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1.
Protein Sci ; 33(6): e4976, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38757374

RESUMO

G-protein coupled receptors (GPCRs) are the largest class of membrane proteins encoded in the human genome with high pharmaceutical relevance and implications to human health. These receptors share a prevalent architecture of seven transmembrane helices followed by an intracellular, amphipathic helix 8 (H8) and a disordered C-terminal tail (Ctail). Technological advancements have led to over 1000 receptor structures in the last two decades, yet frequently H8 and the Ctail are conformationally heterogeneous or altogether absent. Here we synthesize a peptide comprising the neurotensin receptor 1 (NTS1) H8 and Ctail (H8-Ctail) to investigate its structural stability, conformational dynamics, and orientation in the presence of detergent and phospholipid micelles, which mimic the membrane. Circular dichroism (CD) and nuclear magnetic resonance (NMR) measurements confirm that zwitterionic 1,2-diheptanoyl-sn-glycero-3-phosphocholine is a potent stabilizer of H8 structure, whereas the commonly-used branched detergent lauryl maltose neopentyl glycol (LMNG) is unable to completely stabilize the helix - even at amounts four orders of magnitude greater than its critical micellar concentration. We then used NMR spectroscopy to assign the backbone chemical shifts. A series of temperature and lipid titrations were used to define the H8 boundaries as F376-R392 from chemical shift perturbations, changes in resonance intensity, and chemical-shift-derived phi/psi angles. Finally, the H8 azimuthal and tilt angles, defining the helix orientation relative of the membrane normal were measured using paramagnetic relaxation enhancement NMR. Taken together, our studies reveal the H8-Ctail region is sensitive to membrane physicochemical properties and is capable of more adaptive behavior than previously suggested by static structural techniques.


Assuntos
Receptores de Neurotensina , Receptores de Neurotensina/química , Receptores de Neurotensina/metabolismo , Receptores de Neurotensina/genética , Humanos , Micelas , Ressonância Magnética Nuclear Biomolecular , Peptídeos/química , Peptídeos/metabolismo , Dicroísmo Circular , Conformação Proteica em alfa-Hélice , Detergentes/química , Modelos Moleculares
2.
bioRxiv ; 2024 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-37090523

RESUMO

Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain, and the conjugated protein of the ISGylation system. Similar to ubiquitin and other Ubls, ISG15 is ligated to its target proteins with a series of E1, E2, and E3 enzymes known as Uba7, Ube2L6/UbcH8, and HERC5, respectively. Ube2L6/UbcH8 plays a literal central role in ISGylation, underscoring it as an important drug target for boosting innate antiviral immunity. Depending on the type of conjugated protein and the ultimate target protein, E2 enzymes have been shown to function as monomers, dimers, or both. UbcH8 has been crystalized in both monomeric and dimeric forms, but the functional state is unclear. Here, we used a combined approach of small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy to characterize UbcH8's oligomeric state in solution. SAXS revealed a dimeric UbcH8 structure that could be dissociated when fused with an N-terminal glutathione S-transferase molecule. NMR spectroscopy validated the presence of a concentration-dependent monomer-dimer equilibrium and suggested a backside dimerization interface. Chemical shift perturbation and peak intensity analysis further suggest dimer-induced conformational dynamics at ISG15 and E3 interfaces - providing hypotheses for the protein's functional mechanisms. Our study highlights the power of combining NMR and SAXS techniques in providing structural information about proteins in solution.

3.
Nat Commun ; 14(1): 3328, 2023 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-37286565

RESUMO

The neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1 structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used 13CεH3-methionine NMR spectroscopy to show that binding of phosphatidylinositol-4,5-bisphosphate (PIP2) to the receptor's intracellular surface allosterically tunes the timescale of motions at the orthosteric pocket and conserved activation motifs - without dramatically altering the structural ensemble. ß-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on exchange rates. A ß-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.


