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1.
PLoS One ; 19(4): e0300964, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38557973

RESUMO

Human immunoglobulin G (IgG) exists as four subclasses IgG1-4, each of which has two Fab subunits joined by two hinges to a Fc subunit. IgG4 has the shortest hinge with 12 residues. The Fc subunit has two glycan chains, but the importance of glycosylation is not fully understood in IgG4. Here, to evaluate the stability and structure of non-glycosylated IgG4, we performed a multidisciplinary structural study of glycosylated and deglycosylated human IgG4 A33 for comparison with our similar study of human IgG1 A33. After deglycosylation, IgG4 was found to be monomeric by analytical ultracentrifugation; its sedimentation coefficient of 6.52 S was reduced by 0.27 S in reflection of its lower mass. X-ray and neutron solution scattering showed that the overall Guinier radius of gyration RG and its cross-sectional values after deglycosylation were almost unchanged. In the P(r) distance distribution curves, the two M1 and M2 peaks that monitor the two most common distances within IgG4 were unchanged following deglycosylation. Further insight from Monte Carlo simulations for glycosylated and deglycosylated IgG4 came from 111,382 and 117,135 possible structures respectively. Their comparison to the X-ray and neutron scattering curves identified several hundred best-fit models for both forms of IgG4. Principal component analyses showed that glycosylated and deglycosylated IgG4 exhibited different conformations from each other. Within the constraint of unchanged RG and M1-M2 values, the glycosylated IgG4 models showed more restricted Fc conformations compared to deglycosylated IgG4, but no other changes. Kratky plots supported this interpretation of greater disorder upon deglycosylation, also observed in IgG1. Overall, these more variable Fc conformations may demonstrate a generalisable impact of deglycosylation on Fc structures, but with no large conformational changes in IgG4 unlike those seen in IgG1.


Assuntos
Fragmentos Fc das Imunoglobulinas , Imunoglobulina G , Humanos , Imunoglobulina G/química , Estudos Transversais , Modelos Moleculares , Fragmentos Fc das Imunoglobulinas/química
2.
PLoS Comput Biol ; 19(11): e1011248, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-38011290

RESUMO

We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison. These are performed using the SKMT algorithm, a novel method of smoothing the Cα backbone to achieve a minimal complexity curve representation of the manner in which the protein's secondary structure elements fold to form its tertiary structure. Its subsequent complexity is characterised using measures based on the writhe and crossing number quantities heavily utilised in DNA topology studies, and which have shown promising results when applied to proteins recently. The SKMT smoothing is used to derive empirical bounds on a protein's entanglement relative to its number of secondary structure elements. We show that large scale helical geometries dominantly account for the maximum growth in entanglement of protein monomers, and further that this large scale helical geometry is present in a large array of proteins, consistent across a number of different protein structure types and sequences. We also show how these bounds can be used to constrain the search space of protein structure prediction from small angle x-ray scattering experiments, a method highly suited to determining the likely structure of proteins in solution where crystal structure or machine learning based predictions often fail to match experimental data. Finally we develop a structural comparison metric based on the SKMT smoothing which is used in one specific case to demonstrate significant structural similarity between Rossmann fold and TIM Barrel proteins, a link which is potentially significant as attempts to engineer the latter have in the past produced the former. We provide the SWRITHE interactive python notebook to calculate these metrics.


Assuntos
Algoritmos , Proteínas , Proteínas/química , Estrutura Secundária de Proteína
3.
mBio ; 14(5): e0139123, 2023 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-37737607

RESUMO

IMPORTANCE: Genetically diverse paramyxoviruses are united in their presentation of a receptor-binding protein (RBP), which works in concert with the fusion protein to facilitate host-cell entry. The C-terminal head region of the paramyxoviral RBP, a primary determinant of host-cell tropism and inter-species transmission potential, forms structurally distinct classes dependent upon protein and glycan receptor specificity. Here, we reveal the architecture of the C-terminal head region of the RBPs from Nariva virus (NarV) and Mossman virus (MosV), two archetypal rodent-borne paramyxoviruses within the recently established genus Narmovirus, family Paramyxoviridae. Our analysis reveals that while narmoviruses retain the general architectural features associated with paramyxoviral RBPs, namely, a six-bladed ß-propeller fold, they lack the structural motifs associated with known receptor-mediated host-cell entry pathways. This investigation indicates that the RBPs of narmoviruses exhibit pathobiological features that are distinct from those of other paramyxoviruses.


