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1.
Int J Biol Macromol ; 271(Pt 2): 132399, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38754684

RESUMEN

The neutrophil-derived peptide, indolicidin, and the sphere-shaped carbon nanoparticle, C60, are contemporary components capable of acting as bactericides and virucides, among others. Herein, the coarse-grained molecular dynamics simulation method was used to simulate the interactions of gram-negative bacteria, eukaryotes, human immunodeficiency virus (HIV), and SARS-COV-2 membrane models with indolicidin, C60s, and C60-indolicidin hybrids. Our results demonstrated that the carbon nanoparticle penetrated all membrane models, except the bacterial membrane, which remained impenetrable to both the peptide and C60. Additionally, the membrane thickness did not change significantly. The peptide floated above the membranes, with only the side chains of the tryptophan (Trp)-rich site slightly permeating the membranes. After achieving stable contact between the membrane models and nanoparticles, the infiltrated C60s interacted with the unsaturated tail of phospholipids. The density results showed that C60s stayed close to indolicidin and continued to interact with it even after penetration. Indolicidin, especially its Trp-rich site, exhibited more contact with the head and tail of neutral phospholipids compared to other phospholipids. Moreover, both particles interacted with different kinds of glycosphingolipids located in the eukaryote membrane. This investigation has the potential to advance our knowledge of novel approaches to combat antimicrobial resistance.


Asunto(s)
COVID-19 , Fulerenos , Simulación de Dinámica Molecular , SARS-CoV-2 , Fulerenos/química , Fulerenos/farmacología , SARS-CoV-2/efectos de los fármacos , Humanos , COVID-19/virología , Membrana Celular/química , Membrana Celular/metabolismo , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/farmacología , VIH/efectos de los fármacos , Antiinfecciosos/química , Antiinfecciosos/farmacología
2.
Turk J Ophthalmol ; 53(4): 218-221, 2023 08 19.
Artículo en Inglés | MEDLINE | ID: mdl-37602552

RESUMEN

Objectives: Chlamydia trachomatis infects the urogenital tract and eyes. Anatomical tropism is correlated with serovars which are characterized according to the variation in the major outer membrane proteins encoded by the ompA gene. The aim of the present study was to determine the distribution of C. trachomatis serovars among patients with follicular conjunctivitis in Iran. Materials and Methods: A total of 68 conjunctival specimens from symptomatic adults were studied for the presence of C. trachomatis using polymerase chain reaction (PCR) analysis. Serovars were determined by Omp1 PCR-RFLP analysis. Results: C. trachomatis was detected in 38 (55.9%) of patients with follicular conjunctivitis, with higher C. trachomatis prevalence in the younger age groups. Twenty-six (38.2%) of these patients had a history of urinary tract infection. Four distinct serovars were identified in the conjunctiva samples using molecular genotyping. The most prevalent was serovar E, followed by G, I, and F. Conclusion: Our serovar distribution indicated that chlamydial follicular conjunctivitis usually has a genital source. Genital serovars may cause eye diseases, especially in sexually active adults. On the other hand, conjunctivitis might be the only sign of sexually transmitted infection. Therefore, genotyping C. trachomatis in ocular and genital specimens could be beneficial for acquiring more detailed epidemiological information about the etiology of the disease and monitoring treatment success.


Asunto(s)
Chlamydia trachomatis , Conjuntivitis , Adulto , Humanos , Chlamydia trachomatis/genética , Serogrupo , Irán/epidemiología
3.
Clin Lab ; 69(1)2023 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-36649505

RESUMEN

BACKGROUND: The emergence of multidrug resistance and extensively drug-resistant tuberculosis is a serious public health crisis. Using rapid and inexpensive molecular methods such as HRM assay in the detection of second-line drugs resistance in M. tuberculosis would be helpful in the treatment and control of XDR tuberculosis cases. METHODS: MDR-TB isolates were collected from Iranian tuberculosis laboratories. Drug susceptibility test performed via the indirect proportion method utilizing LJ Medium. Susceptibility to ciprofloxacin, ofloxacin, amikacin, kanamycin, and capreomycin, as second-line anti-tuberculosis agents were assessed. Single point mutations in gyrA, rrs and eis genes were detected via HRM assay and DNA sequencing. RESULTS: A DST test was performed for 56 MDR isolates and at least 27 (48.2%) isolates were resistant to CIP or OFL. Also, 14 (25%), 12 (21.4%), and 15 (26.7%) isolates were resistant to capreomycin, amikacin, and kanamycin, respectively. D94G, A90V, and G88C mutations were the most frequent mutations in gyrA gene. Also, A1401G mutation was detected more than the other mutations in rrs gene. CONCLUSIONS: The frequency of CIP/OFL and AMK/CAP/KAN-resistant TB is considerable among Iranian tuberculosis cases. HRM assay is a rapid and inexpensive test and can detect important mutation-based drug resistance in MDR-TB and XDR-TB isolates.


