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1.
PLoS Pathog ; 18(9): e1010760, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-36048802

RESUMO

The impact of artificial intelligence (AI) in understanding biological processes is potentially immense. Structural elucidation of mycobacterial PE_PGRS is sustenance to unveil the role of these enigmatic proteins. We propose a PGRS "sailing" model as a smart tool to diffuse along the mycomembrane, to expose structural motifs for host interactions, and/or to ship functional protein modules at their C-terminus.


Assuntos
Antígenos de Bactérias , Mycobacterium tuberculosis , Antígenos de Bactérias/metabolismo , Inteligência Artificial , Proteínas de Bactérias/metabolismo , Parede Celular/metabolismo , Mycobacterium tuberculosis/metabolismo
2.
Int J Mol Sci ; 24(10)2023 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-37239905

RESUMO

CD59 is an abundant immuno-regulatory human protein that protects cells from damage by inhibiting the complement system. CD59 inhibits the assembly of the Membrane Attack Complex (MAC), the bactericidal pore-forming toxin of the innate immune system. In addition, several pathogenic viruses, including HIV-1, escape complement-mediated virolysis by incorporating this complement inhibitor in their own viral envelope. This makes human pathogenic viruses, such as HIV-1, not neutralised by the complement in human fluids. CD59 is also overexpressed in several cancer cells to resist the complement attack. Consistent with its importance as a therapeutical target, CD59-targeting antibodies have been proven to be successful in hindering HIV-1 growth and counteracting the effect of complement inhibition by specific cancer cells. In this work, we make use of bioinformatics and computational tools to identify CD59 interactions with blocking antibodies and to describe molecular details of the paratope-epitope interface. Based on this information, we design and produce paratope-mimicking bicyclic peptides able to target CD59. Our results set the basis for the development of antibody-mimicking small molecules targeting CD59 with potential therapeutic interest as complement activators.


Assuntos
Proteínas do Sistema Complemento , HIV-1 , Humanos , Sítios de Ligação de Anticorpos , Proteínas do Sistema Complemento/metabolismo , Antígenos CD59/metabolismo , Complexo de Ataque à Membrana do Sistema Complemento/metabolismo , Inativadores do Complemento , HIV-1/fisiologia
3.
Int J Mol Sci ; 23(10)2022 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-35628409

RESUMO

Coronaviruses, including SARS-CoV-2 (the etiological agent of the current COVID-19 pandemic), rely on the surface spike glycoprotein to access the host cells, mainly through the interaction of their receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with the binding of the SARS-CoV-2 spike protein to ACE2 have great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 spike protein and the host ACE2 receptor, we engineered a set of soluble and stable spike interactors, here denoted as S-plugs. Starting from the prototype S-plug, we adopted a computational approach by combining stability prediction, associated to single-point mutations, with molecular dynamics to enhance both S-plug thermostability and binding affinity to the spike protein. The best developed molecule, S-plug3, possesses a highly stable α-helical con-formation (with melting temperature Tm of 54 °C) and can interact with the spike RBD and S1 domains with similar low nanomolar affinities. Importantly, S-plug3 exposes the spike RBD to almost the same interface as the human ACE2 receptor, aimed at the recognition of all ACE2-accessing coronaviruses. Consistently, S-plug3 preserves a low nanomolar dissociation constant with the delta B.1.617.2 variant of SARS-CoV-2 spike protein (KD = 29.2 ± 0.6 nM). Taken together, we provide valid starting data for the development of therapeutical and diagnostic tools against coronaviruses accessing through ACE2.