Assuntos
Receptores Acoplados a Proteínas G , Receptores de Neurotensina , Receptores de Neurotensina/genética , Receptores de Neurotensina/metabolismo , beta-Arrestina 1/genética , beta-Arrestina 1/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , beta-Arrestinas/metabolismo , Proteínas de Ligação ao GTP/metabolismo , Arrestina/metabolismo
4.
Cell Rep ; 42(1): 112015, 2023 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-36680775

RESUMO

Nuclear magnetic resonance (NMR) studies have revealed that fast methyl sidechain dynamics can report on entropically-driven allostery. Yet, NMR applications have been largely limited to the super-microsecond motional regimes of G protein-coupled receptors (GPCRs). We use 13Cε-methionine chemical shift-based global order parameters to test if ligands affect the fast dynamics of a thermostabilized GPCR, neurotensin receptor 1 (NTS1). We establish that the NTS1 solution ensemble includes substates with lifetimes on several, discrete timescales. The longest-lived states reflect those captured in agonist- and inverse agonist-bound crystal structures, separated by large energy barriers. We observe that the rapid fluctuations of individual methionine residues, superimposed on these long-lived states, respond collectively with the degree of fast, global dynamics correlating with ligand pharmacology. This approach lends confidence to interpreting spectra in terms of local structure and methyl dihedral angle geometry. The results suggest a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.


Assuntos
Receptores de Neurotensina , Humanos , Agonismo Inverso de Drogas , Ligantes , Metionina , Ligação Proteica , Conformação Proteica , Receptores de Neurotensina/química , Receptores de Neurotensina/metabolismo
5.
Protein Sci ; 31(11): e4454, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-36116099

RESUMO

Fluorine (19 F) offers several distinct advantages for biomolecular nuclear magnetic resonance spectroscopy such as no background signal, 100% natural abundance, high sensitivity, and a large chemical shift range. Exogenous cysteine-reactive 19 F-probes have proven especially indispensable for characterizing large, challenging systems that are less amenable to other isotopic labeling strategies such as G protein-coupled receptors. As fluorine linewidths are inherently broad, limiting reactions with offsite cysteines is critical for spectral simplification and accurate deconvolution of component peaks-especially when analyzing systems with intermediate to slow timescale conformational exchange. Here, we uncovered noncovalent probe sequestration by detergent proteomicelles as a second source of offsite labeling when using the popular 19 F-probe BTFMA (2-bromo-N-(4-[trifluoromethyl]phenyl)acetamide). The chemical shift and relaxation rates of these unreacted 19 F-BTFMA molecules are insufficient to distinguish them from protein-conjugates, but they can be easily identified using mass spectrometry. We present a simple four-step protocol for Selective Labeling Absent of Probe Sequestration (SLAPS): physically disrupt cell membranes in the absence of detergent, incubate membranes with cysteine-reactive 19 F-BTFMA, remove excess unreacted 19 F-BTFMA molecules via ultracentrifugation, and finally solubilize in the detergent of choice. Our approach builds upon the in-membrane chemical modification method with the addition of one crucial step: removal of unreacted 19 F-probes by ultracentrifugation prior to detergent solubilization. SLAPS is broadly applicable to other lipophilic cysteine-reactive probes and membrane protein classes solubilized in detergent micelles or lipid mimetics.


Assuntos
Detergentes , Flúor , Detergentes/química , Cisteína , Proteínas de Membrana/química
6.
J Am Chem Soc ; 144(23): 10241-10250, 2022 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-35647863

RESUMO

Using a discrete, intracellular 19F nuclear magnetic resonance (NMR) probe on transmembrane helix 6 of the neurotensin receptor 1 (NTS1), we aim to understand how ligands and transducers modulate the receptor's structural ensemble in a solution. For apo NTS1, 19F NMR spectra reveal an ensemble of at least three conformational substates (one inactive and two active-like) in equilibrium that exchange on the millisecond to second timescale. Dynamic NMR experiments reveal that these substates follow a linear three-site exchange process that is both thermodynamically and kinetically remodeled by orthosteric ligands. As previously observed in other G protein-coupled receptors (GPCRs), the full agonist is insufficient to completely stabilize the active-like state. The inactive substate is abolished upon coupling to ß-arrestin-1 (ßArr1) or the C-terminal helix of Gαq, which comprises ≳60% of the GPCR/G protein interface surface area. Whereas ßArr1 exclusively selects for pre-existing active-like substates, the Gαq peptide induces a new substate. Both transducer molecules promote substantial line broadening of active-like states, suggesting contributions from additional microsecond to millisecond exchange processes. Together, our study suggests that (i) the NTS1 allosteric activation mechanism may be alternatively dominated by induced fit or conformational selection depending on the coupled transducer, and (ii) the available static structures do not represent the entire conformational ensemble observed in a solution.