Assuntos
Proteínas de Transporte , Paramyxovirinae , Proteínas de Transporte/metabolismo , Paramyxoviridae , Proteínas Virais de Fusão/metabolismo , Ligação Proteica , Internalização do Vírus
4.
Biol Methods Protoc ; 8(1): bpad001, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36915370

RESUMO

The current SARS-Covid-2 (SARS-CoV-2) pandemic has led to an acceleration of messenger ribonucleic acid (mRNA) vaccine technology. The development of production processes for these large mRNA molecules, especially self-amplifying mRNA (saRNA), has required concomitant development of analytical characterization techniques. Characterizing the purity, shape and structure of these biomolecules is key to their successful performance as drug products. This article describes the biophysical characterization of the Imperial College London Self-amplifying viral RNA vaccine (IMP-1) developed for SARS-CoV-2. A variety of analytical techniques have been used to characterize the IMP-1 RNA molecule. In this article, we use ultraviolet spectroscopy, dynamic light scattering, size-exclusion chromatography small-angle X-ray scattering and circular dichroism to determine key biophysical attributes of IMP-1. Each technique provides important information about the concentration, size, shape, structure and purity of the molecule.

5.
Cell Rep ; 39(11): 110959, 2022 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-35705051

RESUMO

MHC-E regulates NK cells by displaying MHC class Ia signal peptides (VL9) to NKG2A:CD94 receptors. MHC-E can also present sequence-diverse, lower-affinity, pathogen-derived peptides to T cell receptors (TCRs) on CD8+ T cells. To understand these affinity differences, human MHC-E (HLA-E)-VL9 versus pathogen-derived peptide structures are compared. Small-angle X-ray scatter (SAXS) measures biophysical parameters in solution, allowing comparison with crystal structures. For HLA-E-VL9, there is concordance between SAXS and crystal parameters. In contrast, HLA-E-bound pathogen-derived peptides produce larger SAXS dimensions that reduce to their crystallographic dimensions only when excess peptide is supplied. Further crystallographic analysis demonstrates three amino acids, exclusive to MHC-E, that not only position VL9 close to the α2 helix, but also allow non-VL9 peptide binding with re-configuration of a key TCR-interacting α2 region. Thus, non-VL9-bound peptides introduce an alternative peptide-binding motif and surface recognition landscape, providing a likely basis for VL9- and non-VL9-HLA-E immune discrimination.


Assuntos
Antígenos de Histocompatibilidade Classe I , Linfócitos T CD8-Positivos , Antígenos de Histocompatibilidade Classe I/metabolismo , Humanos , Subfamília C de Receptores Semelhantes a Lectina de Células NK/metabolismo , Peptídeos/metabolismo , Ligação Proteica , Conformação Proteica , Espalhamento a Baixo Ângulo , Difração de Raios X , Antígenos HLA-E
6.
J Biol Chem ; 297(3): 100995, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34302810

