines frequently direct the expression of secretory proteins to nonnative host cells. Consequently, it is crucial to understand the maturation and trafficking of proteins in a range of host cells including muscle cells, a popular therapeutic target due to the ease of accessibility by intramuscular injection. Here, we analyzed the production efficiency for α1-antitrypsin (AAT) in Chinese hamster ovary cells, commonly used for biotherapeutic production, and myoblasts (embryonic progenitor cells of muscle cells) and compared it to the production in the major natural cells, liver hepatocytes. AAT is a target protein for gene therapy to address pathologies associated with insufficiencies in native AAT activity or production. AAT secretion and maturation were most efficient in hepatocytes. Myoblasts were the poorest of the cell types tested; however, secretion of active AAT was significantly augmented in myoblasts by treatment with the proteostasis regulator suberoylanilide hydroxamic acid, a histone deacetylase inhibitor. These findings were extended and validated in myotubes (mature muscle cells) where AAT was transduced using an adeno-associated viral capsid transduction method used in gene therapy clinical trials. Overall, our study sheds light on a possible mechanism to enhance the efficacy of gene therapy approaches for AAT and, moreover, may have implications for the production of proteins from mRNA vaccines, which rely on the expression of viral glycoproteins in nonnative host cells upon intramuscular injection.


Asunto(s)
Deficiencia de alfa 1-Antitripsina , alfa 1-Antitripsina , Animales , Células CHO , Cricetinae , Cricetulus , Dependovirus/genética , Terapia Genética , Hepatocitos/metabolismo , Humanos , Fibras Musculares Esqueléticas , Transducción Genética , alfa 1-Antitripsina/biosíntesis , alfa 1-Antitripsina/genética , Deficiencia de alfa 1-Antitripsina/genética
8.
J Chem Inf Model ; 62(24): 6602-6613, 2022 12 26.
Artículo en Inglés | MEDLINE | ID: mdl-35343689

RESUMEN

Peripheral membrane proteins (PMPs) bind temporarily to cellular membranes and play important roles in signaling, lipid metabolism, and membrane trafficking. Obtaining accurate membrane-PMP affinities using experimental techniques is more challenging than for protein-ligand affinities in an aqueous solution. At the theoretical level, calculation of the standard protein-membrane binding free energy using molecular dynamics simulations remains a daunting challenge owing to the size of the biological objects at play, the slow lipid diffusion, and the large variation in configurational entropy that accompanies the binding process. To overcome these challenges, we used a computational framework relying on a series of potential-of-mean-force (PMF) calculations including a set of geometrical restraints on collective variables. This methodology allowed us to determine the standard binding free energy of a PMP to a phospholipid bilayer using an all-atom force field. Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) was chosen due to its importance as a virulence factor and owing to the host of experimental affinity data available. We computed a standard binding free energy of -8.2 ± 1.4 kcal/mol in reasonable agreement with the reported experimental values (-6.6 ± 0.2 kcal/mol). In light of the 2.3-µs separation PMF calculation, we investigated the mechanism whereby BtPI-PLC disengages from interactions with the lipid bilayer during separation. We describe how a short amphipathic helix engages in transitory interactions to ease the passage of its hydrophobes through the interfacial region upon desorption from the bilayer.


Asunto(s)
Membrana Dobles de Lípidos , Fosfolipasas de Tipo C , Entropía , Fosfolipasas de Tipo C/metabolismo , Termodinámica , Membrana Celular/metabolismo , Membrana Dobles de Lípidos/química , Simulación de Dinámica Molecular , Unión Proteica
9.
Angew Chem Int Ed Engl ; 61(6): e202112033, 2022 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-34767659

RESUMEN

The cell membrane is a dynamic and heterogeneous structure composed of distinct sub-compartments. Within these compartments, preferential interactions occur among various lipids and proteins. Currently, it is still challenging to image these short-lived membrane complexes, especially in living cells. In this work, we present a DNA-based probe, termed "DNA Zipper", which allows the membrane order and pattern of transient interactions to be imaged in living cells using standard fluorescence microscopes. By fine-tuning the length and binding affinity of DNA duplex, these probes can precisely extend the duration of membrane lipid interactions via dynamic DNA hybridization. The correlation between membrane order and the activation of T-cell receptor signaling has also been studied. These programmable DNA probes function after a brief cell incubation, which can be easily adapted to study lipid interactions and membrane order during different membrane signaling events.