Assuntos
Receptores Acoplados a Proteínas G , Receptores de Neurotensina , Ligantes , Proteínas de Membrana , Conformação Proteica , Receptores Acoplados a Proteínas G/química , Receptores de Neurotensina/química , Receptores de Neurotensina/metabolismo , Transdutores
7.
J Biomol NMR ; 75(8-9): 293-302, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34480265

RESUMO

Accurate rotational correlation times ([Formula: see text]) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of [Formula: see text] using transverse and longitudinal relaxation rates becomes increasingly unsuitable due to the non-trivial contribution of remote dipole-dipole interactions to longitudinal relaxation. Derivations using cross-correlated relaxation experiments, such as TRACT, overcome these limitations but are erroneously calculated in 65% of the citing literature. Herein, we developed an algebraic solutions to the Goldman relationship that facilitate rapid, point-by-point calculations for straightforward identification of appropriate spectral regions where global tumbling is likely to be dominant. The rigid-body approximation of the Goldman relationship has been previously shown to underestimate TRACT-based rotational correlation time estimates. This motivated us to develop a second algebraic solution that employs a simplified model-free spectral density function including an order parameter term that could, in principle, be set to an average backbone S2 ≈ 0.9 to further improve the accuracy of [Formula: see text] estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the H-N internuclear distance ([Formula: see text]), difference of the two principal components of the axially-symmetric 15N CSA tensor ([Formula: see text]), and angle of the CSA tensor relative to the N-H bond vector ([Formula: see text]). We hope our algebraic solutions and analytical strategies will increase the accuracy and application of the TRACT experiment.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Espectroscopia de Ressonância Magnética
8.
Nat Commun ; 9(1): 3014, 2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30069002

RESUMO

The Bloch-Siegert shift is a phenomenon in NMR spectroscopy and atomic physics in which the observed resonance frequency is changed by the presence of an off-resonance applied field. In NMR, it occurs especially in the context of homonuclear decoupling. Here we develop a practical method for homonuclear decoupling that avoids inducing Bloch-Siegert shifts. This approach enables accurate observation of the resonance frequencies of decoupled nuclear spins. We apply this method to increase the resolution of the HNCA experiment. We also observe a doubling in sensitivity for a 30 kDa protein. We demonstrate the use of band-selective Cß decoupling to produce amino acid-specific line shapes, which are valuable for assigning resonances to the protein sequence. Finally, we assign the backbone of a 30 kDa protein, Human Carbonic Anhydrase II, using only HNCA experiments acquired with band-selective decoupling schemes, and instrument time of one week.


Assuntos
Espectroscopia de Ressonância Magnética , Modelos Teóricos , Aminoácidos/química , Isótopos de Carbono , Simulação por Computador , Humanos , Proteínas/química , Ondas de Rádio , Reprodutibilidade dos Testes
10.
Nat Commun ; 9(1): 356, 2018 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-29367739

RESUMO

Backbone resonance assignment is a critical first step in the investigation of proteins by NMR. This is traditionally achieved with a standard set of experiments, most of which are not optimal for large proteins. Of these, HNCA is the most sensitive experiment that provides sequential correlations. However, this experiment suffers from chemical shift degeneracy problems during the assignment procedure. We present a strategy that increases the effective resolution of HNCA and enables near-complete resonance assignment using this single HNCA experiment. We utilize a combination of 2-13C and 3-13C pyruvate as the carbon source for isotope labeling, which suppresses the one bond (1Jαß) coupling providing enhanced resolution for the Cα resonance and amino acid-specific peak shapes that arise from the residual coupling. Using this approach, we can obtain near-complete (>85%) backbone resonance assignment of a 42 kDa protein using a single HNCA experiment.