RESUMO

Human immunoglobulin G subclass 3 (IgG3) possesses a uniquely long hinge region that separates its Fab antigen-binding and Fc receptor-binding regions. Owing to this hinge length, the molecular structure of full-length IgG3 remains elusive, and the role of the two conserved Fc glycosylation sites are unknown. To address these issues, we subjected glycosylated and deglycosylated human myeloma IgG3 to multidisciplinary solution structure studies. Using analytical ultracentrifugation, the elongated structure of IgG3 was determined from the reduced sedimentation coefficients s020,w of 5.82 to 6.29 S for both glycosylated and deglycosylated IgG3. X-ray and neutron scattering showed that the Guinier RG values were 6.95 nm for glycosylated IgG3 and were unchanged after deglycosylation, again indicating an elongated structure. The distance distribution function P(r) showed a maximum length of 25 to 28 nm and three distinct maxima. The molecular structure of IgG3 was determined using atomistic modeling based on molecular dynamics simulations of the IgG3 hinge and Monte Carlo simulations to identify physically realistic arrangements of the Fab and Fc regions. This resulted in libraries containing 135,135 and 73,905 glycosylated and deglycosylated IgG3 structures, respectively. Comparisons with the X-ray and neutron scattering curves gave 100 best-fit models for each form of IgG3 that accounted for the experimental scattering curves. These models revealed the first molecular structures for full-length IgG3. The structures exhibited relatively restricted Fab and Fc conformations joined by an extended semirigid hinge, which explains the potent effector functions of IgG3 relative to the other subclasses IgG1, IgG2, and IgG4.


Assuntos
Fragmentos Fab das Imunoglobulinas/química , Imunoglobulina G/química , Mieloma Múltiplo/imunologia , Proteínas do Mieloma/química , Receptores Fc/química , Sequência de Aminoácidos , Cromatografia Líquida/métodos , Glicosilação , Humanos , Espectrometria de Massas/métodos , Simulação de Dinâmica Molecular , Nêutrons , Conformação Proteica , Espalhamento a Baixo Ângulo , Homologia de Sequência de Aminoácidos , Ultracentrifugação/métodos , Difração de Raios X
7.
Biophys J ; 120(9): 1814-1834, 2021 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-33675758

RESUMO

The human immunoglobulin G (IgG) class is the most prevalent antibody in serum, with the IgG1 subclass being the most abundant. IgG1 is composed of two Fab regions connected to a Fc region through a 15-residue hinge peptide. Two glycan chains are conserved in the Fc region in IgG; however, their importance for the structure of intact IgG1 has remained unclear. Here, we subjected glycosylated and deglycosylated monoclonal human IgG1 (designated as A33) to a comparative multidisciplinary structural study of both forms. After deglycosylation using peptide:N-glycosidase F, analytical ultracentrifugation showed that IgG1 remained monomeric and the sedimentation coefficients s020,w of IgG1 decreased from 6.45 S by 0.16-0.27 S. This change was attributed to the reduction in mass after glycan removal. X-ray and neutron scattering revealed changes in the Guinier structural parameters after deglycosylation. Although the radius of gyration (RG) was unchanged, the cross-sectional radius of gyration (RXS-1) increased by 0.1 nm, and the commonly occurring distance peak M2 of the distance distribution curve P(r) increased by 0.4 nm. These changes revealed that the Fab-Fc separation in IgG1 was perturbed after deglycosylation. To explain these changes, atomistic scattering modeling based on Monte Carlo simulations resulted in 123,284 and 119,191 trial structures for glycosylated and deglycosylated IgG1 respectively. From these, 100 x-ray and neutron best-fit models were determined. For these, principal component analyses identified five groups of structural conformations that were different for glycosylated and deglycosylated IgG1. The Fc region in glycosylated IgG1 showed a restricted range of conformations relative to the Fab regions, whereas the Fc region in deglycosylated IgG1 showed a broader conformational spectrum. These more variable Fc conformations account for the loss of binding to the Fcγ receptor in deglycosylated IgG1.


Assuntos
Imunoglobulina G , Receptores de IgG , Estudos Transversais , Humanos , Modelos Moleculares , Polissacarídeos , Conformação Proteica
8.
J Vis Exp ; (167)2021 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-33586708

RESUMO

BioSAXS is a popular technique used in molecular and structural biology to determine the solution structure, particle size and shape, surface-to-volume ratio and conformational changes of macromolecules and macromolecular complexes. A high quality SAXS dataset for structural modeling must be from monodisperse, homogeneous samples and this is often only reached by a combination of inline chromatography and immediate SAXS measurement. Most commonly, size-exclusion chromatography is used to separate samples and exclude contaminants and aggregations from the particle of interest allowing SAXS measurements to be made from a well-resolved chromatographic peak of a single protein species. Still, in some cases, even inline purification is not a guarantee of monodisperse samples, either because multiple components are too close to each other in size or changes in shape induced through binding alter perceived elution time. In these cases, it may be possible to deconvolute the SAXS data of a mixture to obtain the idealized SAXS curves of individual components. Here, we show how this is achieved and the practical analysis of SEC-SAXS data is performed on ideal and difficult samples. Specifically, we show the SEC-SAXS analysis of the vaccinia E9 DNA polymerase exonuclease minus mutant.