Assuntos
Enzima de Conversão de Angiotensina 2 , COVID-19 , Enzima de Conversão de Angiotensina 2/genética , Humanos , Glicoproteínas de Membrana/metabolismo , Pandemias , Peptidil Dipeptidase A/metabolismo , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Proteínas do Envelope Viral/química
4.
Mol Microbiol ; 112(3): 800-819, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31145503

RESUMO

The human-adapted pathogen group A Streptococcus (GAS) utilizes wounds as portals of entry into host tissue, wherein surface adhesins interact with the extracellular matrix, enabling bacterial colonization. The streptococcal collagen-like protein 1 (Scl1) is a major adhesin of GAS that selectively binds to two fibronectin type III (FnIII) repeats within cellular fibronectin, specifically the alternatively spliced extra domains A and B, and the FnIII repeats within tenascin-C. Binding to FnIII repeats was mediated through conserved structural determinants present within the Scl1 globular domain and facilitated GAS adherence and biofilm formation. Isoforms of cellular fibronectin that contain extra domains A and B, as well as tenascin-C, are present for several days in the wound extracellular matrix. Scl1-FnIII binding is therefore an example of GAS adaptation to the host's wound environment. Similarly, cellular fibronectin isoforms and tenascin-C are present in the tumor microenvironment. Consistent with this, FnIII repeats mediate GAS attachment to and enhancement of biofilm formation on matrices deposited by cancer-associated fibroblasts and osteosarcoma cells. These data collectively support the premise for utilization of the Scl1-FnIII interaction as a novel method of anti-neoplastic targeting in the tumor microenvironment.


Assuntos
Proteínas de Bactérias/metabolismo , Colágeno/metabolismo , Fibronectinas/metabolismo , Neoplasias/terapia , Streptococcus pyogenes/fisiologia , Adesinas Bacterianas/química , Adesinas Bacterianas/genética , Adesinas Bacterianas/metabolismo , Aderência Bacteriana , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Biofilmes , Linhagem Celular Tumoral , Colágeno/química , Colágeno/genética , Matriz Extracelular/metabolismo , Fibroblastos/metabolismo , Fibroblastos/microbiologia , Fibronectinas/química , Fibronectinas/genética , Humanos , Neoplasias/metabolismo , Ligação Proteica , Domínios Proteicos , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Streptococcus pyogenes/química , Streptococcus pyogenes/genética
5.
J Biol Chem ; 293(20): 7796-7810, 2018 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-29615492

RESUMO

Keratinized epidermis constitutes a powerful barrier of the mucosa and skin, effectively preventing bacterial invasion, unless it is wounded and no longer protective. Wound healing involves deposition of distinct extracellular matrix (ECM) proteins enriched in cellular fibronectin (cFn) isoforms containing extra domain A (EDA). The streptococcal collagen-like protein 1 (Scl1) is a surface adhesin of group A Streptococcus (GAS), which contains an N-terminal variable (V) domain and a C-terminally located collagen-like domain. During wound infection, Scl1 selectively binds EDA/cFn isoforms and laminin, as well as low-density lipoprotein (LDL), through its V domain. The trimeric V domain has a six-helical bundle fold composed of three pairs of anti-parallel α-helices interconnected by hypervariable loops, but the roles of these structures in EDA/cFn binding are unclear. Here, using recombinant Scl (rScl) constructs to investigate structure-function determinants of the Scl1-EDA/cFn interaction, we found that full-length rScl1, containing both the globular V and the collagen domains, is necessary for EDA/cFn binding. We established that the surface-exposed loops, interconnecting conserved α-helices, guide recognition and binding of Scl1-V to EDA and binding to laminin and LDL. Moreover, electrostatic surface potential models of the Scl1-V domains pointed to a conserved, negatively charged pocket, surrounded by positively charged and neutral regions, as a determining factor for the binding. In light of these findings, we propose an updated model of EDA/cFn recognition by the Scl1 adhesin from GAS, representing a significant step in understanding the Scl1-ECM interactions within the wound microenvironment that underlie GAS pathogenesis.


Assuntos
Proteínas de Bactérias/química , Colágeno/química , Matriz Extracelular/química , Fibronectinas/química , Laminina/química , Lipoproteínas LDL/química , Streptococcus pyogenes/química , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Clonagem Molecular , Colágeno/genética , Colágeno/metabolismo , Cristalografia por Raios X , Escherichia coli/genética , Escherichia coli/metabolismo , Matriz Extracelular/metabolismo , Fibronectinas/genética , Fibronectinas/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Humanos , Cinética , Laminina/genética , Laminina/metabolismo , Lipoproteínas LDL/genética , Lipoproteínas LDL/metabolismo , Modelos Moleculares , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Eletricidade Estática , Streptococcus pyogenes/genética , Streptococcus pyogenes/metabolismo , Cicatrização/genética
6.
Biochem J ; 475(19): 3123-3140, 2018 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-30315001

RESUMO

The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.