Asunto(s)
Tuberculosis Extensivamente Resistente a Drogas , Mycobacterium tuberculosis , Tuberculosis Resistente a Múltiples Medicamentos , Humanos , Amicacina/farmacología , Capreomicina/farmacología , Capreomicina/uso terapéutico , Irán , Farmacorresistencia Bacteriana Múltiple/genética , Antituberculosos/farmacología , Kanamicina/farmacología , Kanamicina/uso terapéutico , Tuberculosis Extensivamente Resistente a Drogas/tratamiento farmacológico , Tuberculosis Extensivamente Resistente a Drogas/microbiología , Mutación , Pruebas de Sensibilidad Microbiana , Tuberculosis Resistente a Múltiples Medicamentos/diagnóstico , Tuberculosis Resistente a Múltiples Medicamentos/tratamiento farmacológico , Tuberculosis Resistente a Múltiples Medicamentos/microbiología
4.
J Phys Chem B ; 125(26): 7163-7176, 2021 07 08.
Artículo en Inglés | MEDLINE | ID: mdl-34171196

RESUMEN

The antimicrobial peptide (AMP) pleurocidin has a broad antimicrobial activity against Gram-negative and Gram-positive bacteria by perturbation and permeabilizing their membranes; however, understanding the mechanism of action of pleurocidin, a promising AMP for replacing current antibiotic agents, has tremendous importance for future applications. Hence, we applied all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations to provide molecular-level insights into the pore-forming process. The early stages of pore formation were examined by 500 ns AA simulations. The results demonstrated that pleurocidin has the ability to create a pore with two peptides through which water molecules can flow. However, the results of the 25 µs CG simulations indicate that the final pore will be created by accumulation of more than two peptides. The results show that after 2.5 µs of simulations, peptides will aggregate and create a channel-like pore across the membrane. Pleurocidin can construct a more efficient and stable pore in the anionic membranes than in the zwitterionic membranes. Moreover, the structure amphipathicity, polarity, and basic residues play crucial roles in the pore formation and flow of water molecules across the lipid bilayers. In general, the findings revealed that based on the lipid compositions of the membranes, pleurocidin could act by forming either toroidal or disordered toroidal pores with different peptide arrangements.


Asunto(s)
Simulación de Dinámica Molecular , Agua , Proteínas de Peces , Membrana Dobles de Lípidos , Proteínas Citotóxicas Formadoras de Poros
5.
Infect Drug Resist ; 12: 221-227, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30666137

RESUMEN

INTRODUCTION: Pseudomonas aeruginosa is the most common opportunistic pathogen associated with a broad range of infections, including cystic fibrosis, ocular, otitis media, and burn infections. The aim of this study was to show the frequency of the pilS2 gene, and its association with P. aeruginosa plasmid pKLC102 and PAPI-1 pathogenicity island among P. aeruginosa strains. METHODS: The samples were collected from patients with cystic fibrosis, ocular, otitis media, and burn infections between January 2016 and November 2017. DNA was extracted using the DNA extraction kit and was used for PCR assay. PCR with 4 primer-pairs including 976 F/PAPI-1R, 4542 F/intF, SojR/4541 F, and intF/sojR was performed to identify PAPI-1. pKLC102 was detected using three other primer-pairs including cp10F/cp10R, cp44F/cp44R, and cp97F/cp97R. RESULTS: A total of 112 P. aeruginosa isolates were collected from patients with cystic fibrosis (36), burn (20), otitis media (26), and ocular (30) infections. The results of PCR showed that pilS2 gene was identified in 96 (85%) strains. PAPI-1-attB integration was detected among 38 (33.9%) isolates and the circular form of PAPI-1 detected among 17 (14%) isolates. In addition, 79 (70.5%) strains were found to be positive for pKLC102. CONCLUSION: We found that the majority of the isolates may be susceptible to transfer this significant island and the related element pKLC102 into recipient isolates lacking the island owing to high association of the PilS2 pilus with the islands in the studied strains. It is anticipated that strains isolated from burn and eye with the highest rate of PilS2, PAPI-1, and pKLC102 association have a high level of antibiotic resistance.