Asunto(s)
Membrana Celular/química , Sondas de ADN/química , Colorantes Fluorescentes/química , Células de Riñón Canino Madin Darby/química , Animales , Sondas de ADN/síntesis química , Perros , Transferencia Resonante de Energía de Fluorescencia , Colorantes Fluorescentes/síntesis química
10.
J Phys Chem B ; 125(31): 8827-8838, 2021 08 12.
Artículo en Inglés | MEDLINE | ID: mdl-34320805

RESUMEN

Diverse phospholipid motions are key to membrane function but can be quite difficult to untangle and quantify. High-resolution field cycling 31P NMR spin-lattice relaxometry, where the sample is excited at high field, shuttled in the magnet bore for low-field relaxation, then shuttled back to high field for readout of the residual magnetization, provides data on phospholipid dynamics and structure. This information is encoded in the field dependence of the 31P spin-lattice relaxation rate (R1). In the field range from 11.74 down to 0.003 T, three dipolar nuclear magnetic relaxation dispersions (NMRDs) and one due to 31P chemical shift anisotropy contribute to R1 of phospholipids. Extraction of correlation times and maximum relaxation amplitudes for these NMRDs provides (1) lateral diffusion constants for different phospholipids in the same bilayer, (2) estimates of how additives alter the motion of the phospholipid about its long axis, and (3) an average 31P-1H angle with respect to the bilayer normal, which reveals that polar headgroup motion is not restricted on a microsecond timescale. Relative motions within a phospholipid are also provided by comparing 31P NMRD profiles for specifically deuterated molecules as well as 13C and 1H field dependence profiles to that of 31P. Although this work has dealt exclusively with phospholipids in small unilamellar vesicles, these same NMRDs can be measured for phospholipids in micelles and nanodisks, making this technique useful for monitoring lipid behavior in a variety of structures and assessing how additives alter specific lipid motions.


Asunto(s)
Imagen por Resonancia Magnética , Fosfolípidos , Difusión , Membrana Dobles de Lípidos , Espectroscopía de Resonancia Magnética , Movimiento (Física)
11.
J Vis Exp ; (171)2021 05 17.
Artículo en Inglés | MEDLINE | ID: mdl-34057447

RESUMEN

Fast Photochemical Oxidation of proteins (FPOP) coupled with mass spectrometry (MS) has become an invaluable tool in structural proteomics to interrogate protein interactions, structure, and protein conformational dynamics as a function of solvent accessibility. In recent years, the scope of FPOP, a hydroxyl radical protein foot printing (HRPF) technique, has been expanded to protein labeling in live cell cultures, providing the means to study protein interactions in the convoluted cellular environment. In-cell protein modifications can provide insight into ligand induced structural changes or conformational changes accompanying protein complex formation, all within the cellular context. Protein footprinting has been accomplished employing a customary flow-based system and a 248 nm KrF excimer laser to yield hydroxyl radicals via photolysis of hydrogen peroxide, requiring 20 minutes of analysis for one cell sample.To facilitate time-resolved FPOP experiments, the use of a new 6-well plate-based IC-FPOP platform was pioneered. In the current system, a single laser pulse irradiates one entire well, which truncates the FPOP experimental time frame resulting in 20 seconds of analysis time, a 60-fold decrease. This greatly reduced analysis time makes it possible to research cellular mechanisms such as biochemical signaling cascades, protein folding, and differential experiments (i.e., drug-free vs. drug bound) in a time-dependent manner. This new instrumentation, entitled Platform Incubator with Movable XY Stage (PIXY), allows the user to perform cell culture and IC-FPOP directly on the optical bench using a platform incubator with temperature, CO2 and humidity control. The platform also includes a positioning stage, peristaltic pumps, and mirror optics for laser beam guidance. IC-FPOP conditions such as optics configuration, flow rates, transient transfections, and H2O2 concentration in PIXY have been optimized and peer-reviewed. Automation of all components of the system will reduce human manipulation and increase throughput.