Assuntos
Colágeno/metabolismo , Mycobacterium tuberculosis/metabolismo , Proteólise , Animais , Colágeno/química , Matriz Extracelular/química , Matriz Extracelular/metabolismo , Humanos , Metaloproteinases da Matriz/química , Metaloproteinases da Matriz/metabolismo , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína
7.
Mol Microbiol ; 103(6): 919-930, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27997716

RESUMO

The collagen domain, which is defined by the presence of the Gly-X-Y triplet repeats, is amongst the most versatile and widespread known structures found in proteins from organisms representing all three domains of life. The streptococcal collagen-like (Scl) proteins are widely present in pathogenic streptococci, including Streptococcus pyogenes, S. agalactiae, S. pneumoniae, and S. equi. Experiments and bioinformatic analyses support the hypothesis that all Scl proteins are homotrimeric and cell wall-anchored. These proteins contain the rod-shaped collagenous domain proximal to cell surface, as well as a variety of outermost non-collagenous domains that generally lack predicted functions but can be grouped into one of six clusters based on sequence similarity. The well-characterized Scl1 proteins of S. pyogenes show a dichotomous switch in ligand binding between human tissue and blood environments. In tissue, Scl1 adhesin specifically recognizes the wound microenvironment, promotes adhesion and biofilm formation, decreases bacterial killing by neutrophil extracellular traps, and modulates S. pyogenes virulence. In blood, ligands include components of complement and coagulation-fibrinolytic systems, as well as plasma lipoproteins. In all, the Scl proteins signify a large family of structurally related surface proteins, which contribute to the ability of streptococci to colonize and cause diseases in humans and animals.


Assuntos
Adesinas Bacterianas/metabolismo , Aderência Bacteriana/fisiologia , Proteínas de Bactérias/metabolismo , Colágeno/metabolismo , Streptococcus agalactiae/patogenicidade , Streptococcus pneumoniae/patogenicidade , Streptococcus pyogenes/patogenicidade , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/genética , Biofilmes/crescimento & desenvolvimento , Colágeno/genética , Humanos , Ligação Proteica , Domínios Proteicos/genética , Fatores de Virulência/genética
8.
Biochim Biophys Acta Proteins Proteom ; 1866(9): 952-962, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29860047

RESUMO

Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.


Assuntos
Arginina/química , Proteínas de Bactérias/química , Thermotoga maritima/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/fisiologia , Técnicas Biossensoriais , Clonagem Molecular , Ligantes , Modelos Moleculares , Ligação Proteica , Domínios Proteicos
9.
Chemistry ; 24(11): 2533-2546, 2018 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-28925518

RESUMO

The cell wall envelope of mycobacteria is structurally distinct from that of both Gram-positive and Gram-negative bacteria. In Mycobacterium tuberculosis, this cell wall has unique structural features and plays a crucial role in drug resistance and macrophage survival under stress conditions. Peptidoglycan is the major constituent of this cell wall, with an important structural role, giving structural strength, and counteracting the osmotic pressure of the cytoplasm. Synthesis of this complex polymer takes place in three stages that occur at three different locations in the cell, from the cytoplasm to the external side of the cell membrane, where polymerization occurs. A fine balance of peptidoglycan synthesis and degradation is responsible for a plethora of molecular mechanisms which are key to the pathogenicity of M. tuberculosis. Enlargement of mycobacterial cells can occur through the synthesis of new peptidoglycan, autolysis of old peptidoglycan, or a combination of both processes. Here, we discuss the chemical aspects of peptidoglycan synthesis and degradation, in relation to metabolic stages of M. tuberculosis. Going from inside the mycobacterial cytoplasm to outside its membrane, we describe the assembly line of peptidoglycan synthesis and polymerization, and continue with its depolymerization events and their consequences on mycobacterial life and resuscitation from dormancy.


