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1.
Cell ; 184(1): 194-206.e14, 2021 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-33357447

RESUMO

Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi). We report the 3.2 Å resolution cryogenic electron microscopy (cryo-EM) structure of palmitoleated human WNT8A in complex with WLS. This is accompanied by biochemical experiments to probe the physiological implications of the observed association. The WLS membrane domain has close structural homology to G protein-coupled receptors (GPCRs). A Wnt hairpin inserts into a conserved hydrophobic cavity in the GPCR-like domain, and the palmitoleate protrudes between two helices into the bilayer. A conformational switch of highly conserved residues on a separate Wnt hairpin might contribute to its transfer to receiving cells. This work provides molecular-level insights into a central mechanism in animal body plan development and stem cell biology.


Assuntos
Peptídeos e Proteínas de Sinalização Intracelular/química , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Proteínas Wnt/metabolismo , Sequência de Aminoácidos , Animais , Dissulfetos/metabolismo , Glicosilação , Humanos , Interações Hidrofóbicas e Hidrofílicas , Peptídeos e Proteínas de Sinalização Intracelular/isolamento & purificação , Modelos Moleculares , Ligação Proteica , Domínios Proteicos , Estrutura Secundária de Proteína , Transporte Proteico , Receptores Acoplados a Proteínas G/isolamento & purificação , Receptores Acoplados a Proteínas G/ultraestrutura , Homologia Estrutural de Proteína , Relação Estrutura-Atividade , Proteínas Wnt/química , Proteínas Wnt/isolamento & purificação , Proteínas Wnt/ultraestrutura
2.
Cell ; 152(3): 532-42, 2013 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-23374348

RESUMO

G-protein-coupled receptors (GPCRs) can modulate diverse signaling pathways, often in a ligand-specific manner. The full range of functionally relevant GPCR conformations is poorly understood. Here, we use NMR spectroscopy to characterize the conformational dynamics of the transmembrane core of the ß(2)-adrenergic receptor (ß(2)AR), a prototypical GPCR. We labeled ß(2)AR with (13)CH(3)ε-methionine and obtained HSQC spectra of unliganded receptor as well as receptor bound to an inverse agonist, an agonist, and a G-protein-mimetic nanobody. These studies provide evidence for conformational states not observed in crystal structures, as well as substantial conformational heterogeneity in agonist- and inverse-agonist-bound preparations. They also show that for ß(2)AR, unlike rhodopsin, an agonist alone does not stabilize a fully active conformation, suggesting that the conformational link between the agonist-binding pocket and the G-protein-coupling surface is not rigid. The observed heterogeneity may be important for ß(2)AR's ability to engage multiple signaling and regulatory proteins.


Assuntos
Simulação de Dinâmica Molecular , Ressonância Magnética Nuclear Biomolecular , Receptores Adrenérgicos beta 2/química , Receptores Adrenérgicos beta 2/metabolismo , Agonistas de Receptores Adrenérgicos beta 2/metabolismo , Sequência de Aminoácidos , Humanos , Dados de Sequência Molecular , Conformação Proteica , Transdução de Sinais , Termodinâmica
3.
Nature ; 604(7905): 371-376, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35388216

RESUMO

The outer membrane of Gram-negative bacteria has an external leaflet that is largely composed of lipopolysaccharide, which provides a selective permeation barrier, particularly against antimicrobials1. The final and crucial step in the biosynthesis of lipopolysaccharide is the addition of a species-dependent O-antigen to the lipid A core oligosaccharide, which is catalysed by the O-antigen ligase WaaL2. Here we present structures of WaaL from Cupriavidus metallidurans, both in the apo state and in complex with its lipid carrier undecaprenyl pyrophosphate, determined by single-particle cryo-electron microscopy. The structures reveal that WaaL comprises 12 transmembrane helices and a predominantly α-helical periplasmic region, which we show contains many of the conserved residues that are required for catalysis. We observe a conserved fold within the GT-C family of glycosyltransferases and hypothesize that they have a common mechanism for shuttling the undecaprenyl-based carrier to and from the active site. The structures, combined with genetic, biochemical, bioinformatics and molecular dynamics simulation experiments, offer molecular details on how the ligands come in apposition, and allows us to propose a mechanistic model for catalysis. Together, our work provides a structural basis for lipopolysaccharide maturation in a member of the GT-C superfamily of glycosyltransferases.