Asunto(s)
Peróxido de Hidrógeno , Proteínas , Humanos , Peróxido de Hidrógeno/química , Incubadoras , Oxidación-Reducción , Procesos Fotoquímicos , Conformación Proteica , Proteínas/química
12.
Environ Sci Technol ; 54(8): 5159-5166, 2020 04 21.
Artículo en Inglés | MEDLINE | ID: mdl-32182039

RESUMEN

Most bacteria in natural and engineered environments grow and exist in biofilms. Recent investigations have shown that nanoparticles (NPs) interact with environmental biofilms, but these interactions are still not well characterized. Extracellular polymeric substances (EPS) are polymers secreted by bacteria to establish the functional and structural integrity of biofilms, and EPS porosity is a major contributor to NP access to and diffusion in biofilms. We used a synergistic combination of total internal reflection fluorescence microscopy and image correlation spectroscopy to monitor and map diffusion of fluorescent NPs in alginate yielding a detailed picture of the heterogeneous structure and connectivity of pores within a model EPS polymer. Using different sizes (20, 100, and 200 nm) of carboxylated polystyrene NPs, we examined how NP diffusive behaviors change as a result of calcium-induced cross-linking of the alginate matrix. This study reveals that cross-linking decreases NP diffusion coefficients and pore accessibility in an NP size-dependent manner and that NP movement through alginate matrices is anisotropic and heterogeneous. These results on heterogeneous and size-dependent movement within biofilms have important implications for future studies and simulations of NP-biofilm interactions.


Asunto(s)
Nanopartículas , Poliestirenos , Alginatos , Biopelículas , Tamaño de la Partícula
13.
J Biol Chem ; 295(1): 15-33, 2020 01 03.
Artículo en Inglés | MEDLINE | ID: mdl-31712314

RESUMEN

Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Go and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.


Asunto(s)
Simulación de Dinámica Molecular , Pliegue de Proteína , Animales , Humanos , Serpinas/química , Serpinas/metabolismo
14.
Anal Chem ; 92(2): 1691-1696, 2020 01 21.
Artículo en Inglés | MEDLINE | ID: mdl-31860269

RESUMEN

Fast photochemical oxidation of proteins (FPOP) is a protein footprinting technique that is being increasingly used in MS-based proteomics. FPOP is utilized to study protein-protein interactions, protein-ligand interactions, and protein conformational dynamics. This method has recently been extended to protein labeling in live cells (IC-FPOP), allowing the study of protein conformations in the complex cellular environment. Traditionally, IC-FPOP has been executed using a single cell flow system, in which hydrodynamic focusing drives cells along in a single file line, keeping the cells from clumping and thus ensuring equal exposure to the laser irradiation required for photochemical oxidation. Here, we introduce a novel platform that allows IC-FPOP to occur in a sterile incubation system complete with a mobile stage for XY movement, peristaltic pumps equipped with perfusion lines for chemical transport, and mirrors for laser beam guidance. This new system, called Platform Incubator with movable XY stage (PIXY), also utilizes software enabling automated communication between equipment and execution of the entire system. Further, comparison with a standard IC-FPOP flow system results reveal that this platform can successfully be used in lieu of the flow system while also decreasing the time to complete analysis of a single sample.


Asunto(s)
Incubadoras , Proteínas/química , Análisis de la Célula Individual , Programas Informáticos , Hidrodinámica , Modelos Moleculares , Oxidación-Reducción , Procesos Fotoquímicos , Conformación Proteica , Análisis de la Célula Individual/instrumentación
15.
J Biol Chem ; 294(50): 18992-19011, 2019 12 13.
Artículo en Inglés | MEDLINE | ID: mdl-31662433