Assuntos
Parede Celular/metabolismo , Mycobacterium tuberculosis/metabolismo , Peptidoglicano/química , Alquil e Aril Transferases/metabolismo , Citoplasma/metabolismo , Peptidoglicano/metabolismo , Estrutura Terciária de Proteína
10.
Cell Microbiol ; 19(5)2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-27886433

RESUMO

The Burkholderia cepacia complex (Bcc) is a group of Gram-negative opportunistic pathogens causing infections in people with cystic fibrosis (CF). Bcc is highly antibiotic resistant, making conventional antibiotic treatment problematic. The identification of novel targets for anti-virulence therapies should improve therapeutic options for infected CF patients. We previously identified that the peptidoglycan-associated lipoprotein (Pal) was immunogenic in Bcc infected CF patients; however, its role in Bcc pathogenesis is unknown. The virulence of a pal deletion mutant (Δpal) in Galleria mellonella was 88-fold reduced (p < .001) compared to wild type. The lipopolysaccharide profiles of wild type and Δpal were identical, indicating no involvement of Pal in O-antigen transport. However, Δpal was more susceptible to polymyxin B. Structural elucidation by X-ray crystallography and calorimetry demonstrated that Pal binds peptidoglycan fragments. Δpal showed a 1.5-fold reduced stimulation of IL-8 in CF epithelial cells relative to wild type (p < .001), demonstrating that Pal is a significant driver of inflammation. The Δpal mutant had reduced binding to CFBE41o- cells, but adhesion of Pal-expressing recombinant E. coli to CFBE41o- cells was enhanced compared to wild-type E. coli (p < .0001), confirming that Pal plays a direct role in host cell attachment. Overall, Bcc Pal mediates host cell attachment and stimulation of cytokine secretion, contributing to Bcc pathogenesis.


Assuntos
Proteínas de Bactérias/química , Infecções por Burkholderia/imunologia , Burkholderia cenocepacia/imunologia , Células Epiteliais/fisiologia , Lipoproteínas/química , Animais , Aderência Bacteriana , Proteínas de Bactérias/fisiologia , Sítios de Ligação , Infecções por Burkholderia/microbiologia , Burkholderia cenocepacia/patogenicidade , Adesão Celular , Células Cultivadas , Cristalografia por Raios X , Fibrose Cística/microbiologia , Citocinas/metabolismo , Farmacorresistência Bacteriana , Células Epiteliais/microbiologia , Escherichia coli , Humanos , Larva/microbiologia , Lipopolissacarídeos/fisiologia , Lipoproteínas/fisiologia , Modelos Moleculares , Mariposas , Peptidoglicano/química , Polimixinas/farmacologia , Ligação Proteica , Domínios Proteicos
11.
Amino Acids ; 50(10): 1441-1450, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30032416

RESUMO

PASTA domains are small modules expressed in bacteria and found in one or multiple copies at the C-terminal end of several penicillin binding proteins (PBPs) and Ser/Thr protein kinases (STPKs) and represent potential targets for a new class of antibiotics. PASTA domains are currently annotated as sensor domains, as they are thought to activate their cognate proteins in response to binding to opportune ligands. However, recent studies have shown that PASTA domains linked to proteins of different classes, STPKs or PBPs, do not share the same binding abilities. Despite this, there is currently no way to distinguish between PASTA domains from the two classes, since all of them share the same fold, independent of the class they belong to. To identify a predictive tool of class identification, we here analyse a pool of parameters, including amino acid compositions and total charges of PASTA domains either linked to PBPs or to STPKs. We screened sequences from Actinobacteria, Firmicutes and Bacteroidetes. The first two phyla include some of the most dangerous micro-organisms for human health such as Mycobacterium tuberculosis and Staphylococcus aureus. Based on this analysis, our study proposes a predictive method to assign PASTA domains with unknown origin to their corresponding enzyme class, based solely on sequence information.