6.
J Chem Inf Model ; 59(1): 550-563, 2019 01 28.
Artículo en Inglés | MEDLINE | ID: mdl-30475620

RESUMEN

Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation process of peptide and protein-based drugs. Herein, the self-assembly of different polymers and block copolymers with combinations of the various molecular weight of blocks and the effects of resultant polymer and copolymer nanomicelles on the stability of magainin2, an α-helical antimicrobial peptide, were investigated by means of all-atom molecular dynamics (MD) simulation. The micelle forming, morphology of micellar aggregations and changes in the first hydration shell of the micelles during micelles formation were explored as well. The results showed that the peptide binds to the polymer and copolymer micelles and never detaches during the MD simulation time. In general, all polymers and copolymers simultaneously encapsulated the peptide during micelles formation and had the ability to maintain the helical structure of the peptide, whereas the first hydration shell of the peptide remained unchanged. Among the micelles, the polyethylene glycol (PEG) micelles completely encapsulated magainin2 and, surprisingly, the NMR structure of the peptide was perfectly kept during the encapsulation process. The MD results also indicated that the aromatic and basic residues of the peptide strongly interact with polymers/copolymers and play important roles in the encapsulation mechanism. This research will provide a good opportunity in the design of polymer surfaces for drug delivery applications such as controlled-release peptide delivery systems.


Asunto(s)
Péptidos Catiónicos Antimicrobianos/química , Interacciones Hidrofóbicas e Hidrofílicas , Simulación de Dinámica Molecular , Nanopartículas/química , Polímeros/química , Conformación Proteica en Hélice alfa , Agua/química
7.
Int Ophthalmol ; 39(7): 1581-1587, 2019 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-29982958

RESUMEN

BACKGROUND: Pseudomonas is the most common cause of microbial keratitis especially in people who use contact lens. The virulence of Pseudomonas aeruginosa in different eye infections is associated with different virulence factors . METHODS: In this study, 54 P. aeruginosa isolates including 39 isolates from keratitis and 15 isolates from conjunctivitis were evaluated for their ability to form biofilm, production of protease, elastase, alkaline protease and their antibiotic-resistant patterns. The distribution of the exoS and exoU genes in the test strains were determined using PCR assays. RESULTS: Most of the eye infections (90.74%) were seen in people who used contact lenses, and in most of patients (72.22%), the infection was presented as keratitis. None of the isolates were resistant to a single antibiotic as tested. Multidrug resistance (MDR) was detected in two isolates (3.5%) which were resistant to more than one category of antibiotics. The exoU+/exoS+ isolates were in majority although in total, compared to exoS, there were more exoU in a greater number of samples. Most of the strains produce elastase but among all of ocular isolates, only 5.8% of the strains showed alkaline protease activity. Most of the ocular isolates were not capable of producing biofilm. CONCLUSIONS: In our study, a high prevalence of virulence factors was observed in P. aeruginosa isolates from contact lens wearer with keratitis. As the P. aeruginosa isolates from different infection origins and different geographic region may have different virulence factors, having a better perception of these differences could help to improve development of clinical instructions for the control of keratitis.


Asunto(s)
Biopelículas/crecimiento & desarrollo , ADN Bacteriano/análisis , Infecciones Bacterianas del Ojo/microbiología , Queratitis/microbiología , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/genética , Adulto , Infecciones Bacterianas del Ojo/diagnóstico , Infecciones Bacterianas del Ojo/epidemiología , Femenino , Genotipo , Humanos , Incidencia , Irán/epidemiología , Queratitis/diagnóstico , Queratitis/epidemiología , Masculino , Infecciones por Pseudomonas/diagnóstico , Infecciones por Pseudomonas/epidemiología , Pseudomonas aeruginosa/aislamiento & purificación , Estudios Retrospectivos , Adulto Joven
8.
Int J Mycobacteriol ; 7(3): 268-274, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30198509