Assuntos
Algoritmos , Cromatografia em Gel , Análise de Dados , Espalhamento a Baixo Ângulo , Difração de Raios X , DNA/química , Proteínas/química
9.
J Synchrotron Radiat ; 28(Pt 1): 318-321, 2021 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-33399583

RESUMO

The design of a multipurpose sample cell holder for the high-throughput (HT) beamline B21 is presented. The device is compatible with the robot bioSAXS sample changer currently installed on BM29, ESRF, and P12 Petra IV synchrotrons. This work presents an approach that uses 3D-printing to make hardware alterations which can expand the versatility of HT beamlines at low cost.

10.
J Am Chem Soc ; 142(49): 20640-20650, 2020 12 09.
Artigo em Inglês | MEDLINE | ID: mdl-33252237

RESUMO

Controlling the assembly and disassembly of nanoscale protein cages for the capture and internalization of protein or non-proteinaceous components is fundamentally important to a diverse range of bionanotechnological applications. Here, we study the reversible, pressure-induced dissociation of a natural protein nanocage, E. coli bacterioferritin (Bfr), using synchrotron radiation small-angle X-ray scattering (SAXS) and circular dichroism (CD). We demonstrate that hydrostatic pressures of 450 MPa are sufficient to completely dissociate the Bfr 24-mer into protein dimers, and the reversibility and kinetics of the reassembly process can be controlled by selecting appropriate buffer conditions. We also demonstrate that the heme B prosthetic group present at the subunit dimer interface influences the stability and pressure lability of the cage, despite its location being discrete from the interdimer interface that is key to cage assembly. This indicates a major cage-stabilizing role for heme within this family of ferritins.


Assuntos
Proteínas de Bactérias/metabolismo , Grupo dos Citocromos b/metabolismo , Escherichia coli/metabolismo , Ferritinas/metabolismo , Proteínas de Bactérias/química , Dicroísmo Circular , Grupo dos Citocromos b/química , Dimerização , Ferritinas/química , Pressão Hidrostática , Cinética , Espalhamento a Baixo Ângulo , Termodinâmica , Difração de Raios X
11.
J Synchrotron Radiat ; 27(Pt 5): 1438-1446, 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32876621

RESUMO

B21 is a small-angle X-ray scattering (SAXS) beamline with a bending magnet source in the 3 GeV storage ring at the Diamond Light Source Ltd synchrotron in the UK. The beamline utilizes a double multi-layer monochromator and a toroidal focusing optic to deliver 2 × 1012 photons per second to a 34 × 40 µm (FWHM) focal spot at the in-vacuum Eiger 4M (Dectris) detector. A high-performance liquid chromatography system and a liquid-handling robot make it possible to load solution samples into a temperature-controlled in-vacuum sample cell with a high level of automation. Alternatively, a range of viscous or solid materials may be loaded manually using a range of custom sample cells. A default scattering vector range from 0.0026 to 0.34 Å-1 and low instrument background make B21 convenient for measuring a wide range of biological macromolecules. The beamline has run a full user programme since 2013.