Assuntos
Ligases , Lipopolissacarídeos , Antígenos O , Proteínas de Bactérias/química , Carbono-Oxigênio Ligases/química , Carbono-Oxigênio Ligases/genética , Microscopia Crioeletrônica , Glicosiltransferases , Bactérias Gram-Negativas , Lipopolissacarídeos/química , Lipopolissacarídeos/metabolismo
4.
N Engl J Med ; 385(14): 1292-1301, 2021 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-34587386

RESUMO

BACKGROUND: Structural birth defects occur in approximately 3% of live births; most such defects lack defined genetic or environmental causes. Despite advances in surgical approaches, pharmacologic prevention remains largely out of reach. METHODS: We queried worldwide databases of 20,248 families that included children with neurodevelopmental disorders and that were enriched for parental consanguinity. Approximately one third of affected children in these families presented with structural birth defects or microcephaly. We performed exome or genome sequencing of samples obtained from the children, their parents, or both to identify genes with biallelic pathogenic or likely pathogenic mutations present in more than one family. After identifying disease-causing variants, we generated two mouse models, each with a pathogenic variant "knocked in," to study mechanisms and test candidate treatments. We administered a small-molecule Wnt agonist to pregnant animals and assessed their offspring. RESULTS: We identified homozygous mutations in WLS, which encodes the Wnt ligand secretion mediator (also known as Wntless or WLS) in 10 affected persons from 5 unrelated families. (The Wnt ligand secretion mediator is essential for the secretion of all Wnt proteins.) Patients had multiorgan defects, including microcephaly and facial dysmorphism as well as foot syndactyly, renal agenesis, alopecia, iris coloboma, and heart defects. The mutations affected WLS protein stability and Wnt signaling. Knock-in mice showed tissue and cell vulnerability consistent with Wnt-signaling intensity and individual and collective functions of Wnts in embryogenesis. Administration of a pharmacologic Wnt agonist partially restored embryonic development. CONCLUSIONS: Genetic variations affecting a central Wnt regulator caused syndromic structural birth defects. Results from mouse models suggest that what we have named Zaki syndrome is a potentially preventable disorder. (Funded by the National Institutes of Health and others.).


Assuntos
Anormalidades Múltiplas/genética , Anormalidades Congênitas/genética , Pleiotropia Genética , Peptídeos e Proteínas de Sinalização Intracelular/genética , Mutação , Receptores Acoplados a Proteínas G/genética , Proteínas Wnt/metabolismo , Animais , Modelos Animais de Doenças , Fibroblastos/metabolismo , Técnicas de Introdução de Genes , Genes Recessivos , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Camundongos , Camundongos Transgênicos , Linhagem , Fenótipo , Receptores Acoplados a Proteínas G/metabolismo , Síndrome , Via de Sinalização Wnt
5.
Biochem Soc Trans ; 50(6): 1763-1772, 2022 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-36416660

RESUMO

Wnts are short-range signaling proteins, expressed in all metazoans from sponges to humans, critical for cell development and fate. There are 19 different Wnts in the human genome with varying expression levels and patterns, and post-translational modifications. Common to essentially all Wnts is the palmitoleation of a conserved serine by the O-acyltransferase PORCN in the endoplasmic reticulum (ER). All lipidated Wnts then bind a dedicated carrier Wntless (WLS), endowed with the task of transporting them from the ER to the plasma membrane, and ultimately facilitating their release to receptors on the Wnt-receiving cell to initiate signaling. Here, we will focus on the WLS-mediated transport step. There are currently two published structures, both obtained by single-particle cryo-electron microscopy of the Wnt/WLS complex: human Wnt8A-bound and human Wnt3A-bound WLS. We analyze the two Wnt/WLS structures - remarkably similar despite the sequence similarity between Wnt8A and Wnt3A being only ∼39% - to begin to understand the conserved nature of this binding mechanism, and ultimately how one carrier can accommodate a family of 19 different Wnts. By comparing how Wnt associates with WLS with how it binds to PORCN and FZD receptors, we can begin to speculate on mechanisms of Wnt transfer from PORCN to WLS, and from WLS to FZD, thus providing molecular-level insight into these essential steps of the Wnt signaling pathway.