RESUMEN

Background: In this study, we have experimentally investigated the effects of different osmolytes including sucrose, sorbitol, urea, and guanidinium chloride (GdmCl) on the stability and structure of the Mycobacterium tuberculosis pyrazinamidase (PZase). PZase converts pyrazinamide to its active form. Methods: In addition, in order to gain molecular insight into the interactions between osmolytes and PZase, we have conducted 1000-ns molecular dynamics simulations. Results: The results indicated that sucrose and sorbitol increase the stability and compactness of the enzyme, whereas in the presence of urea and GdmCl, PZase loses its stability and compactness. Furthermore, the activity of PZase in the presence of sucrose was more than the other solutions. The energetic analyses imply that the electrostatic and van der Waals interactions are the major factors in the osmolyte-PZase interactions. Sorbitol and sucrose, as protective osmolytes, protect the protein structure by utilizing the van der Waals interaction from denaturation. In addition, urea molecules affect the structure of the protein using the hydrogen bonds and van der Waals interactions. Conclusion: The results show that the most important factor in the denaturing effect of GdmCl is the strong interactions of positively charged guanidinium ions with the aspartate and glutamate residues.


Asunto(s)
Amidohidrolasas/química , Estabilidad de Enzimas/efectos de los fármacos , Simulación de Dinámica Molecular , Mycobacterium tuberculosis/enzimología , Guanidina/farmacología , Humanos , Enlace de Hidrógeno , Sorbitol/farmacología , Electricidad Estática , Sacarosa/farmacología , Temperatura , Urea/farmacología
9.
Eye Contact Lens ; 44 Suppl 2: S277-S280, 2018 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-29280751

RESUMEN

BACKGROUND: Staphylococcus epidermidis is one of the common causes of bacterial keratitis and post-operation infections. One of the most important virulence factors of S. epidermidis is biofilm formation. Poly-N-acetylglucosamine (PNAG) production is critical for biofilm formation in S. epidermidis. The intercellular adhesion (ica) operon is formed by icaA, icaD, icaB, and icaC genes, which participate in the biosynthesis of PNAG. Strains of S. epidermidis from different infections show different genotypes in relation to adhesion operon genes. Therefore, regarding the fact that the pathogenic strain in each community has unique genotypes, this study investigated the relation between ica operon genotypes and various ocular infections. However, the correlation between the ica operon genes and the mecA gene was analyzed in the isolates. METHODS: For this study, samples of the conjunctiva, cornea, and intraocular fluid of patients with ocular infection were collected. After culture and incubation, detection of S. epidermidis was performed using biochemical and coagulase tests. The antibiotic susceptibility of the bacteria was evaluated by the disk diffusion method. After this, DNA was extracted from the bacteria and the presence of icaA, icaD, is256, and mecA genes was analyzed using polymerase chain reaction. RESULTS: All 50 coagulase-negative Staphylococcus samples isolated from different eye infections were characterized as S. epidermidis. Most of the samples (36%) were isolated from the cornea and the others were, respectively, from the conjunctiva (24%), vitreous (20%), anterior chamber (8%), eyelid (6%), and nasolacrimal duct (6%). The icaA, icaD, and is256 genes were detected with different genotypes in isolates from keratitis and endophthalmities compared with conjunctivitis. Overall, the most isolated genotype from ocular infections was icaA+. icaD+. is256+. (46%). Most of the isolates (82.60%) had mecA, icaA, and icaD genes simultaneously, which indicates a strong relationship between the adhesion genes and the antibiotic resistance gene. CONCLUSIONS: The adhesion operon genes were observed with different genotypes in S. epidermidis samples isolated from various ocular infections.


Asunto(s)
Adhesión Bacteriana/genética , Proteínas Bacterianas/genética , Infecciones Bacterianas del Ojo/microbiología , Operón/genética , Infecciones Estafilocócicas/genética , Staphylococcus epidermidis/genética , Factores de Virulencia/genética , Antibacterianos/farmacología , ADN Bacteriano/genética , Genotipo , Humanos , Polisacáridos Bacterianos , Infecciones Estafilocócicas/microbiología , Staphylococcus epidermidis/efectos de los fármacos , Staphylococcus epidermidis/aislamiento & purificación
10.
PLoS One ; 12(11): e0187216, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-29125878

RESUMEN

Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD) simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers. As well as, the structure of zwitterionic membranes was more affected by the peptide than the anionic bilayers. Taken together, the study demonstrated that the cationic residues of pardaxin snorkeled toward the interface of lipid bilayers and all phenylalanine residues of the peptide played important roles in the peptide-membrane interactions. We hope that this work will provide a better understanding of the interactions of antimicrobial peptides with the membranes.