Assuntos
Espectroscopia de Ressonância Magnética Nuclear de Carbono-13/métodos , Proteínas de Escherichia coli/análise , Marcação por Isótopo/métodos , Proteínas Ligantes de Maltose/análise , Ácido Pirúvico/química , Escherichia coli , Espectroscopia de Ressonância Magnética
11.
J Biomol NMR ; 68(2): 139-154, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28332026

RESUMO

Non-Uniform Sampling has the potential to exploit the optimal resolution of high-field NMR instruments. This is not possible in 3D and 4D NMR experiments when using traditional uniform sampling due to the long overall measurement time. Nominally, uniformly sampled time domain data acquired to a maximum evolution time tmax can be extended to high resolution via a virtual maximum evolution time t*max while extrapolating with linear prediction or iterative soft thresholding (IST). At the high resolution obtainable with extrapolation of US data, however, the accuracy of peak positions is compromised as observed when comparing inter- and intra-residue peaks in a 3D HNCA experiment. However, the accuracy of peak positions is largely improved by spreading the same number of acquired time domain data points non-uniformly over a larger evolution time to an optimal tmax followed by extrapolation to a total t*max and processing the data with an appropriate reconstruction method, such as hmsIST. To explore the optimum value of experimentally measured tmax to be reached non-uniformly with a given number of sampling points we have created test situations of time-equivalent experiments and evaluate sensitivity and accuracy of peak positions. Here we use signal-to-maximum-noise ratio as the decisive measure of sensitivity. We find that both sensitivity and resolution are optimal when PoissonGap sampling to a tmax of about ½*T2*. Digital resolution is further enhanced by extrapolating the range of acquired time domain data to 2*T2* but without measuring experimental points beyond ½*T2*.


Assuntos
Algoritmos , Ressonância Magnética Nuclear Biomolecular/métodos , Análise de Fourier , Sensibilidade e Especificidade , Razão Sinal-Ruído
12.
Biomol NMR Assign ; 9(2): 387-91, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25967379

RESUMO

Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into (15)N(2)H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA.


Assuntos
Aminoácidos/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Geobacillus stearothermophilus/metabolismo , Ressonância Magnética Nuclear Biomolecular , Sequência de Aminoácidos , Modelos Moleculares , Dados de Sequência Molecular , Ligação Proteica , Espectroscopia de Prótons por Ressonância Magnética
13.
J Magn Reson ; 241: 60-73, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24656081

RESUMO

Multi-dimensional NMR spectra have traditionally been processed with the fast Fourier transformation (FFT). The availability of high field instruments, the complexity of spectra of large proteins, the narrow signal dispersion of some unstructured proteins, and the time needed to record the necessary increments in the indirect dimensions to exploit the resolution of the highfield instruments make this traditional approach unsatisfactory. New procedures need to be developed beyond uniform sampling of the indirect dimensions and reconstruction methods other than the straight FFT are necessary. Here we discuss approaches of non-uniform sampling (NUS) and suitable reconstruction methods. We expect that such methods will become standard for multi-dimensional NMR data acquisition with complex biological macromolecules and will dramatically enhance the power of modern biological NMR.


Assuntos
Análise de Fourier , Ressonância Magnética Nuclear Biomolecular/métodos , Algoritmos , Animais , Humanos , Distribuição de Poisson
14.
J Biomol NMR ; 55(2): 167-78, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23274692

RESUMO

It is well established that non-uniform sampling (NUS) allows acquisition of multi-dimensional NMR spectra at a resolution that cannot be obtained with traditional uniform acquisition through the indirect dimensions. However, the impact of NUS on the signal-to-noise ratio (SNR) and sensitivity are less well documented. SNR and sensitivity are essential aspects of NMR experiments as they define the quality and extent of data that can be obtained. This is particularly important for spectroscopy with low concentration samples of biological macromolecules. There are different ways of defining the SNR depending on how to measure the noise, and the distinction between SNR and sensitivity is often not clear. While there are defined procedures for measuring sensitivity with high concentration NMR standards, such as sucrose, there is no clear or generally accepted definition of sensitivity when comparing different acquisition and processing methods for spectra of biological macromolecules with many weak signals close to the level of noise. Here we propose tools for estimating the SNR and sensitivity of NUS spectra with respect to sampling schedule and reconstruction method. We compare uniformly acquired spectra with NUS spectra obtained in the same total measuring time. The time saving obtained when only 1/k of the Nyquist grid points are sampled is used to measure k-fold more scans per increment. We show that judiciously chosen NUS schedules together with suitable reconstruction methods can yield a significant increase of the SNR within the same total measurement time. Furthermore, we propose to define the sensitivity as the probability to detect weak peaks and show that time-equivalent NUS can considerably increase this detection sensitivity. The sensitivity gain increases with the number of NUS indirect dimensions. Thus, well-chosen NUS schedules and reconstruction methods can significantly increase the information content of multidimensional NMR spectra of challenging biological macromolecules.