Assuntos
Peptídeos e Proteínas de Sinalização Intracelular , Via de Sinalização Wnt , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Microscopia Crioeletrônica , Aciltransferases/metabolismo , Membrana Celular/metabolismo , Proteínas de Membrana/metabolismo
6.
Int J Mol Sci ; 23(18)2022 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-36142855

RESUMO

Macrophages synthesize active vitamin D (1,25-dihydroxy-vitamin D) and express the vitamin D receptor in the nucleus; however, vitamin D metabolism in relation to macrophage polarization and function is not well understood. We studied monocyte-derived macrophages (MDMs) from human buffy coats polarized into M0, M1 (LPS + IFNγ), M2a (IL4 + IL13) and M2c (IL10) macrophage subtypes stimulated with 25-hydroxy-vitamin D (1000 and 10,000 nanomolar). We measured vitamin D metabolites (25-hydroxy-vitamin D, 1,25-dihydroxy-vitamin D, 24,25-dihydroxy-vitamin D and 3-epi-25-hydroxy-vitamin D) in cell media with liquid chromatography-mass spectrometry-mass spectrometry. The mRNA expression (CYP27B1, CYP24A1 and CYP24A1-SV) was measured with qPCR. We found that reparative MDMs (M2a) had significantly more 1,25-dihydroxy-vitamin D compared to the other MDMs (M0, M1 and M2c). All MDMs were able to produce 3-epi-25-hydroxy-vitamin D, but this pathway was almost completely attenuated in inflammatory M1 MDMs. All MDM subtypes degraded vitamin D through the 24-hydroxylase pathway, although M1 MDMs mainly expressed an inactive splice variant of CYP24A1, coding the degrading enzyme. In conclusion, this study shows that vitamin D metabolism is highly dependent on macrophage polarization and that the C3-epimerase pathway for vitamin D is active in macrophages.


Assuntos
Lipopolissacarídeos , Receptores de Calcitriol , 25-Hidroxivitamina D3 1-alfa-Hidroxilase/genética , 25-Hidroxivitamina D3 1-alfa-Hidroxilase/metabolismo , Calcifediol , Humanos , Interleucina-10/metabolismo , Interleucina-13/metabolismo , Interleucina-4/metabolismo , Lipopolissacarídeos/metabolismo , Macrófagos/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Racemases e Epimerases/metabolismo , Receptores de Calcitriol/genética , Receptores de Calcitriol/metabolismo , Vitamina D/metabolismo , Vitamina D3 24-Hidroxilase/genética , Vitamina D3 24-Hidroxilase/metabolismo
7.
Eur J Appl Physiol ; 118(7): 1301-1307, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29623400

RESUMO

PURPOSE: Hereditary connective tissue disorders (HCTDs), such as classic Ehlers-Danlos syndrome (cEDS) and Marfan syndrome (MS) share overlapping features like hypermobility and tissue fragility. In clinical practice it remains a challenge to distinguish children and adolescents with HCTD from healthy children. The purpose of this study was to investigate the biomechanical properties of the patellar tendon and joint laxity (Beighton score) in children with HCTDs (n = 7) compared to healthy controls (n = 14). METHODS: The mechanical properties of the patellar tendon were assessed using simultaneous force and ultrasonographic measurements during isometric ramp contractions. Ultrasonography was also used to measure tendon dimensions. The HCTD children were matched with 2 healthy controls with regard to age, body mass index (BMI), sex and physical activity level. RESULTS: The HCTD children had a greater degree of joint laxity (P < 0.01). Although, the patellar tendon dimensions did not differ significantly between the two groups, the HCTD children showed a tendency toward a larger patellar tendon cross-sectional area (CSA) (35%, P = 0.19). Moreover, stiffness did not differ between the two groups, but secant modulus was 27% lower in children with a HCTD (P = 0.05) at common force and 34% lower at maximum force (P = 0.02). CONCLUSIONS: The present study demonstrates for the first time that children with HCTDs have lower material properties (modulus) of their patellar tendon, which may be indicative of general impairment of connective tissue mechanics related to their increased joint laxity.