Asunto(s)
Péptidos Catiónicos Antimicrobianos/química , Membrana Dobles de Lípidos/química , Proteínas de la Membrana/química , Simulación de Dinámica Molecular
11.
J Infect ; 74(6): 545-554, 2017 06.
Artículo en Inglés | MEDLINE | ID: mdl-28366687

RESUMEN

INTRODUCTION: The measurement of adenosine deaminase (ADA) level in cerebrospinal fluid (CSF) has generated as a suitable test for tuberculous meningitis (TBM) diagnosis. The main objective in the present meta-analysis focused on analyzing the ADA test accuracy in order to diagnose TBM. METHODS: We searched several databases including Medline, Embase and Cochrane databases to identify studies addressing the diagnosis of TBM. The quality of included reports were assessed by RevMan5 software (via QUADS2 checklist). Accuracy measures of ADA test (sensitivity, specificity and others) pooled with random effects models. In addition, the data was elicited by using midas and metan packages in stata (version 12). RESULT: Twenty studies were eligible for inclusion within the meta-analysis. The pooled sensitivity and specificity for TBM diagnosis hallmarks were 89% (95% CI: 0.84-0.92) and 91% (95% CI: 0.87-0.93), respectively. The positive likelihood ratio was 9.4 (95% CI: 7-12.8), negative likelihood ratio was 0.12 (95% CI: 0.09-0.17), and diagnostic odds ratio was 77 (95% CI: 45-132). Indeed, the area under the summary receiver operating characteristic (SROC) was 0.96. CONCLUSION: It was magnificently attained that ADA test had a relatively high accuracy for TBM diagnosis.


Asunto(s)
Adenosina Desaminasa/líquido cefalorraquídeo , Tuberculosis Meníngea/diagnóstico , Pruebas Enzimáticas Clínicas , Humanos , Oportunidad Relativa , Curva ROC , Sensibilidad y Especificidad , Tuberculosis Meníngea/enzimología , Tuberculosis Meníngea/microbiología
12.
J Chem Inf Model ; 57(4): 929-941, 2017 04 24.
Artículo en Inglés | MEDLINE | ID: mdl-28301157

RESUMEN

Antimicrobial peptides (AMPs) are part of the innate host defense system, and they are produced by living organisms to defend themselves against infections. Pardaxin is a cationic AMP with antimicrobial and antitumor activities that has potential to be used as a novel antibiotic or for drug delivery in cancer therapy. This peptide acts on the membrane of target cells and can lead to lysis using different mechanisms of action. Here, we conducted 4.5 µs all-atom molecular dynamics (MD) simulations to determine the critical fragments and residues of Pardaxin for early insertion into different lipid bilayers. Our results revealed that the N-terminal domain of the peptide, particularly the Phe 2 and (/or) Phe 3 residues, has a crucial role in early insertion, independent of the type of lipid bilayers.


Asunto(s)
Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/metabolismo , Venenos de los Peces/química , Venenos de los Peces/metabolismo , Membrana Dobles de Lípidos/metabolismo , Simulación de Dinámica Molecular , Fosfolípidos/metabolismo , Difusión , Conformación Proteica
13.
Int J Mycobacteriol ; 5 Suppl 1: S138-S139, 2016 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-28043510