12.
Nat Commun ; 11(1): 1837, 2020 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32296055

RESUMO

Guanosine 5'-monophosphate reductase (GMPR) is involved in the purine salvage pathway and is conserved throughout evolution. Nonetheless, the GMPR of Trypanosoma brucei (TbGMPR) includes a unique structure known as the cystathionine-ß-synthase (CBS) domain, though the role of this domain is not fully understood. Here, we show that guanine and adenine nucleotides exert positive and negative effects, respectively, on TbGMPR activity by binding allosterically to the CBS domain. The present structural analyses revealed that TbGMPR forms an octamer that shows a transition between relaxed and twisted conformations in the absence and presence of guanine nucleotides, respectively, whereas the TbGMPR octamer dissociates into two tetramers when ATP is available instead of guanine nucleotides. These findings demonstrate that the CBS domain plays a key role in the allosteric regulation of TbGMPR by facilitating the transition of its oligomeric state depending on ligand nucleotide availability.


Assuntos
Cistationina beta-Sintase/química , Cistationina beta-Sintase/metabolismo , GMP Redutase/química , GMP Redutase/metabolismo , Trypanosoma brucei brucei/enzimologia , Regulação Alostérica , Cristalografia por Raios X , Cinética , Domínios Proteicos , Multimerização Proteica , Estrutura Secundária de Proteína
13.
Langmuir ; 36(33): 9649-9657, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32202793

RESUMO

Bioproduction of poly(methyl methacrylate) is a fast growing global industry that is limited by cellular toxicity of monomeric methacrylate intermediates to the producer strains. Maintaining high methacrylate concentrations during biofermentation, required by economically viable technologies, challenges bacterial membrane stability and cellular viability. Studying the stability of model lipid membranes in the presence of methacrylates offers unique molecular insights into the mechanisms of methacrylate toxicity, as well as into the fundamental structural bases of membrane assembly. We investigate the structure and stability of model membranes in the presence of high levels of methacrylate esters using solid-state nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS). Wide-line 31P NMR spectroscopy shows that butyl methacrylate (BMA) can be incorporated into the lipid bilayer at concentrations as high as 75 mol % without significantly disrupting membrane integrity and that lipid acyl chain composition can influence membrane tolerance and ability to accommodate BMA. Using high resolution 13C magic angle spinning (MAS) NMR, we show that the presence of 75 mol % BMA lowers the lipid main transition temperature by over 12 degrees, which suggests that BMA intercalates between the lipid chains, causing uncoupling of collective lipid motions that are typically dominated by chain trans-gauche isomerization. Potential uncoupling of the bilayer leaflets to accommodate a separate BMA subphase was not supported by the SAXS experiments, which showed that membrane thickness remained unchanged even at 80% BMA. Reduced X-ray scattering contrast at the polar/apolar interface suggests BMA localization in that region between the lipid molecules.

14.
Nat Commun ; 11(1): 500, 2020 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-31980625

RESUMO

The CRISPR system provides adaptive immunity against mobile genetic elements in prokaryotes. On binding invading RNA species, Type III CRISPR systems generate cyclic oligoadenylate (cOA) signalling molecules, potentiating a powerful immune response by activating downstream effector proteins, leading to viral clearance, cell dormancy or death. Here we describe the structure and mechanism of a cOA-activated CRISPR defence DNA endonuclease, CRISPR ancillary nuclease 1 (Can1). Can1 has a unique monomeric structure with two CRISPR associated Rossman fold (CARF) domains and two DNA nuclease-like domains. The crystal structure of the enzyme has been captured in the activated state, with a cyclic tetra-adenylate (cA4) molecule bound at the core of the protein. cA4 binding reorganises the structure to license a metal-dependent DNA nuclease activity specific for nicking of supercoiled DNA. DNA nicking by Can1 is predicted to slow down viral replication kinetics by leading to the collapse of DNA replication forks.