Assuntos
Síndrome de Ehlers-Danlos/fisiopatologia , Instabilidade Articular/fisiopatologia , Síndrome de Marfan/fisiopatologia , Ligamento Patelar/fisiopatologia , Adolescente , Fenômenos Biomecânicos , Criança , Feminino , Humanos , Masculino , Ligamento Patelar/diagnóstico por imagem
8.
Nature ; 463(7277): 108-12, 2010 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-20054398

RESUMO

G-protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters. They are the largest group of therapeutic targets for a broad spectrum of diseases. Recent crystal structures of GPCRs have revealed structural conservation extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the native ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the beta(2) adrenergic receptor: a salt bridge linking extracellular loops 2 and 3. Small-molecule drugs that bind within the transmembrane core and exhibit different efficacies towards G-protein activation (agonist, neutral antagonist and inverse agonist) also stabilize distinct conformations of the ECS. We thereby demonstrate conformational coupling between the ECS and the orthosteric binding site, showing that drugs targeting this diverse surface could function as allosteric modulators with high subtype selectivity. Moreover, these studies provide a new insight into the dynamic behaviour of GPCRs not addressable by static, inactive-state crystal structures.


Assuntos
Receptores Adrenérgicos beta 2/química , Receptores Adrenérgicos beta 2/metabolismo , Agonistas de Receptores Adrenérgicos beta 2 , Antagonistas de Receptores Adrenérgicos beta 2 , Regulação Alostérica/efeitos dos fármacos , Sítios de Ligação , Cristalografia por Raios X , Agonismo Inverso de Drogas , Etanolaminas/farmacologia , Fumarato de Formoterol , Humanos , Ligantes , Lisina/análogos & derivados , Lisina/metabolismo , Metilação , Modelos Moleculares , Proteínas Mutantes , Ressonância Magnética Nuclear Biomolecular , Propanolaminas/metabolismo , Propanolaminas/farmacologia , Estrutura Terciária de Proteína/efeitos dos fármacos , Eletricidade Estática , Especificidade por Substrato
9.
Biophys J ; 108(6): 1380-1389, 2015 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-25809251

RESUMO

Gram-positive bacteria surround themselves with a thick cell wall that is essential to cell survival and is a major target of antibiotics. Quantifying alterations in cell-wall composition are crucial to evaluating drug modes of action, particularly important for human pathogens that are now resistant to multiple antibiotics such as Staphylococcus aureus. Macromolecular and whole-cell NMR spectroscopy allowed us to observe the full panel of carbon and nitrogen pools in S. aureus cell walls and intact whole cells. We discovered that one-dimensional (13)C and (15)N NMR spectra, together with spectroscopic selections based on dipolar couplings as well as two-dimensional spin-diffusion measurements, revealed the dramatic compositional differences between intact cells and cell walls and allowed the identification of cell-wall signatures in whole-cell samples. Furthermore, the whole-cell NMR approach exhibited the sensitivity to detect distinct compositional changes due to treatment with the antibiotics fosfomycin (a cell-wall biosynthesis inhibitor) and chloramphenicol (a protein synthesis inhibitor). Whole cells treated with fosfomycin exhibited decreased peptidoglycan contributions while those treated with chloramphenicol contained a higher percentage of peptidoglycan as cytoplasmic protein content was reduced. Thus, general antibiotic modes of action can be identified by profiling the total carbon pools in intact whole cells.


Assuntos
Antibacterianos/farmacologia , Parede Celular/química , Parede Celular/efeitos dos fármacos , Staphylococcus aureus/química , Staphylococcus aureus/efeitos dos fármacos , Carbono/análise , Cloranfenicol/farmacologia , Fosfomicina/farmacologia , Espectroscopia de Ressonância Magnética/métodos , Nitrogênio/análise , Peptidoglicano/análise , Polissacarídeos Bacterianos/análise , Inibidores da Síntese de Proteínas/farmacologia , Protoplastos/química , Ácidos Teicoicos/análise
10.
Eur J Endocrinol ; 190(6): K53-K56, 2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38788201

RESUMO

A 29-year-old female, born to consanguineous parents, was found with unmeasurable levels of vitamin D (<10 nmol/L) after routine biochemical screening during her first pregnancy. She did not respond to either oral or intramuscular vitamin D supplementation and was an otherwise healthy young woman, with no signs of rickets, osteomalacia, osteoporosis, or secondary hyperparathyroidism. Western blot analysis revealed total lack of vitamin D binding protein, and next generation sequencing confirmed a novel, pathogenic homozygote loss-of-function mutation in exon 13 of the group-specific component gene, that encodes the poly A tail for vitamin D binding protein. She was therefore diagnosed with hereditary DBP deficiency, and vitamin D supplementation was diminished to life-long regular vitamin D supplementation (25 µg per day). This case is extremely interesting, as it expands our knowledge of vitamin D physiology and supports the free hormone hypothesis, given that the patient was asymptomatic despite no measurable levels of vitamin D.