Assuntos
Bactérias/classificação , Proteínas de Bactérias/química , Bactérias/química , Bactérias/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Ligação às Penicilinas/química , Proteínas de Ligação às Penicilinas/genética , Proteínas de Ligação às Penicilinas/metabolismo , Filogenia , Domínios Proteicos , Proteínas Serina-Treonina Quinases/química , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo
12.
Biochim Biophys Acta ; 1860(2): 445-51, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26549874

RESUMO

BACKGROUND: RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D). METHODS: The structural features of RpfB3D have been investigated combining x-ray crystallography and biophysical studies. RESULTS AND CONCLUSIONS: The crystal structure of RpfB3D provides the first structural characterization of a DUF348 domain and revealed an unexpected structural relationship with ubiquitin. The crystal structure also provides specific structural features of these domains explaining their frequent association with G5 domains. GENERAL SIGNIFICANCE: Results provided novel insights into the mechanism of peptidoglycan degradation necessary to the resuscitation of M. tuberculosis. Features of the DUF348 domain add structural data to a large set of proteins embedding this domain. Based on its structural similarity to ubiquitin and frequent association to the G5 domain, we propose to name this domain as G5-linked-Ubiquitin-like domain, UBLG5.


Assuntos
Proteínas de Bactérias/química , Mycobacterium tuberculosis/química , Ubiquitina/química , Cristalização , Estrutura Terciária de Proteína , Soluções
13.
J Virol ; 90(7): 3745-59, 2016 Jan 27.
Artigo em Inglês | MEDLINE | ID: mdl-26819303

RESUMO

UNLABELLED: The hepatitis C virus (HCV) E2 envelope glycoprotein is crucial for virus entry into hepatocytes. A conserved region of E2 encompassing amino acids 412 to 423 (epitope I) and containing Trp420, a residue critical for virus entry, is recognized by several broadly neutralizing antibodies. Peptides embodying this epitope I sequence adopt a ß-hairpin conformation when bound to neutralizing monoclonal antibodies (MAbs) AP33 and HCV1. We therefore generated new mouse MAbs that were able to bind to a cyclic peptide containing E2 residues 412 to 422 (C-epitope I) but not to the linear counterpart. These MAbs bound to purified E2 with affinities of about 50 nM, but they were unable to neutralize virus infection. Structural analysis of the complex between C-epitope I and one of our MAbs (C2) showed that the Trp420 side chain is largely buried in the combining site and that the Asn417 side chain, which is glycosylated in E2 and solvent exposed in other complexes, is slightly buried upon C2 binding. Also, the orientation of the cyclic peptide in the antibody-combining site is rotated by 180° compared to the orientations of the other complexes. All these structural features, however, do not explain the lack of neutralization activity. This is instead ascribed to the high degree of selectivity of the new MAbs for the cyclic epitope and to their inability to interact with the epitope in more flexible and extended conformations, which recent data suggest play a role in the mechanisms of neutralization escape. IMPORTANCE: Hepatitis C virus (HCV) remains a major health care burden, affecting almost 3% of the global population. The conserved epitope comprising residues 412 to 423 of the viral E2 glycoprotein is a valid vaccine candidate because antibodies recognizing this region exhibit potent neutralizing activity. This epitope adopts a ß-hairpin conformation when bound to neutralizing MAbs. We explored the potential of cyclic peptides mimicking this structure to elicit anti-HCV antibodies. MAbs that specifically recognize a cyclic variant of the epitope bind to soluble E2 with a lower affinity than other blocking antibodies and do not neutralize virus. The structure of the complex between one such MAb and the cyclic epitope, together with new structural data showing the linear peptide bound to neutralizing MAbs in extended conformations, suggests that the epitope displays a conformational flexibility that contributes to neutralization escape. Such features can be of major importance for the design of epitope-based anti-HCV vaccines.