RESUMEN

OBJECTIVE/BACKGROUND: Mycobacterium tuberculosis pyrazinamidase (PZase) is known an enzyme that is involved in degradation of pyrazinamide to ammonia and pyrazinoic acid. Pyrazinamide is an important first-line drug used in the short-course treatment of tuberculosis. Previous investigations have indicated that the pyrazinamide (PZA)-resistant M. tuberculosis strains are caused by point mutations in the PZase enzyme which is the activator of the prodrug PZA. Although the general fold of PZase was determined, the structural and functional properties of the enzyme in solution were not understood very well. In this study, the PZase enzyme was overexpressed and purified. In addition, two polyols, namely sorbitol and glycerol, were chosen to study their effects on the structure, dynamics, and stability of the enzyme. To gain a deeper insight, molecular dynamics simulation and spectroscopic methods, such as fluorescence spectroscopy and circular dichroism (CD), were used. METHODS: The genes were cloned in Escherichia coli BL21 (DE3), harboring the recombinant pET-28a (+) plasmid, overexpressed and purified by Ni-NTA Sepharose. The far UV-visible CD spectra were measured by a Jasco-810 spectropolarimeter. The intrinsic fluorescence spectra were measured on a Cary Varian Eclipse spectrofluorometer. For molecular dynamics (MD) simulations, we have applied GROMACS4.6.5. RESULTS: The results showed that glycerol and sorbitol increased the enzyme activity up to 130% and 110%, respectively, at 37°C. The stability of PZase was decreased and the half-life was 20 min. Glycerol and sorbitol increased the PZase half-life to 99 min and 23 min, respectively. The far UV CD measurements of PZase indicated that the CD spectra in glycerol and sorbitol give rise to an increase in the content of α-helix and ß-sheets elements. The average enzyme root mean square deviation (RMSD) in sorbitol solution was about 0.416nm, a value that is higher than the enzyme RMSD in the pure water (0.316). In dictionary of protein secondary structure (DSSP) results, we observed that the secondary structures of the protein are partially increased as compared to the native state in water. The experimental and simulation data clearly indicated that the polyols increased the PZase stabilization in the order: glycerol>sorbitol. CONCLUSION: It can be concluded that the native conformation of the enzyme was stabilized in the sorbitol and glycerol and tend to exclude from the PZase surface, forcing the enzyme to keep it in the compactly folded conformation. The glycerol molecules stabilized PZase by decreasing the loops flexibility and then compacting the enzyme structure. It appears that more stability of PZase in glycerol solution correlates with its amphiphilic orientation, which decreases the unfavorable interactions of hydrophobic regions.

14.
Protein J ; 34(3): 181-92, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25972249

RESUMEN

Pyrazinamide (PZA) is one the first line anti-tuberculosis drugs that require activation by the pyrazinamidase (PZase). Most PZA-resistant Mycobacterium tuberculosis strains have mutations in the pncA gene which encoding PZase that result in the reduction or loss of the enzyme activity. Herein, we have examined how various mutations, which have been found from the PZA-resistant M. tuberculosis strains in Iran, modify the PZase activity. To elucidate the possible role of these mutations, namely A143T (MUT1), L151S (MUT2), A143T/T168A/E173K (MUT3), in the bioactivity of the enzyme, the PZase and mutant genes were cloned, functionally expressed and biochemically and computationally characterized. In comparison to the PZase enzyme, the enzymatic efficiency of mutant enzymes was decreased, with MUT2 indicating the largest enzymatic efficiency reduction. Homology models of mutants were constructed based on the PZase X-ray crystal structure. Molecular modeling and substrate docking revealed that the wild-type has much stronger binding affinity to PZA than the mutants whereas MUT2 has the weakest binding affinity. In addition, the molecular dynamics simulations and the essential dynamics results illustrated that the positions of the 51st to 71st residues were more dynamics in MUT2 as compared to the other atoms in PZase, MUT1 and MUT3 which could decrease the K(m) and k(cat) values of the enzymes.


Asunto(s)
Amidohidrolasas/química , Proteínas Bacterianas/química , Farmacorresistencia Bacteriana , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/enzimología , Pirazinamida/farmacología , Tuberculosis/microbiología , Amidohidrolasas/genética , Amidohidrolasas/metabolismo , Secuencia de Aminoácidos , Antituberculosos/farmacología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Humanos , Enlace de Hidrógeno , Irán , Simulación de Dinámica Molecular , Datos de Secuencia Molecular , Mutación , Mycobacterium tuberculosis/genética , Alineación de Secuencia
15.
Chem Biol Drug Des ; 84(2): 242-52, 2014 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-24581146

RESUMEN

LAH4 is an antimicrobial peptide that is believed to possess both antibiotic and DNA delivery capabilities. It is one of a number of membrane-active peptides that show increased affinity toward anionic lipids. Herein, we have performed molecular dynamics simulations to compare LAH4 effects on anionic palmitoyl-oleoyl-phosphatidylglycerol bilayer, which approximate a prokaryotic membrane environment and zwitterionic palmitoyl-oleoyl-phosphatidylcholine bilayer, which approximate a eukaryotic membrane environment. One particular interest in this work is to study how different kinds of lipid bilayers respond to the attraction of LAH4. Remarkably, our data have shown that the depth of peptide penetration strongly depends on membrane composition and pH. At acidic pH, LAH4 has exhibited a high tendency to interact strongly with and be adsorbed on anionic membrane. We have also shown that electrostatic interactions between His11 and the phosphor atoms of bilayers should have a significant impact on the penetration of LAH4. These results provide insights into the interactions of LAH4 and lipid bilayers at the atomic level, which is useful to understand cell selectivity and mechanism of the peptide action.