Assuntos
Nucleotídeos de Adenina/farmacologia , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Endonucleases/química , Endonucleases/metabolismo , Oligorribonucleotídeos/farmacologia , Sítios de Ligação , DNA/metabolismo , Modelos Moleculares , Plasmídeos/genética , Domínios Proteicos , Homologia Estrutural de Proteína , Thermus thermophilus/genética
15.
ACS Appl Bio Mater ; 2(5): 2208-2218, 2019 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-31157325

RESUMO

The self-assembly and antimicrobial activity of two novel arginine-capped bola-amphiphile peptides, namely RA6R and RA9R (R, arginine; A, alanine) are investigated. RA6R does not self-assemble in water due to its high solubility, but RA9R self-assembles above a critical aggregation concentration into ordered nanofibers due to the high hydrophobicity of the A9block. The structure of the RA9R nanofibers is studied by cryogenic transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). Circular dichroism spectroscopy shows that both RA6R and RA9R adopt coil conformations in water at low concentration, but only RA9R adopts a ß-sheet conformation at high concentration. SAXS and differential scanning calorimetry are used to study RA6R and RA9R interactions with a mixed lipid membrane that models a bacterial cell wall, consisting of multilamellar 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol/1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine vesicles. Cytotoxicity studies show that RA6R is more cytocompatible than RA9R. RA6R has enhanced activity against the Gram-negative pathogen P. aeruginosa at a concentration where viability of mammalian cells is retained. RA9R has little antimicrobial activity, independently of concentration. Our results highlight the influence of the interplay between relative charge and hydrophobicity on the self-assembly, cytocompatibility, and bioactivity of peptide bola-amphiphiles.

16.
Org Biomol Chem ; 17(18): 4543-4553, 2019 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-30994696

RESUMO

We investigate the self-assembly of a palmitoylated (C16-chain at the N terminus) peptide fragment in comparison to the unlipidated peptide EELNRYY, a fragment of the gut hormone peptide PYY3-36. The lipopeptide C16-EELNRYY shows remarkable pH-dependent self-assembly above measured critical aggregation concentrations, forming fibrils at pH 7, but micelles at pH 10. The parent peptide does not show self-assembly behaviour. The lipopeptide forms hydrogels at sufficiently high concentration at pH 7, the dynamic mechanical properties of which were measured. We also show that the tyrosine functionality at the C terminus of EELNRYY can be used to enzymatically produce the pigment melanin. The enzyme tyrosinase oxidises tyrosine into 3,4-dihydroxyphenylalanine (DOPA), DOPA-quinone and further products, eventually forming eumelanin. This is a mechanism of photo-protection in the skin, for this reason controlling tyrosinase activity is a major target for skin care applications and EELNRYY has potential to be developed for such uses.


Assuntos
Lipopeptídeos/química , Melaninas/síntese química , Monofenol Mono-Oxigenase/química , Oligopeptídeos/química , Fragmentos de Peptídeos/química , Peptídeo YY/química , Sequência de Aminoácidos , Corantes Fluorescentes/química , Hidrogéis/química , Concentração de Íons de Hidrogênio , Lipopeptídeos/metabolismo , Micelas , Oligopeptídeos/metabolismo , Fragmentos de Peptídeos/metabolismo , Peptídeo YY/metabolismo , Conformação Proteica em Folha beta , Multimerização Proteica , Pirenos/química , Tirosina/química
17.
Sci Rep ; 9(1): 4933, 2019 03 20.
Artigo em Inglês | MEDLINE | ID: mdl-30894561

RESUMO

Group 21 and 5 allergens are homologous house dust mite proteins known as mid-tier allergens. To reveal the biological function of group 21 allergens and to understand better the allergenicity of the rDer f 21 allergen, we determined the 1.5 Å crystal structure of rDer f 21 allergen from Dermatophagoides farinae. The rDer f 21 protein consists of a three helical bundle, similar to available structures of group 21 and homologous group 5 allergens. The rDer f 21 dimer forms a hydrophobic binding pocket similar to the one in the Der p 5 allergen, which indicates that both of the homologous groups could share a similar function. By performing structure-guided mutagenesis, we mutated all 38 surface-exposed polar residues of the rDer f 21 allergen and carried out immuno-dot blot assays using 24 atopic sera. Six residues, K10, K26, K42, E43, K46, and K48, which are located in the region between the N-terminus and the loop 1 of rDer f 21 were identified as the major IgE epitopes of rDer f 21. Epitope mapping of all potential IgE epitopes on the surface of the rDer f 21 crystal structure revealed heterogeneity in the sIgE recognition of the allergen epitopes in atopic individuals. The higher the allergen-sIgE level of an individual, the higher the number of epitope residues that are found in the allergen. The results illustrate the clear correlation between the number of specific major epitope residues in an allergen and the sIgE level of the atopic population.