Assuntos
Anticorpos Monoclonais/imunologia , Anticorpos Monoclonais/isolamento & purificação , Epitopos de Linfócito B/imunologia , Hepacivirus/imunologia , Anticorpos Anti-Hepatite C/imunologia , Anticorpos Anti-Hepatite C/isolamento & purificação , Proteínas do Envelope Viral/imunologia , Animais , Anticorpos Monoclonais/química , Anticorpos Anti-Hepatite C/química , Camundongos Endogâmicos BALB C , Modelos Moleculares , Testes de Neutralização , Ligação Proteica , Conformação Proteica , Proteínas do Envelope Viral/química
14.
Proc Natl Acad Sci U S A ; 111(3): E404-13, 2014 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-24395781

RESUMO

Perception of microbe-associated molecular patterns (MAMPs) through pattern recognition receptors (PRRs) triggers various defense responses in plants. This MAMP-triggered immunity plays a major role in the plant resistance against various pathogens. To clarify the molecular basis of the specific recognition of chitin oligosaccharides by the rice PRR, CEBiP (chitin-elicitor binding protein), as well as the formation and activation of the receptor complex, biochemical, NMR spectroscopic, and computational studies were performed. Deletion and domain-swapping experiments showed that the central lysine motif in the ectodomain of CEBiP is essential for the binding of chitin oligosaccharides. Epitope mapping by NMR spectroscopy indicated the preferential binding of longer-chain chitin oligosaccharides, such as heptamer-octamer, to CEBiP, and also the importance of N-acetyl groups for the binding. Molecular modeling/docking studies clarified the molecular interaction between CEBiP and chitin oligosaccharides and indicated the importance of Ile122 in the central lysine motif region for ligand binding, a notion supported by site-directed mutagenesis. Based on these results, it was indicated that two CEBiP molecules simultaneously bind to one chitin oligosaccharide from the opposite side, resulting in the dimerization of CEBiP. The model was further supported by the observations that the addition of (GlcNAc)8 induced dimerization of the ectodomain of CEBiP in vitro, and the dimerization and (GlcNAc)8-induced reactive oxygen generation were also inhibited by a unique oligosaccharide, (GlcNß1,4GlcNAc)4, which is supposed to have N-acetyl groups only on one side of the molecule. Based on these observations, we proposed a hypothetical model for the ligand-induced activation of a receptor complex, involving both CEBiP and Oryza sativa chitin-elicitor receptor kinase-1.


Assuntos
Quitina/química , Oryza/imunologia , Imunidade Vegetal , Proteínas de Plantas/metabolismo , Receptores de Superfície Celular/metabolismo , Transdução de Sinais , Motivos de Aminoácidos , Sequência de Aminoácidos , Sítios de Ligação , Epitopos/imunologia , Ligantes , Lisina/química , Espectroscopia de Ressonância Magnética , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Oligossacarídeos/química , Oryza/metabolismo , Multimerização Proteica , Estrutura Terciária de Proteína , Espécies Reativas de Oxigênio/metabolismo , Homologia de Sequência de Aminoácidos , Nicotiana
15.
Biochim Biophys Acta ; 1854(5): 402-9, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25668224

RESUMO

Eukaryotic-type Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases (STPK) are widespread in gram positive bacteria, where they regulate several cellular functions. STPKs belong to the protein kinase family named as one-component signal transduction systems, which combine both sensing and regulating properties. Thermodynamic investigations of sensing extra-cellular portions of two important Ser-Thr kinases, PrkC, from Staphylococcus aureus and Bacillus subtilis were conducted by differential scanning calorimetry (DSC) and circular dichroism (CD) melting measurements, coupled with modelling studies. The study of thermodynamic properties of the two domains is challenging since they share a modular domain organization. Consistently, DSC and CD data show that they present similar thermodynamic behaviours and that folding/unfolding transitions do not fit a two-state folding model. However, the thermal unfolding of the two proteins is differentially sensitive to pH. In particular, their unfolding is characteristic of modular structures at the neutral pH, with independent contributions of individual domains to folding. Differently, a cooperative unfolding is evidenced at acidic pH for the B. subtilis member, suggesting that a significant interaction between domains becomes valuable.