Assuntos
Homozigoto , Deficiência de Vitamina D , Proteína de Ligação a Vitamina D , Vitamina D , Humanos , Feminino , Adulto , Vitamina D/sangue , Deficiência de Vitamina D/genética , Deficiência de Vitamina D/sangue , Proteína de Ligação a Vitamina D/genética , Mutação com Perda de Função
11.
bioRxiv ; 2024 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-39345506

RESUMO

Tuberculosis (TB), exceeded in mortality only by COVID-19 among global infectious diseases, is caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of Mtb is largely attributed to its complex cell envelope, which includes a class of glycolipids called phosphatidyl-myo-inositol mannosides (PIMs), found uniquely in mycobacteria and its related corynebacterineae. These glycolipids maintain the integrity of the mycobacterial cell envelope, regulate its permeability, and mediate host-pathogen interactions. PIMs consist of a phosphatidyl-myo-inositol core decorated with one to six mannose residues and up to four acyl chains. The mannosyltransferase PimE catalyzes the transfer of the fifth PIM mannose residue from a polyprenyl phosphate-mannose (PPM) donor. This step in the biosynthesis of higher-order PIMs contributes to the proper assembly and function of the mycobacterial cell envelope; however, the structural basis for substrate recognition and the catalytic mechanism of PimE remain poorly understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of PimE from Mycobacterium abscessus captured in its apo form and in a product-bound complex with the reaction product Ac1PIM5 and the by-product polyprenyl phosphate (PP), determined at 3.0 Å and 3.5 Å, respectively. The structures reveal the active site within a distinctive binding cavity that accommodates both donor and acceptor substrates/products. Within the cavity, we identified residues involved in substrate coordination and catalysis, which we confirmed through in vitro enzymatic assays and further validated by in vivo complementation experiments. Molecular dynamics simulations were applied to identify the access pathways and the dynamics involved in substrate binding. Integrating structural, biochemical, genetic, and computational experiments, our study provides comprehensive insights into how PimE functions, opening potential avenues for development of novel anti-TB therapeutics.

12.
bioRxiv ; 2024 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-39345558

RESUMO

The emergence of drug-resistant strains exacerbates the global challenge of tuberculosis caused by Mycobacterium tuberculosis (Mtb). Central to the pathogenicity of Mtb is its complex cell envelope, which serves as a barrier against both immune system and pharmacological attacks. Two key components of this envelope, arabinogalactan (AG) and lipoarabinomannan (LAM) are complex polysaccharides that contain integral arabinan domains important for cell wall structural and functional integrity. The arabinofuranosyltransferase AftB terminates the synthesis of these arabinan domains by catalyzing the addition of the addition of ß-(1→2)-linked terminal arabinofuranose residues. Here, we present the cryo-EM structures of Mycobacterium chubuense AftB in its apo and donor substrate analog-bound form, determined to 2.9 Å and 3.4 Å resolution, respectively. Our structures reveal that AftB has a GT-C fold transmembrane (TM) domain comprised of eleven TM helices and a periplasmic cap domain. AftB has an irregular tube-shaped cavity that bridges the two proposed substrate binding sites. By integrating structural analysis, biochemical assays, and molecular dynamics simulations, we elucidate the molecular basis of the reaction mechanism of AftB and propose a model for catalysis.

13.
J Biol Chem ; 287(38): 31973-82, 2012 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-22843684

RESUMO

Recent high resolution x-ray structures of the ß2-adrenergic receptor confirmed a close salt-bridge interaction between the suspected micro-switch residue ArgIII:26 (Arg3.50) and the neighboring AspIII:25 (Asp3.49). However, neither the expected "ionic lock" interactions between ArgIII:26 and GluVI:-06 (Glu6.30) in the inactive conformation nor the interaction with TyrV:24 (Tyr5.58) in the active conformation were observed in the x-ray structures. Here we find through molecular dynamics simulations, after removal of the stabilizing T4 lysozyme, that the expected salt bridge between ArgIII:26 and GluVI:-06 does form relatively easily in the inactive receptor conformation. Moreover, mutational analysis of GluVI:-06 in TM-VI and the neighboring AspIII:25 in TM-III demonstrated that these two residues do function as locks for the inactive receptor conformation as we observed increased G(s) signaling, arrestin mobilization, and internalization upon alanine substitutions. Conversely, TyrV:24 appears to play a role in stabilizing the active receptor conformation as loss of function of G(s) signaling, arrestin mobilization, and receptor internalization was observed upon alanine substitution of TyrV:24. The loss of function of the TyrV:24 mutant could partly be rescued by alanine substitution of either AspIII:25 or GluVI:-06 in the double mutants. Surprisingly, removal of the side chain of the ArgIII:26 micro-switch itself had no effect on G(s) signaling and internalization and only reduced arrestin mobilization slightly. It is suggested that ArgIII:26 is equally important for stabilizing the inactive and the active conformation through interaction with key residues in TM-III, -V, and -VI, but that the ArgIII:26 micro-switch residue itself apparently is not essential for the actual G protein activation.