Assuntos
Antígenos de Dermatophagoides/imunologia , Proteínas de Artrópodes/imunologia , Dermatophagoides farinae/imunologia , Epitopos/ultraestrutura , Hipersensibilidade Imediata/imunologia , Imunoglobulina E/sangue , Animais , Antígenos de Dermatophagoides/metabolismo , Antígenos de Dermatophagoides/ultraestrutura , Proteínas de Artrópodes/metabolismo , Proteínas de Artrópodes/ultraestrutura , Cristalografia por Raios X , Mapeamento de Epitopos , Epitopos/imunologia , Epitopos/metabolismo , Humanos , Hipersensibilidade Imediata/sangue , Imunoglobulina E/imunologia
18.
J Biol Chem ; 293(33): 12862-12876, 2018 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-29880640

RESUMO

Mitochondrial tRNAs are transcribed as long polycistronic transcripts of precursor tRNAs and undergo posttranscriptional modifications such as endonucleolytic processing and methylation required for their correct structure and function. Among them, 5'-end processing and purine 9 N1-methylation of mitochondrial tRNA are catalyzed by two proteinaceous complexes with overlapping subunit composition. The Mg2+-dependent RNase P complex for 5'-end cleavage comprises the methyltransferase domain-containing protein tRNA methyltransferase 10C, mitochondrial RNase P subunit (TRMT10C/MRPP1), short-chain oxidoreductase hydroxysteroid 17ß-dehydrogenase 10 (HSD17B10/MRPP2), and metallonuclease KIAA0391/MRPP3. An MRPP1-MRPP2 subcomplex also catalyzes the formation of 1-methyladenosine/1-methylguanosine at position 9 using S-adenosyl-l-methionine as methyl donor. However, a lack of structural information has precluded insights into how these complexes methylate and process mitochondrial tRNA. Here, we used a combination of X-ray crystallography, interaction and activity assays, and small angle X-ray scattering (SAXS) to gain structural insight into the two tRNA modification complexes and their components. The MRPP1 N terminus is involved in tRNA binding and monomer-monomer self-interaction, whereas the C-terminal SPOUT fold contains key residues for S-adenosyl-l-methionine binding and N1-methylation. The entirety of MRPP1 interacts with MRPP2 to form the N1-methylation complex, whereas the MRPP1-MRPP2-MRPP3 RNase P complex only assembles in the presence of precursor tRNA. This study proposes low-resolution models of the MRPP1-MRPP2 and MRPP1-MRPP2-MRPP3 complexes that suggest the overall architecture, stoichiometry, and orientation of subunits and tRNA substrates.


Assuntos
3-Hidroxiacil-CoA Desidrogenases/química , Metiltransferases/química , Modelos Moleculares , Complexos Multienzimáticos/química , RNA Mitocondrial/química , RNA de Transferência/química , Ribonuclease P/química , 3-Hidroxiacil-CoA Desidrogenases/metabolismo , Cristalografia por Raios X , Humanos , Metiltransferases/metabolismo , Complexos Multienzimáticos/metabolismo , RNA Mitocondrial/metabolismo , RNA de Transferência/metabolismo , Ribonuclease P/metabolismo , Espalhamento a Baixo Ângulo
19.
Biomacromolecules ; 19(7): 2782-2794, 2018 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-29738229