Assuntos
Proteína Quinase C/química , Estabilidade Proteica , Termodinâmica , Sequência de Aminoácidos , Bacillus subtilis/enzimologia , Varredura Diferencial de Calorimetria , Dicroísmo Circular , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Desdobramento de Proteína , Homologia de Sequência de Aminoácidos , Staphylococcus aureus/enzimologia
16.
J Biol Chem ; 289(8): 5122-33, 2014 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-24356966

RESUMO

The arsenal of virulence factors deployed by streptococci includes streptococcal collagen-like (Scl) proteins. These proteins, which are characterized by a globular domain and a collagen-like domain, play key roles in host adhesion, host immune defense evasion, and biofilm formation. In this work, we demonstrate that the Scl2.3 protein is expressed on the surface of invasive M3-type strain MGAS315 of Streptococcus pyogenes. We report the crystal structure of Scl2.3 globular domain, the first of any Scl. This structure shows a novel fold among collagen trimerization domains of either bacterial or human origin. Despite there being low sequence identity, we observed that Scl2.3 globular domain structurally resembles the gp41 subunit of the envelope glycoprotein from human immunodeficiency virus type 1, an essential subunit for viral fusion to human T cells. We combined crystallographic data with modeling and molecular dynamics techniques to gather information on the entire lollipop-like Scl2.3 structure. Molecular dynamics data evidence a high flexibility of Scl2.3 with remarkable interdomain motions that are likely instrumental to the protein biological function in mediating adhesive or immune-modulatory functions in host-pathogen interactions. Altogether, our results provide molecular tools for the understanding of Scl-mediated streptococcal pathogenesis and important structural insights for the future design of small molecular inhibitors of streptococcal invasion.


Assuntos
Proteínas de Bactérias/química , Colágeno/química , Proteína gp41 do Envelope de HIV/química , Fatores Imunológicos/química , Streptococcus pyogenes/metabolismo , Homologia Estrutural de Proteína , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Colágeno/metabolismo , Cristalografia por Raios X , Humanos , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Alinhamento de Sequência , Soluções
17.
Chemistry ; 21(2): 500-19, 2015 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-25353096

RESUMO

In many Gram-negative bacteria, lipopolysaccharide (LPS) and its lipid A moiety are pivotal for bacterial survival. Depending on its structure, lipid A carries the toxic properties of the LPS and acts as a potent elicitor of the host innate immune system via the Toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD-2) receptor complex. It often causes a wide variety of biological effects ranging from a remarkable enhancement of the resistance to the infection to an uncontrolled and massive immune response resulting in sepsis and septic shock. Since the bioactivity of lipid A is strongly influenced by its primary structure, a broad range of chemical syntheses of lipid A derivatives have made an enormous contribution to the characterization of lipid A bioactivity, providing novel pharmacological targets for the development of new biomedical therapies. Here, we describe and discuss the chemical aspects regarding lipid A and its role in innate immunity, from the (bio)synthesis, isolation and characterization to the molecular recognition at the atomic level.


Assuntos
Bactérias Gram-Negativas/química , Bactérias Gram-Negativas/imunologia , Infecções por Bactérias Gram-Negativas/imunologia , Imunidade Inata , Lipídeo A/química , Lipídeo A/imunologia , Animais , Infecções por Bactérias Gram-Negativas/microbiologia , Humanos , Lipídeo A/análogos & derivados , Antígeno 96 de Linfócito/imunologia , Modelos Moleculares , Receptor 4 Toll-Like/imunologia
18.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 9): 2295-300, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25195744

RESUMO

RipA is a key cysteine protease of Mycobacterium tuberculosis as it is responsible for bacterial daughter-cell separation. Although it is an important target for antimicrobial development, its mechanism of action and its interaction pattern with its substrate are hitherto unknown. By combining crystallographic and mutational studies with functional assays and molecular modelling, it is shown that the catalytic activity of the enzyme relies on a Cys-His-Glu triad and the impact of the mutation of each residue of the triad on the structure and function of RipA is analysed. Unexpectedly, the crystallographic analyses reveal that mutation of the glutamic acid to alanine results in inversion of the configuration of the catalytic cysteine. The consequent burial of the catalytic cysteine side chain explains the enzyme inactivation upon mutation. These data point to a novel role of the acidic residue often present in the triad of cysteine proteases as a supervisor of cysteine configuration through preservation of the local structural integrity.