RESUMEN

The protein quality control machinery of the endoplasmic reticulum (ERQC) ensures that client proteins are properly folded. ERQC substrates may be recognized as nonnative by the presence of exposed hydrophobic surfaces, free thiols, or processed N-glycans. How these features dictate which ERQC pathways engage a given substrate is poorly understood. Here, using metabolic labeling, immunoprecipitations, various biochemical assays, and the human serpin antithrombin III (ATIII) as a model, we explored the role of ERQC systems in mammalian cells. Although ATIII has N-glycans and a hydrophobic core, we found that its quality control depended solely on free thiol content. Mutagenesis of all six Cys residues in ATIII to Ala resulted in its efficient secretion even though the product was not natively folded. ATIII variants with free thiols were retained in the endoplasmic reticulum but not degraded. These results provide insight into the hierarchy of ERQC systems and reveal a fundamental vulnerability of ERQC in a case of reliance on the thiol-dependent quality control pathway.


Asunto(s)
Antitrombina III/metabolismo , Control de Calidad , Serpinas/metabolismo , Compuestos de Sulfhidrilo/metabolismo , Animales , Células CHO , Células Cultivadas , Cricetulus , Retículo Endoplásmico/metabolismo , Humanos
16.
J Phys Chem Lett ; 10(14): 3972-3977, 2019 Jul 18.
Artículo en Inglés | MEDLINE | ID: mdl-31246477

RESUMEN

Membrane-binding interfaces of peripheral proteins are restricted to a small part of their exposed surface, so the ability to engage in strong selective interactions with membrane lipids at various depths in the interface, both below and above the phosphates, is an advantage. Driven by their hydrophobicity, aromatic amino acids preferentially partition into membrane interfaces, often below the phosphates, yet enthalpically favorable interactions with the lipid headgroups, above the phosphate plane, are likely to further stabilize high interfacial positions. Using free-energy perturbation, we calculate the energetic cost of alanine substitution for 11 interfacial aromatic amino acids from 3 peripheral proteins. We show that the involvement in cation-π interactions with the headgroups (i) increases the ΔΔGtransfer as compared with insertion at the same depth without cation-π stabilization and (ii) can contribute at least as much as deeper insertion below the phosphates, highlighting the multiple roles of aromatics in peripheral membrane protein affinity.


Asunto(s)
Aminoácidos Aromáticos/química , Colina/química , Lípidos/química , Proteínas de la Membrana/química , Fosfatos/química , Cationes/química , Modelos Moleculares , Termodinámica
17.
Elife ; 82019 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-30720429

RESUMEN

RNA polymerases (RNAPs) contain a conserved 'secondary channel' which binds regulatory factors that modulate transcription initiation. In Escherichia coli, the secondary channel factors (SCFs) GreB and DksA both repress ribosomal RNA (rRNA) transcription, but SCF loading and repression mechanisms are unclear. We observed in vitro fluorescently labeled GreB molecules binding to single RNAPs and initiation of individual transcripts from an rRNA promoter. GreB arrived and departed from promoters only in complex with RNAP. GreB did not alter initial RNAP-promoter binding but instead blocked a step after conformational rearrangement of the initial RNAP-promoter complex. Strikingly, GreB-RNAP complexes never initiated at an rRNA promoter; only RNAP molecules arriving at the promoter without bound GreB produced transcript. The data reveal that a model SCF functions by a 'delayed inhibition' mechanism and suggest that rRNA promoters are inhibited by GreB/DksA because their short-lived RNAP complexes do not allow sufficient time for SCFs to dissociate.


Asunto(s)
Proteínas de Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , ARN Ribosómico/genética , Transcripción Genética , Factores de Elongación Transcripcional/genética , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , ARN Polimerasas Dirigidas por ADN/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Cinética , Modelos Genéticos , Regiones Promotoras Genéticas/genética , Unión Proteica , ARN Ribosómico/metabolismo , Factores de Elongación Transcripcional/metabolismo
18.
Chem Rev ; 118(18): 8435-8473, 2018 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-30148347