Asunto(s)
Membrana Dobles de Lípidos/metabolismo , Péptidos/metabolismo , Fosfatidilcolinas/metabolismo , Fosfatidilgliceroles/metabolismo , Péptidos Catiónicos Antimicrobianos , Concentración de Iones de Hidrógeno , Simulación de Dinámica Molecular
16.
J Chem Phys ; 134(3): 035104, 2011 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-21261393

RESUMEN

Co-solvents such as glycerol and sorbitol are small organic molecules solvated in the cellular solutions that can have profound effects on the protein structures. Here, the molecular dynamics simulations and comparative structural analysis of magainin, as a peptide model, in pure water, 2,2,2-trifluoroethanol∕water, glycerol∕water, and sorbitol∕water are reported. Our results show that the peptide NMR structure is largely maintained its native structure in osmolytes-water mixtures. The simulation data indicates that the stabilizing effect of glycerol and sorbitol is induced by preferential accumulation of glycerol and sorbitol molecules around the nonpolar and aromatic residues. Thus, the presence of glycerol and sorbitol molecules decreases the interactions of water molecules with the hydrophobic residues of the peptide, and the alpha helical structure is stabilized.


Asunto(s)
Glicerol/química , Magaininas/química , Simulación de Dinámica Molecular , Sorbitol/química , Modelos Moleculares , Estructura Secundaria de Proteína , Agua/química
17.
J Comput Aided Mol Des ; 24(10): 829-41, 2010 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-20697778

RESUMEN

Urea and GdmCl are widely used to denature proteins at high concentrations. Here, we used MD simulations to study the denaturation mechanisms of helical peptide in different concentrations of GdmCl and urea. It was found that the helical structure of the peptide in water simulation is disappeared after 5 ns while the helicity of the peptide is disappeared after 70 ns in 2 M urea and 25 ns in 1 M GdmCl. Surprisingly, this result shows that the helical structure in low concentration of denaturants is remained more with respect to that solvated in water. The present work strongly suggests that urea interact more preferentially to non-polar and aromatic side chains in 2 M urea; therefore, hydrophobic residues are in more favorable environment in 2 M urea. Our results also reveal that the hydrogen bonds between urea and the backbone is the dominant mechanism by which the peptide is destabilized in high concentration of urea. In 1 M and 2 M GdmCl, GdmCl molecules tend to engage in transient stacking interactions with aromatics and hydrophobic planar side chains that lead to displacement of water from the hydration surface, providing more favorable environment for them. This shows that accumulation of GdmCl around hydrophobic surfaces in 1 M and 2 M GdmCl solutions prevents proper solvation of the peptide at the beginning. In high GdmCl concentrations, water solvate the peptide better than 1 M and 2 M GdmCl. Therefore, our results strongly suggest that hydrogen bonds between water and the peptide are important factors in the destabilization of peptide in GdmCl solutions.


Asunto(s)
Guanidina/química , Péptidos/química , Desnaturalización Proteica , Urea/química , Secuencia de Aminoácidos , Simulación de Dinámica Molecular , Datos de Secuencia Molecular , Estructura Secundaria de Proteína
18.
Microb Drug Resist ; 15(4): 251-6, 2009 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-19857130

RESUMEN

Pyrazinamide (PZA) is an important first-line drug used for the short-course treatment of tuberculosis in combination with isoniazid and rifampin. It has been reported that mutations in pncA gene correlate well with PZA resistance depending on the geographic area. On the other hand, different genotypes of Mycobacterium tuberculosis show different affinities to acquire resistance-related mutations. To determine the relative significance of various mutations in the pncA gene in Iranian PZA-resistant M. tuberculosis isolates and to analyze the association of different genotypes of M. tuberculosis with PZA resistance, 34 PZA-resistant M. tuberculosis isolates were analyzed for their pncA mutations using direct sequencing. These isolates were genotyped by IS6110 fingerprinting and spoligotyping methods. Mutations in the pncA gene were identified in 24 of 34 of these isolates (70.58%). No mutations were found in 10 PZA-resistant isolates, which implied that alternative mechanisms of resistance existed in these strains. PZA resistance was strongly (41.2%) associated with multidrug-resistant tuberculosis. Genotyping revealed the Central Asian (CAS) and East-African Indian families as the most prevalent families between PZA-monoresistant isolates versus the Beijing and Haarlem families which were the most frequent families between PZA including multidrug-resistant isolates.