RESUMO

The activity of antimicrobial peptides stems from their interaction with bacterial membranes, which are disrupted according to a number of proposed mechanisms. Here, we investigate the interaction of a model antimicrobial peptide that contains a single arginine residue with vesicles containing model lipid membranes. The surfactant-like peptide Ala6-Arg (A6R) is studied in the form where both termini are capped (CONH-A6R-NH2, capA6R) or uncapped (NH2-A6R-OH, A6R). Lipid membranes are selected to correspond to model anionic membranes (POPE/POPG) resembling those in bacteria or model zwitterionic membranes (POPC/DOPC) similar to those found in mammalian cells. Viable antimicrobial agents should show activity against anionic membranes but not zwitterionic membranes. We find, using small-angle X-ray scattering (SAXS) and cryogenic-TEM (transmission electron microscopy) that, uniquely, capA6R causes structuring of anionic membranes due to the incorporation of the peptide in the lipid bilayer with peptide ß-sheet conformation revealed by circular dichroism spectroscopy (CD). There is a preferential interaction of the peptide with POPG (which is the only anionic lipid in the systems studied) due to electrostatic interactions and bidentate hydrogen bonding between arginine guanidinium and lipid phosphate groups. At a certain composition, this peptide leads to the remarkable tubulation of zwitterionic phosphatidylcholine (PC) vesicles, which is ascribed to the interaction of the peptide with the outer lipid membrane, which occurs without penetration into the membrane. In contrast, peptide A6R has a minimal influence on the anionic lipid membranes (and no ß-sheet peptide structure is observed) but causes thinning (lamellar decorrelation) of zwitterionic membranes. We also investigated the cytotoxicity (to fibroblasts) and antimicrobial activity of these two peptides against model Gram positive and Gram negative bacteria. A strong selective antimicrobial activity against Gram positive Listeria monocytogenes, which is an important food-borne pathogen, is observed for capA6R. Peptide A6R is active against all three studied bacteria. The activity of the peptides against bacteria and mammalian cells is related to the specific interactions uncovered through our SAXS, cryo-TEM, and CD measurements. Our results highlight the exquisite sensitivity to the charge distribution in these designed peptides and its effect on the interaction with lipid membranes bearing different charges, and ultimately on antimicrobial activity.


Assuntos
Anti-Infecciosos/química , Peptídeos Catiônicos Antimicrobianos/química , Tensoativos/química , Anti-Infecciosos/farmacologia , Peptídeos Catiônicos Antimicrobianos/farmacologia , Arginina/química , Linhagem Celular , Escherichia coli/efeitos dos fármacos , Fibroblastos/efeitos dos fármacos , Humanos , Bicamadas Lipídicas/química , Listeria monocytogenes/efeitos dos fármacos , Fosfatidilcolinas/química , Staphylococcus aureus/efeitos dos fármacos , Tensoativos/farmacologia
20.
Biomacromolecules ; 19(1): 167-177, 2018 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-29195274

RESUMO

We investigate the self-assembly of two telechelic star polymer-peptide conjugates based on poly(ethylene oxide) (PEO) four-arm star polymers capped with oligotyrosine. The conjugates were prepared via N-carboxy anhydride-mediated ring-opening polymerization from PEO star polymer macroinitiators. Self-assembly occurs above a critical aggregation concentration determined via fluorescence probe assays. Peptide conformation was examined using circular dichroism spectroscopy. The structure of self-assembled aggregates was probed using small-angle X-ray scattering and cryogenic transmission electron microscopy. In contrast to previous studies on linear telechelic PEO-oligotyrosine conjugates that show self-assembly into ß-sheet fibrils, the star architecture suppresses fibril formation and micelles are generally observed instead, a small population of fibrils only being observed upon pH adjustment. Hydrogelation is also suppressed by the polymer star architecture. These peptide-functionalized star polymer solutions are cytocompatible at sufficiently low concentration. These systems present tyrosine at high density and may be useful in the development of future enzyme or pH-responsive biomaterials.


Assuntos
Polietilenoglicóis/química , Tirosina/química , Água/química , Linhagem Celular , Cromatografia em Gel , Dicroísmo Circular , Humanos , Hidrogéis/química , Espectroscopia de Ressonância Magnética , Microscopia Eletrônica de Transmissão , Peptídeos/química , Polimerização , Espalhamento a Baixo Ângulo , Soluções , Espectroscopia de Infravermelho com Transformada de Fourier , Difração de Raios X
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