Assuntos
Arginina/química , Receptores Adrenérgicos beta 2/química , Alanina/química , Motivos de Aminoácidos , Animais , Arrestina/química , Células CHO , Células COS , Membrana Celular/metabolismo , Chlorocebus aethiops , Cricetinae , Proteínas de Ligação ao GTP/metabolismo , Inativação Gênica , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Ligação Proteica , Receptores Adrenérgicos beta 2/metabolismo , Relação Estrutura-Atividade
14.
Nat Commun ; 14(1): 5151, 2023 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-37620344

RESUMO

Peptidoglycan (PG) is an essential structural component of the bacterial cell wall that is synthetized during cell division and elongation. PG forms an extracellular polymer crucial for cellular viability, the synthesis of which is the target of many antibiotics. PG assembly requires a glycosyltransferase (GT) to generate a glycan polymer using a Lipid II substrate, which is then crosslinked to the existing PG via a transpeptidase (TP) reaction. A Shape, Elongation, Division and Sporulation (SEDS) GT enzyme and a Class B Penicillin Binding Protein (PBP) form the core of the multi-protein complex required for PG assembly. Here we used single particle cryo-electron microscopy to determine the structure of a cell elongation-specific E. coli RodA-PBP2 complex. We combine this information with biochemical, genetic, spectroscopic, and computational analyses to identify the Lipid II binding sites and propose a mechanism for Lipid II polymerization. Our data suggest a hypothesis for the movement of the glycan strand from the Lipid II polymerization site of RodA towards the TP site of PBP2, functionally linking these two central enzymatic activities required for cell wall peptidoglycan biosynthesis.


Assuntos
Escherichia coli , Peptidil Transferases , Microscopia Crioeletrônica , Escherichia coli/genética , Peptidoglicano , Biologia Molecular , Antibacterianos , Glicosiltransferases
15.
J Biol Chem ; 285(25): 19625-36, 2010 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-20395291

RESUMO

Five highly conserved polar residues connected by a number of structural water molecules together with two rotamer micro-switches, TrpVI:13 and TyrVII:20, constitute an extended hydrogen bond network between the intracellular segments of TM-I, -II, -VI, and -VII of 7TM receptors. Molecular dynamics simulations showed that, although the fewer water molecules in rhodopsin were relatively movable, the hydrogen bond network of the beta2-adrenergic receptor was fully loaded with water molecules that were surprisingly immobilized between the two rotamer switches, both apparently being in their closed conformation. Manipulations of the rotamer state of TyrVII:20 and TrpVI:13 demonstrated that these residues served as gates for the water molecules at the intracellular and extracellular ends of the hydrogen bond network, respectively. TrpVI:13 at the bottom of the main ligand-binding pocket was shown to apparently function as a catching trap for water molecules. Mutational analysis of the beta2-adrenergic receptor demonstrated that the highly conserved polar residues of the hydrogen bond network were all important for receptor signaling but served different functions, some dampening constitutive activity (AsnI:18, AspII:10, and AsnVII:13), whereas others (AsnVII:12 and AsnVII:16) located one helical turn apart and sharing a water molecule were shown to be essential for agonist-induced signaling. It is concluded that the conserved water hydrogen bond network of 7TM receptors constitutes an extended allosteric interface between the transmembrane segments being of crucial importance for receptor signaling and that part of the function of the rotamer micro-switches, TyrVII:20 and TrpVI:13, is to gate or trap the water molecules.