Assuntos
Ressonância Magnética Nuclear Biomolecular/métodos , Razão Sinal-Ruído , Algoritmos , Sensibilidade e Especificidade
15.
J Biol Chem ; 288(2): 1065-78, 2013 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-23132864

RESUMO

Staphylococcus aureus is a leading cause of life-threatening infections in the United States. It requires iron to grow, which must be actively procured from its host to successfully mount an infection. Heme-iron within hemoglobin (Hb) is the most abundant source of iron in the human body and is captured by S. aureus using two closely related receptors, IsdH and IsdB. Here we demonstrate that each receptor captures heme using two conserved near iron transporter (NEAT) domains that function synergistically. NMR studies of the 39-kDa conserved unit from IsdH (IsdH(N2N3), Ala(326)-Asp(660)) reveals that it adopts an elongated dumbbell-shaped structure in which its NEAT domains are properly positioned by a helical linker domain, whose three-dimensional structure is determined here in detail. Electrospray ionization mass spectrometry and heme transfer measurements indicate that IsdH(N2N3) extracts heme from Hb via an ordered process in which the receptor promotes heme release by inducing steric strain that dissociates the Hb tetramer. Other clinically significant Gram-positive pathogens capture Hb using receptors that contain multiple NEAT domains, suggesting that they use a conserved mechanism.


Assuntos
Antígenos de Bactérias/metabolismo , Proteínas de Transporte de Cátions/metabolismo , Heme/metabolismo , Hemoglobinas/metabolismo , Receptores de Superfície Celular/metabolismo , Staphylococcus aureus/metabolismo , Clonagem Molecular , Humanos , Ressonância Magnética Nuclear Biomolecular , Proteólise
16.
Biochemistry ; 51(48): 9624-37, 2012 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-23163963

RESUMO

Human defensin 5 (HD5) is a 32-residue host-defense peptide expressed in the gastrointestinal, reproductive, and urinary tracts that has antimicrobial activity. It exhibits six cysteine residues that are regiospecifically oxidized to form three disulfide bonds (Cys(3)-Cys(31), Cys(5)-Cys(20), and Cys(10)-Cys(30)) in the oxidized form (HD5(ox)). To probe the solution structure and oligomerization properties of HD5(ox), and select mutant peptides lacking one or more disulfide bonds, NMR solution studies and analytical ultracentrifugation experiments are reported in addition to in vitro peptide stability assays. The NMR solution structure of HD5(ox), solved at pH 4.0 in 90:10 H(2)O/D(2)O, is presented (PDB: 2LXZ ). Relaxation T(1)/T(2) measurements and the rotational correlation time (τ(c)) estimated from a (15)N-TRACT experiment demonstrate that HD5(ox) is dimeric under these experimental conditions. Exchange broadening of the Hα signals in the NMR spectra suggests that residues 19-21 (Val(19)-Cys(20)-Glu(21)) contribute to the dimer interface in solution. Exchange broadening is also observed for residues 7-14 comprising the loop. Sedimentation velocity and equilibrium studies conducted in buffered aqueous solution reveal that the oligomerization state of HD5(ox) is pH-dependent. Sedimentation coefficients of ca. 1.8 S and a molecular weight of 14 363 Da were determined for HD5(ox) at pH 7.0, supporting a tetrameric form ([HD5(ox)] ≥ 30 µM). At pH 2.0, a sedimentation coefficient of ca. 1.0 S and a molecular weight of 7079 Da, corresponding to a HD5(ox) dimer, were obtained. Millimolar concentrations of NaCl, CaCl(2), and MgCl(2) have a negligible effect on the HD5(ox) sedimentation coefficients in buffered aqueous solution at neutral pH. Removal of a single disulfide bond results in a loss of peptide fold and quaternary structure. These biophysical investigations highlight the dynamic and environmentally sensitive behavior of HD5(ox) in solution, and provide important insights into HD5(ox) structure/activity relationships and the requirements for antimicrobial action.


