1,721,018 research outputs found
Structural and functional characterization of proteins involved in bacterial cell growth and division
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Structures of free and inhibited forms of theL,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis
No full textThe modelling of peptidoglycan is responsible for key cellular processes in Mycobacterium tuberculosis such as cell growth, division and resuscitation from dormancy. The structure of M. tuberculosis peptidoglycan is atypical since it contains a majority of 3,3 cross-links synthesized by L,D-transpeptidases that replace the 4,3 cross-links formed by the D,D-transpeptidase activity of classical penicillin-binding proteins. Carbapenems inactivate these L,D-transpeptidases and in combination with clavulanic acid are bactericidal against extensively drug-resistant M. tuberculosis. Here, crystal structures of the L,D-transpeptidase Ldt(Mt1) from M. tuberculosis in a ligand-free form and in complex with the carbapenem imipenem are reported. Elucidation of the structural features of Ldt(Mt1) unveils analogies and differences between the two key transpeptidases of M. tuberculosis: Ldt(Mt1) and Ldt(Mt2). In addition, the structure of imipenemin-activated Ldt(Mt1) provides a detailed structural view of the interactions between a carbapenem drug and Ldt(Mt1). By providing the key interactions in the binding of carbapenem to Ldt(Mt1), this work will facilitate structure-guided discovery of L,D-transpeptidase inhibitors as novel antitubercular agents against drug-resistant M. tuberculosis
PASTA sequence composition is a predictive tool for protein class identification
No full textAbstract
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
Antimicrobial peptides as an opportunity against bacterial diseases
No full textAntimicrobial peptides (AMPs) are an heterogeneous group of small amino acidic molecules produced by the innate immune system of a variety of organisms encompassing all orders of life from eukaryotes to amphibians, insects and plants. Numerous AMPs have been isolated from natural sources and many others have been de novo designed and synthetically produced. AMPs have antimicrobial activity in the micromolar range and compared with traditional antibiotics, they kill bacteria very rapidly. They act, principally, by the electrostatic attraction to negatively charged bacterial cells and consequently membrane disruption, but their antibacterial activity may also involve interference with metabolic processes or different cytoplasmic targets. AMPs are a group of unique and incredible compounds that may be directed to a therapeutic use either alone or in combination with existing antibiotics
PASTA in penicillin binding proteins and serine/threonine kinases: a recipe of structural, dynamic and binding properties
No full textPenicillin binding proteins (PBPs) and Serine Threonine kinases (STPKs) are two classes of bacterial enzymes whose involvement in a series of vital processes in bacterial growth and division is well assessed. Many components belonging to both classes share an ancillary domain named PASTA, whose functional role is not completely deciphered so far. Indeed, why PASTA motives decorate, often in multiple copies, PBPs and STPKs is yet an unanswered question. At present, PASTA is annotated as a sensor domain. It has been proposed that its binding to opportune ligands, i.e. muropeptides, is able to activate the cognate proteins to their functions. However, some experimental data proved that such role might not be a general property of PASTA. Furthermore, many PASTA modules, recognized in bacterial genomes, are not associated with either PBPs or STPKs enzymes. Thus, which is the function and/or if there is a context-dependent function of PASTA modules is still an open question. Here we present a survey of the structural, binding and dynamic properties so far described for PASTA domains. We also propose a possible criterion to discriminate between PASTA modules of STPKs or PBPs solely based on their sequences
Structural Basis of PE_PGRS Polymorphism, a Tool for Functional Modulation
No full textBackground: The mycobacterial PE_PGRS protein family is present only in pathogenic strains of the genus mycobacterium, such as Mtb and members of the MTB complex, suggesting a likely important role of this family in pathogenesis. Their PGRS domains are highly polymorphic and have been suggested to cause antigenic variations and facilitate pathogen survival. The availability of AlphaFold2.0 offered us a unique opportunity to better understand structural and functional properties of these domains and a role of polymorphism in Mtb evolution and dissemination. Methods: We made extensive use of AlphaFold2.0 computations and coupled them with sequence distribution phylogenetic and frequency analyses, and antigenic predictions. Results: Modeling of several polymorphic forms of PE_PGRS33, the prototype of the PE_PGRS family and sequence analyses allowed us to predict the structural impact of mutations/deletions/insertions present in the most frequent variants. These analyses well correlate with the observed frequency and with the phenotypic features of the described variants. Conclusions: Here, we provide a thorough description of structural impacts of the observed polymorphism of PE_PGRS33 protein and we correlate predicted structures to the known fitness of strains containing specific variants. Finally, we also identify protein variants associated with bacterial evolution, showing sophisticated modifications likely endowed with a gain-of-function role during bacterial evolution
Structural and enzymatic properties of Ageritin, a novel metal-dependent ribotoxin-like protein with antitumor activity
No full textAgeritin has been recently described as the first ribotoxin-like from Basidiomycota division (mushroom Agrocybe aegerita) with known antitumor activity (BBA 2017, 1861: 1113-1121). By investigating structural, catalytic and binding properties, we demonstrate that Ageritin is a unique ribotoxin-like protein. Indeed, typical of the ribotoxin family, it shows the specific ribonucleolytic activity against the ribosomal Sarcin-Ricin Loop in a rabbit reticulocytes assay. However, it displays several elements of novelty, as this activity is strongly metal-dependent and completely suppressed in the presence of EDTA, different from other representative members of the ribotoxin family. Consistently, we prove that Ageritin is able to bind magnesium ions with low micromolar affinity. We also show that Ageritin is significantly more stable than other ribotoxins in thermal and chemical denaturation experiments. These peculiar features make Ageritin the prototype of a new ribotoxin-like family present in basidiomycetes. Finally, given its high stability, this enzyme is a promising candidate as a new tool in immunoconjugates and nanoconstructs
Resveratrol Reverts Tolerance and Restores Susceptibility to Chlorhexidine and Benzalkonium in Gram-Negative Bacteria, Gram-Positive Bacteria and Yeasts
Full text linkThe spread of microorganisms causing health-care associated infection (HAI) is contributed to by their intrinsic tolerance to a variety of biocides, used as antiseptics or disinfectants. The natural monomeric stilbenoid resveratrol (RV) is able to modulate the susceptibility to the chlorhexidine digluconate (CHX) biocide in Acinetobacter baumannii. In this study, a panel of reference strains and clinical isolates of Gram-negative bacteria, Gram-positive bacteria and yeasts were analyzed for susceptibility to CHX and benzalkonium chloride (BZK) and found to be tolerant to one or both biocides. The carbonyl cyanide m-chlorophenylhydrazine protonophore (CCCP) efflux pump inhibitor reduced the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of CHX and BZK in the majority of strains. RV reduced dose-dependently MIC and MBC of CHX and BZK biocides when used as single agents or in combination in all analyzed strains, but not CHX MIC and MBC in Pseudomonas aeruginosa, Candida albicans, Klebsiella pneumoniae, Stenotrophomonas maltophilia and Burkholderia spp. strains. In conclusion, RV reverts tolerance and restores susceptibility to CHX and BZK in the majority of microorganisms responsible for HAI. These results indicates that the combination of RV, CHX and BZK may represent a useful strategy to maintain susceptibility to biocides in several nosocomial pathogens
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