Assuntos
Água/química , Motivos de Aminoácidos , Animais , Células COS , Chlorocebus aethiops , Análise Mutacional de DNA , Ligação de Hidrogênio , Ligantes , Modelos Biológicos , Conformação Molecular , Mutagênese , Estrutura Terciária de Proteína , Receptores Adrenérgicos beta 2/química , Receptores Acoplados a Proteínas G/química , Transdução de Sinais
16.
J Biol Chem ; 285(6): 3973-3985, 2010 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-19920139

RESUMO

The conserved tryptophan in position 13 of TM-VI (Trp-VI:13 or Trp-6.48) of the CWXP motif located at the bottom of the main ligand-binding pocket in TM-VI is believed to function as a rotameric microswitch in the activation process of seven-transmembrane (7TM) receptors. Molecular dynamics simulations in rhodopsin demonstrated that rotation around the chi1 torsion angle of Trp-VI:13 brings its side chain close to the equally highly conserved Phe-V:13 (Phe-5.47) in TM-V. In the ghrelin receptor, engineering of high affinity metal-ion sites between these positions confirmed their close spatial proximity. Mutational analysis was performed in the ghrelin receptor with multiple substitutions and with Ala substitutions in GPR119, GPR39, and the beta(2)-adrenergic receptor as well as the NK1 receptor. In all of these cases, it was found that mutation of the Trp-VI:13 rotameric switch itself eliminated the constitutive signaling and strongly impaired agonist-induced signaling without affecting agonist affinity and potency. Ala substitution of Phe-V:13, the presumed interaction partner for Trp-VI:13, also in all cases impaired both the constitutive and the agonist-induced receptor signaling, but not to the same degree as observed in the constructs where Trp-VI:13 itself was mutated, but again without affecting agonist potency. In a proposed active receptor conformation generated by molecular simulations, where the extracellular segment of TM-VI is tilted inwards in the main ligand-binding pocket, Trp-VI:13 could rotate into a position where it obtained an ideal aromatic-aromatic interaction with Phe-V:13. It is concluded that Phe-V:13 can serve as an aromatic lock for the proposed active conformation of the Trp-VI:13 rotameric switch, being involved in the global movement of TM-V and TM-VI in 7TM receptor activation.


Assuntos
Fenilalanina/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Triptofano/metabolismo , Regulação Alostérica , Sequência de Aminoácidos , Animais , Sítios de Ligação , Células COS , Chlorocebus aethiops , Humanos , Modelos Moleculares , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Mutação , Fenilalanina/química , Fenilalanina/genética , Ligação Proteica , Conformação Proteica , Receptores Adrenérgicos beta 2/genética , Receptores Adrenérgicos beta 2/metabolismo , Receptores Acoplados a Proteínas G/agonistas , Receptores Acoplados a Proteínas G/antagonistas & inibidores , Receptores Acoplados a Proteínas G/genética , Receptores de Grelina/genética , Receptores de Grelina/metabolismo , Retinaldeído/farmacologia , Rodopsina/agonistas , Rodopsina/química , Rodopsina/metabolismo , Triptofano/química , Triptofano/genética
17.
Trends Pharmacol Sci ; 30(5): 249-59, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19375807

RESUMO

The past couple of years have seen several novel X-ray structures of 7 transmembrane (7TM) receptors in complex with antagonists and even with a peptide fragment of a G protein. These structures demonstrate that the main ligand-binding pocket in 7TM receptors is like a funnel with a partial 'lid' in which extracellular loop 2b, in particular, functions as a gating element. Small-molecule antagonists and inverse agonists bind in very different modes: some very deeply and others more superficially, even reaching out above the transmembranes. Several highly conserved residues seem to function as micro-switches of which ArgIII:26 (Arg3.50) in its active conformation interacts directly with the G protein. These micro-switches together with a hydrogen-bond network between conserved polar residues and structural water molecules are proposed to constitute an extended allosteric interface between the domains (i.e. especially TM-VI), which performs the large, global toggle switch movements connecting ligand binding with intracellular signaling.


Assuntos
Modelos Moleculares , Domínios e Motivos de Interação entre Proteínas , Receptores Acoplados a Proteínas G/química , Regulação Alostérica , Sítios de Ligação , Agonismo de Drogas , Antagonismo de Drogas , Ligantes , Conformação Molecular , Estrutura Molecular , Receptores Acoplados a Proteínas G/agonistas , Receptores Acoplados a Proteínas G/antagonistas & inibidores
18.
Curr Opin Struct Biol ; 64: 26-33, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32603877

RESUMO

Recent advances in single-particle cryogenic-electron microscopy have facilitated an exponential growth in the number of membrane protein structures determined to close to atomic resolution. Nevertheless, despite improvements in microscope hardware, cryo-EM software and sample preparation techniques, challenges remain for structural analysis of small-sized membrane proteins (i.e.<150 kilodalton). Here we discuss recent examples of structures of macromolecules from this category determined by cryo-EM. We analyze the underlying difficulties, the enabling technologies such as the use of antibody fragments to gain size and provide fiducials for particle alignment, and the unresolved issues like dislocation of complexes at the air-water interface. Finally, we briefly highlight the biological relevance of some of these success stories, and our predictions for the future.