RESUMEN

Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes from Gram-positive bacteria are secreted virulence factors that aid in downregulating host immunity. These PI-PLCs are minimalist peripheral membrane enzymes with a distorted (ßα)8 TIM barrel fold offering a conserved and stable scaffold for the conserved catalytic amino acids while membrane recognition is achieved mostly through variable loops. Decades of experimental and computational research on these enzymes have revealed the subtle interplay between molecular mechanisms of catalysis and membrane binding, leading to a semiquantitative model for how they find, bind, and cleave their respective substrates on host cell membranes. Variations in sequence and structure of their membrane binding sites may correlate with how enzymes from different Gram-positive bacteria search for their particular targets on the membrane. Detailed molecular characterization of protein-lipid interactions have been aided by cutting-edge methods ranging from 31P field-cycling NMR relaxometry to monitor protein-induced changes in phospholipid dynamics to molecular dynamics simulations to elucidate the roles of electrostatic and cation-π interactions in lipid binding to single molecule fluorescence measurements of dynamic interactions between PI-PLCs and vesicles. This toolkit is readily applicable to other peripheral membrane proteins including orthologues in Gram-negative bacteria and more recently discovered eukaryotic minimalist PI-PLCs.


Asunto(s)
Bacterias/enzimología , Fosfatidilinositol Diacilglicerol-Liasa/química , Fosfatidilinositol Diacilglicerol-Liasa/metabolismo , Fosfatidilinositoles/metabolismo , Regulación Alostérica/fisiología , Biocatálisis , Dominio Catalítico , Membrana Celular/metabolismo , Cinética , Unión Proteica , Conformación Proteica , Especificidad por Sustrato
19.
Biophys J ; 114(9): 2083-2094, 2018 05 08.
Artículo en Inglés | MEDLINE | ID: mdl-29742402

RESUMEN

Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α1-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α1-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, whereas the relatively benign S mutant shows late-stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation, and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.


Asunto(s)
Simulación de Dinámica Molecular , Proteínas Mutantes/química , Mutación Puntual , Pliegue de Proteína , alfa 1-Antitripsina/química , Proteínas Mutantes/genética , Conformación Proteica , alfa 1-Antitripsina/genética
20.
J Biol Chem ; 292(40): 16787-16801, 2017 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-28842497

RESUMEN

Upon activation by the Gq family of Gα subunits, Gßγ subunits, and some Rho family GTPases, phospholipase C-ß (PLC-ß) isoforms hydrolyze phosphatidylinositol 4,5-bisphosphate to the second messengers inositol 1,4,5-trisphosphate and diacylglycerol. PLC-ß isoforms also function as GTPase-activating proteins, potentiating Gq deactivation. To elucidate the mechanism of this mutual regulation, we measured the thermodynamics and kinetics of PLC-ß3 binding to Gαq FRET and fluorescence correlation spectroscopy, two physically distinct methods, both yielded Kd values of about 200 nm for PLC-ß3-Gαq binding. This Kd is 50-100 times greater than the EC50 for Gαq-mediated PLC-ß3 activation and for the Gαq GTPase-activating protein activity of PLC-ß. The measured Kd was not altered either by the presence of phospholipid vesicles, phosphatidylinositol 4,5-bisphosphate and Ca2+, or by the identity of the fluorescent labels. FRET-based kinetic measurements were also consistent with a Kd of 200 nm We determined that PLC-ß3 hysteresis, whereby PLC-ß3 remains active for some time following either Gαq-PLC-ß3 dissociation or PLC-ß3-potentiated Gαq deactivation, is not sufficient to explain the observed discrepancy between EC50 and Kd These results indicate that the mechanism by which Gαq and PLC-ß3 mutually regulate each other is far more complex than a simple, two-state allosteric model and instead is probably kinetically determined.


Asunto(s)
Subunidades alfa de la Proteína de Unión al GTP Gq-G11/química , Modelos Químicos , Fosfolipasa C beta/química , Regulación Alostérica/fisiología , Calcio/química , Calcio/metabolismo , Activación Enzimática , Transferencia Resonante de Energía de Fluorescencia , Subunidades alfa de la Proteína de Unión al GTP Gq-G11/genética , Subunidades alfa de la Proteína de Unión al GTP Gq-G11/metabolismo , Humanos , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Cinética , Fosfolipasa C beta/genética , Fosfolipasa C beta/metabolismo , Unión Proteica
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