Assuntos
Proteínas de Bactérias/genética , Divisão Celular , Citosina/metabolismo , Mutação , Mycobacterium tuberculosis/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sequência de Bases , Biocatálise , Dicroísmo Circular , Clonagem Molecular , Primers do DNA , Modelos Moleculares , Mycobacterium tuberculosis/citologia , Reação em Cadeia da Polimerase , Conformação Proteica
19.
Biopolymers ; 101(7): 712-9, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24281824

RESUMO

PonA2 is one of the two class A penicillin binding proteins of Mycobacterium tuberculosis, the etiologic agent of tuberculosis. It plays a complex role in mycobacterial physiology and is spotted as a promising target for inhibitors. PonA2 is involved in adaptation of M. tuberculosis to dormancy, an ability which has been attributed to the presence in its sequence of a C-terminal PASTA domain. Since PASTA modules are typically considered as ß-lactam antibiotic binding domains, we determined the solution structure of the PASTA domain from PonA2 and analyzed its binding properties versus a plethora of potential binders, including the ß-lactam antibiotics, two typical muropeptide mimics, and polymeric peptidoglycan. We show that, despite a high structural similarity with other PASTA domains, the PASTA domain of PonA2 displays different binding properties, as it is not able to bind muropeptides, or ß-lactams, or polymeric peptidoglycan. These results indicate that the role of PASTA domains cannot be generalized, as their specific binding properties strongly depend on surface residues, which are widely variable.


Assuntos
Proteínas de Bactérias/química , Mycobacterium tuberculosis/metabolismo , Proteínas de Ligação às Penicilinas/química , Estrutura Terciária de Proteína , Proteínas de Bactérias/metabolismo , Calorimetria/métodos , Dicroísmo Circular , Espectroscopia de Ressonância Magnética/métodos , Modelos Moleculares , Proteínas de Ligação às Penicilinas/metabolismo , Peptidoglicano/química , Peptidoglicano/metabolismo , Ligação Proteica , Desdobramento de Proteína , Temperatura , beta-Lactamas/química , beta-Lactamas/metabolismo
20.
Biomolecules ; 14(4)2024 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-38672487

RESUMO

Tuberculosis (TB) is the leading global cause of death f rom an infectious bacterial agent. Therefore, limiting its epidemic spread is a pressing global health priority. The chaperone-like protein HtpG of M. tuberculosis (Mtb) is a large dimeric and multi-domain protein with a key role in Mtb pathogenesis and promising antigenic properties. This dual role, likely associated with the ability of Heat Shock proteins to act both intra- and extra-cellularly, makes HtpG highly exploitable both for drug and vaccine development. This review aims to gather the latest updates in HtpG structure and biological function, with HtpG operating in conjunction with a large number of chaperone molecules of Mtb. Altogether, these molecules help Mtb recovery after exposure to host-like stress by assisting the whole path of protein folding rescue, from the solubilisation of aggregated proteins to their refolding. Also, we highlight the role of structural biology in the development of safer and more effective subunit antigens. The larger availability of structural information on Mtb antigens and a better understanding of the host immune response to TB infection will aid the acceleration of TB vaccine development.


Assuntos
Antígenos de Bactérias , Proteínas de Bactérias , Mycobacterium tuberculosis , Vacinas contra a Tuberculose , Fatores de Virulência , Mycobacterium tuberculosis/imunologia , Antígenos de Bactérias/imunologia , Antígenos de Bactérias/química , Fatores de Virulência/imunologia , Fatores de Virulência/química , Humanos , Vacinas contra a Tuberculose/imunologia , Proteínas de Bactérias/imunologia , Proteínas de Bactérias/química , Tuberculose/imunologia , Tuberculose/prevenção & controle , Tuberculose/microbiologia , Animais , Chaperonas Moleculares/imunologia , Chaperonas Moleculares/química , Chaperonas Moleculares/metabolismo
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