Assuntos
Proteínas de Membrana , Imagem Individual de Molécula , Microscopia Crioeletrônica , Substâncias Macromoleculares , Software
19.
J Phys Chem B ; 121(40): 9331-9335, 2017 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-28901760

RESUMO

Solid-state NMR is a powerful tool for quantifying chemical composition and structure in complex assemblies and even whole cells. We employed N{P} REDOR NMR to obtain atomic-level distance propensities in intact 15N-labeled E. coli ribosomes. The experimental REDOR dephasing of shift-resolved lysyl amine nitrogens by phosphorus was comparable to that expected from a calculation of N-P distances involving the lysines included in the crystal structure coordinates. Among the nitrogen contributions to the REDOR spectra, the strongest dephasing emerged from the dipolar couplings to phosphorus involving nitrogen peaks ascribed primarily to rRNA, and the weakest dephasing arose from protein amide nitrogens. This approach is applicable to any macromolecular system and provides quantitative comparisons of distance proximities between shift-resolved nuclei of one type and heteronuclear dephasing spins. Enhanced molecular specificity could be achieved through the use of spectroscopic filters or specific labeling. Furthermore, ribosome 13C and 15N CPMAS spectra were compared with those of whole cells from which the ribosomes were isolated. Whole-cell signatures of ribosomes were identified and should be of value in comparing overall cellular ribosome content in whole-cell samples.


Assuntos
Espectroscopia de Ressonância Magnética Nuclear de Carbono-13/métodos , Proteínas de Escherichia coli/química , RNA Ribossômico/química , Proteínas Ribossômicas/química , Ribossomos/química , Escherichia coli , Proteínas de Escherichia coli/isolamento & purificação , Lisina/química , RNA Ribossômico/isolamento & purificação , Proteínas Ribossômicas/isolamento & purificação
20.
J Appl Physiol (1985) ; 123(2): 482-488, 2017 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-28596275

RESUMO

Patients with Ehlers-Danlos syndrome (EDS) are known to have genetically impaired connective tissue and skeletal muscle symptoms in form of pain, fatigue, and cramps; however earlier studies have not been able to link these symptoms to morphological muscle changes. We obtained skeletal muscle biopsies in patients with classic EDS [cEDS; n = 5 (Denmark)+ 8 (The Netherlands)] and vascular EDS (vEDS; n = 3) and analyzed muscle fiber morphology and content (Western blotting and muscle fiber type/area distributions) and muscle mRNA expression and protein synthesis rate (RT-PCR and stable isotope technique). The cEDS patients did not differ from healthy controls (n = 7-11) with regard to muscle fiber type/area, myosin/α-actin ratio, muscle protein synthesis rate, or mRNA expression. In contrast, the vEDS patients demonstrated higher expression of matrix proteins compared with cEDS patients (fibronectin and MMP-2). The cEDS patients had surprisingly normal muscle morphology and protein synthesis, whereas vEDS patients demonstrated higher mRNA expression for extracellular matrix remodeling in skeletal musculature compared with cEDS patients.NEW & NOTEWORTHY This study is the first of its kind to systematically investigate muscle biopsies from Ehlers-Danlos patients, focusing on muscle structure and function. These patients suffer from severe muscle symptoms, but in our study they show surprisingly normal muscle findings, which points toward indirect muscle symptoms originating from the surrounding connective tissue. These findings have basal physiological importance and implications for future physiotherapeutic treatment options for these patients.


Assuntos
Síndrome de Ehlers-Danlos/fisiopatologia , Expressão Gênica/genética , Músculo Esquelético/fisiologia , Biossíntese de Proteínas/genética , Actinas/genética , Adulto , Dinamarca , Matriz Extracelular/genética , Fadiga/genética , Feminino , Fibronectinas/genética , Humanos , Masculino , Metaloproteinase 2 da Matriz/genética , Miosinas/genética , Países Baixos , RNA Mensageiro/genética
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