Assuntos
Biopolímeros/química , Defensinas/química , Sequência de Aminoácidos , Cromatografia Líquida de Alta Pressão , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular , Conformação Proteica , Espectrofotometria Ultravioleta , Staphylococcus aureus/química
17.
Biochemistry ; 51(40): 7953-63, 2012 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-22974341

RESUMO

Bacillus anthracis forms metabolically dormant endospores that upon germination can cause lethal anthrax disease in humans. Efficient sporulation requires the activity of the SrtC sortase (BaSrtC), a cysteine transpeptidase that covalently attaches the BasH and BasI proteins to the peptidoglycan of the forespore and predivisional cell, respectively. To gain insight into the molecular basis of protein display, we used nuclear magnetic resonance to determine the structure and backbone dynamics of the catalytic domain of BaSrtC (residues Ser(56)-Lys(198)). The backbone and heavy atom coordinates of structurally ordered amino acids have coordinate precision of 0.42 ± 0.07 and 0.82 ± 0.05 Å, respectively. BaSrtC(Δ55) adopts an eight-stranded ß-barrel fold that contains two short helices positioned on opposite sides of the protein. Surprisingly, the protein dimerizes and contains an extensive, structurally disordered surface that is positioned adjacent to the active site. The surface is formed by two loops (ß2-ß3 and ß4-H1 loops) that surround the active site histidine, suggesting that they may play a key role in associating BaSrtC with its lipid II substrate. BaSrtC anchors proteins bearing a noncanonical LPNTA sorting signal. Modeling studies suggest that the enzyme recognizes this substrate using a rigid binding pocket and reveals the presence of a conserved subsite for the signal. This first structure of a class D member of the sortase superfamily unveils class-specific features that may facilitate ongoing efforts to discover sortase inhibitors for the treatment of bacterial infections.


Assuntos
Aminoaciltransferases/metabolismo , Bacillus anthracis/enzimologia , Bacillus anthracis/fisiologia , Proteínas de Bactérias/metabolismo , Cisteína Endopeptidases/metabolismo , Esporos Bacterianos/fisiologia , Sequência de Aminoácidos , Aminoaciltransferases/genética , Proteínas de Bactérias/genética , Clonagem Molecular , Cisteína Endopeptidases/genética , Regulação Bacteriana da Expressão Gênica/fisiologia , Regulação Enzimológica da Expressão Gênica , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Sinais Direcionadores de Proteínas , Ultracentrifugação
18.
J Am Chem Soc ; 133(36): 14176-9, 2011 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-21834592

RESUMO

Iron is an essential nutrient for the bacterial pathogen Staphylococcus aureus . Heme in hemoglobin (Hb) is the most abundant source of iron in the human body and during infections is captured by S. aureus using iron-regulated surface determinant (Isd) proteins. A central step in this process is the transfer of heme between the cell wall associated IsdA and IsdC hemoproteins. Biochemical evidence indicates that heme is transferred via an activated IsdA:heme:IsdC heme complex. Transfer is rapid and occurs up to 70,000 times faster than indirect mechanisms in which heme is released into the solvent. To gain insight into the mechanism of transfer, we modeled the structure of the complex using NMR paramagnetic relaxation enhancement (PRE) methods. Our results indicate that IsdA and IsdC transfer heme via an ultraweak affinity "handclasp" complex that juxtaposes their respective 3(10) helices and ß7/ß8 loops. Interestingly, PRE also identified a set of transient complexes that could represent high-energy pre-equilibrium encounter species that form prior to the stereospecific handclasp complex. Targeted amino acid mutagenesis and stopped-flow measurements substantiate the functional relevance of a PRE-derived model, as mutation of interfacial side chains significantly slows the rate of transfer. IsdA and IsdC bind heme using NEAr Transporter (NEAT) domains that are conserved in many species of pathogenic Gram-positive bacteria. Heme transfer in these microbes may also occur through structurally similar transient stereospecific complexes.