Asunto(s)
Antituberculosos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Mycobacterium tuberculosis/efectos de los fármacos , Pirazinamida/farmacología , Amidohidrolasas/genética , ADN Bacteriano , Genotipo , Humanos , Irán/epidemiología , Pruebas de Sensibilidad Microbiana , Mutación , Mycobacterium tuberculosis/genética , Análisis de Secuencia de ADN , Tuberculosis Resistente a Múltiples Medicamentos/tratamiento farmacológico , Tuberculosis Resistente a Múltiples Medicamentos/epidemiología , Tuberculosis Resistente a Múltiples Medicamentos/microbiología
19.
Microb Drug Resist ; 14(4): 273-9, 2008 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-19090721

RESUMEN

Considering the significant increase of isoniazid (INH) resistance in Iranian Mycobacterium tuberculosis isolates in the last few years and to investigate the prevalence and diagnostic potential of the most commonly reported mutations associated with INH resistance in Iran, we analyzed parts of the katG gene and fabG1-inhA and oxyR-ahpC regulatory regions in a sample of 48 INH-resistant and 25 INH-sensitive isolates. Mutations in the katG 315, fabG1-inhA, and oxyR-ahpC regulatory regions were detected in 58.3%, 18.7%, and 39.6% of isolates, respectively. The R463L polymorphism in the katG gene and the ahpC46A were detected with high frequency in both INH-resistant and -sensitive isolates. Spoligotyping and IS6110-based restriction fragment length polymorphism patterns revealed that most of the isolates containing ahpC46A and katG 463Leu polymorphism belonged to the Central Asian (CAS) super family. The tight relationship between ahpC46A and katG 463Leu polymorphisms and the CAS super family highlights the importance of the CAS super family in INH resistance in Iran. In conclusion, mutations at katG codon 315 or the fabG1-inhA regulatory region were identified in 77.0% of the INH-resistant isolates and in none of the INH-sensitive strains, and are highly predictive of isonizid resistance in Iranian isolates.


Asunto(s)
Antituberculosos/farmacología , Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana/genética , Isoniazida/farmacología , Mycobacterium tuberculosis/efectos de los fármacos , Genotipo , Humanos , Irán/epidemiología , Pruebas de Sensibilidad Microbiana , Datos de Secuencia Molecular , Mutación , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/aislamiento & purificación , Oxidorreductasas/genética , Peroxidasas/genética , Peroxirredoxinas/genética , Valor Predictivo de las Pruebas , Análisis de Secuencia de ADN , Tuberculosis/epidemiología , Tuberculosis/microbiología
20.
Appl Biochem Biotechnol ; 149(2): 109-18, 2008 May.
Artículo en Inglés | MEDLINE | ID: mdl-18401741

RESUMEN

Brevinin-2R, a member of a new family of antimicrobial peptides isolated from the skin of Rana ridibunda, displays antimicrobial activity against bacteria and fungi. In this study, we have used an assembly PCR method for the fast and extremely accurate synthesis of the brevinin-2R gene. A total of six primers were assembled in a single step PCR, and the assembly was then amplified by PCR to produce the final gene. The synthetic gene was cloned into the pET32a (+) vector to allow the expression of brevinin-2R as a Trx fusion protein in Escherichia coli. The results indicated that the expression level of the fusion protein could reach up to 25% of the total cell proteins. The expression products could be easily purified by Ni-NTA chromatography and released from the fusion protein by factor Xa protease. The peptide displayed antimicrobial activity similar to that of the purified brevinin that was reported earlier. This method allows the fast synthesis of a gene that optimized the overexpression in the E. coli system and production of sufficiently large amounts of peptide for functional and structural characterizations.


Asunto(s)
Proteínas Anfibias , Antiinfecciosos/farmacología , Péptidos Catiónicos Antimicrobianos , Escherichia coli/química , Secuencia de Aminoácidos , Proteínas Anfibias/genética , Proteínas Anfibias/aislamiento & purificación , Proteínas Anfibias/metabolismo , Proteínas Anfibias/farmacología , Péptidos Catiónicos Antimicrobianos/genética , Péptidos Catiónicos Antimicrobianos/aislamiento & purificación , Péptidos Catiónicos Antimicrobianos/metabolismo , Péptidos Catiónicos Antimicrobianos/farmacología , Clonación Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Datos de Secuencia Molecular , Péptidos/farmacología , Reacción en Cadena de la Polimerasa
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