Assuntos
Antígenos de Bactérias/metabolismo , Proteínas de Transporte/metabolismo , Parede Celular/metabolismo , Heme/metabolismo , Staphylococcus aureus/metabolismo , Antígenos de Bactérias/química , Transporte Biológico , Proteínas de Transporte/química , Parede Celular/química , Heme/química , Ressonância Magnética Nuclear Biomolecular , Estrutura Secundária de Proteína , Staphylococcus aureus/química
19.
Appl Environ Microbiol ; 77(14): 4849-58, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21622797

RESUMO

To cost-efficiently produce biofuels, new methods are needed to convert lignocellulosic biomass into fermentable sugars. One promising approach is to degrade biomass using cellulosomes, which are surface-displayed multicellulase-containing complexes present in cellulolytic Clostridium and Ruminococcus species. In this study we created cellulolytic strains of Bacillus subtilis that display one or more cellulase enzymes. Proteins containing the appropriate cell wall sorting signal are covalently anchored to the peptidoglycan by coexpressing them with the Bacillus anthracis sortase A (SrtA) transpeptidase. This approach was used to covalently attach the Cel8A endoglucanase from Clostridium thermocellum to the cell wall. In addition, a Cel8A-dockerin fusion protein was anchored on the surface of B. subtilis via noncovalent interactions with a cell wall-attached cohesin module. We also demonstrate that it is possible to assemble multienzyme complexes on the cell surface. A three-enzyme-containing minicellulosome was displayed on the cell surface; it consisted of a cell wall-attached scaffoldin protein noncovalently bound to three cellulase-dockerin fusion proteins that were produced in Escherichia coli. B. subtilis has a robust genetic system and is currently used in a wide range of industrial processes. Thus, grafting larger, more elaborate minicellulosomes onto the surface of B. subtilis may yield cellulolytic bacteria with increased potency that can be used to degrade biomass.


Assuntos
Bacillus subtilis/metabolismo , Parede Celular/metabolismo , Celulossomas/metabolismo , Lignina/metabolismo , Proteínas de Membrana/metabolismo , Aminoaciltransferases/biossíntese , Aminoaciltransferases/genética , Bacillus subtilis/genética , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/genética , Bioengenharia , Proteínas de Ciclo Celular , Celulase/metabolismo , Proteínas Cromossômicas não Histona , Clostridium thermocellum/enzimologia , Cisteína Endopeptidases/biossíntese , Cisteína Endopeptidases/genética , Escherichia coli/metabolismo , Immunoblotting , Proteínas de Membrana/genética , Microscopia de Fluorescência , Complexos Multienzimáticos/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Coesinas
20.
J Bacteriol ; 192(23): 6116-25, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20870765

RESUMO

Bacterial cytokinesis is achieved through the coordinated action of a multiprotein complex known as the divisome. The Escherichia coli divisome is comprised of at least 10 essential proteins whose individual functions are mostly unknown. Most divisomal proteins have multiple binding partners, making it difficult to pinpoint epitopes that mediate pairwise interactions between these proteins. We recently introduced an artificial septal targeting approach that allows the interaction between pairs of proteins to be studied in vivo without the complications introduced by other interacting proteins (C. Robichon, G. F. King, N. W. Goehring, and J. Beckwith, J. Bacteriol. 190:6048-6059, 2008). We have used this approach to perform a molecular dissection of the interaction between Bacillus subtilis DivIB and the divisomal transpeptidase PBP 2B, and we demonstrate that this interaction is mediated exclusively through the extracytoplasmic domains of these proteins. Artificial septal targeting in combination with mutagenesis experiments revealed that the C-terminal region of the ß domain of DivIB is critical for its interaction with PBP 2B. These findings are consistent with previously defined loss-of-function point mutations in DivIB as well as the recent demonstration that the ß domain of DivIB mediates its interaction with the FtsL-DivIC heterodimer. These new results have allowed us to construct a model of the DivIB/PBP 2B/FtsL/DivIC quaternary complex that strongly implicates DivIB, FtsL, and DivIC in modulating the transpeptidase activity of PBP 2B.


Assuntos
Bacillus subtilis/fisiologia , Proteínas de Bactérias/metabolismo , Divisão Celular , Proteínas de Membrana/metabolismo , Proteínas de Ligação às Penicilinas/metabolismo , Mapeamento de Interação de Proteínas , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Membrana/genética , Microscopia de Fluorescência , Modelos Biológicos , Modelos Químicos , Modelos Moleculares , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Transporte Proteico , Alinhamento de Sequência
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