Comparative homology of<i>Pleurotus ostreatus</i>laccase enzyme: Swiss model or Modeller?

Silva, Marco Antonio; Júnior, José Cordeiro do Nascimento; Thomaz, Douglas Vieira; Maia, Rafael Trindade; Amador, Vinícius Costa; Tommaso, Giovana; Coelho, Glauciane Danusa

doi:10.1080/07391102.2022.2138975

Cited by 7 publications

(3 citation statements)

References 93 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Protein sequences, coupled with their three-dimensional (3D) structures, provide critical information for understanding protein functions, interactions, and biological processes [ 38 ]. In this study, three-dimensional structures of proteins with non-synonymous mutations were constructed by SWOSS-MODEL, the online server for automated protein homology modeling [ 39 ]. The SWISS-MODEL could incorporate features to predict the structure and stoichiometry parameters of complexes based on the amino acid sequences of interacting proteins.…”

Section: Methodsmentioning

confidence: 99%

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis

Qian,

Ma,

Zeng

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

Background Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium. Methods In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool. Results We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins. Conclusion This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.

show abstract

Section: Methodsmentioning

confidence: 99%

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis

Qian,

Ma,

Zeng

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…In practical applications, this electrochemical transduction process offers numerous advantages. It enables real-time and rapid detection of target analytes with high sensitivity and selectivity, making it ideal for applications in healthcare [28][29][30], environmental monitoring [31][32][33][34][35][36][37][38][39][40][41], food safety [42][43][44][45][46][47][48][49], and pharmaceutical research [50][51][52][53][54][55]. This field's continuous research and development strives to further optimise the electrochemical transduction process, aiming for enhanced performance, increased versatility and expanded applications across a broad spectrum of analytical domains.…”

Section: Mip-based Electrochemical Sensors: Principles and Mechanismsmentioning

confidence: 99%

Molecularly Imprinted Polymer-Based Electrochemical Sensing in Protein Detection

Rodrigues,

Tierno,

Carvalho

et al. 2023

PoS

View full text Add to dashboard Cite

Protein detection is paramount across various scientific, clinical, and industrial domains. Accurate and sensitive detection of proteins is pivotal for understanding biological processes, diagnosing diseases, drug development, environmental monitoring, and ensuring food safety. Traditional protein detection methods encounter sensitivity, specificity, and ease of use challenges. Molecularly imprinted polymers (MIPs), with their tailored molecular recognition sites, offer a novel approach to address these limitations. When combined with electrochemical techniques, MIP-based electrochemical methods have emerged as a revolutionary technology, showcasing enhanced sensitivity and selectivity. This article provides a comprehensive overview of MIPbased electrochemical methods for protein detection, including the principles, engineering aspects, advantages, and potential applications. The aim is to elucidate the potential of this cutting-edge technology in reshaping protein detection and its promising role in advancing biosensing technologies.

show abstract

“…In silico studies3.2.1 | GABA homology modelThe period between experimentally validated protein structures and known protein sequences has been drastically cut down, thanks to the development of homology modeling into a powerful structural biology tool(Silva et al, 2022). The homology process model is improved and standardized using fully automated systems and databases, making it possible for people without a specific supercomputing background to directly connect protein maps and serve as a clear and uncomplicated reference for creating discoveries, representations, and evaluations(Hameduh et al, 2020).…”

mentioning

confidence: 99%

Quercetin increases the antidepressant‐like effects of sclareol and antagonizes diazepam in thiopental sodium‐induced sleeping mice: A possible GABAergic transmission intervention

Bappi,

Mia,

Ansari

et al. 2024

Phytotherapy Research

View full text Add to dashboard Cite

Quercetin is the most common polyphenolic flavonoid present in fruits and vegetables demonstrating versatile health‐promoting effects. This study aimed to examine the effects of quercetin (QR) and sclareol (SCL) on the thiopental sodium (TS)‐induced sleeping and forced swimming test (FST) mouse models. SCL (1, 5, and 10 mg/kg, p.o.) or QR (50 mg/kg, p.o.) and/or diazepam (DZP) (3 mg/kg, i.p.) were employed. After 30 min of TS induction, individual or combined effects on the animals were checked. In the FST test, the animals were subjected to forced swimming after 30 min of administration of the test and/or controls for 5 min. In this case, immobility time was measured. In silico studies were conducted to evaluate the involvement of GABA receptors. SCL (5 and 10 mg/kg) significantly increased the latency and decreased sleeping time compared to the control in the TS‐induced sleeping time study. DZP (3 mg/kg) showed a sedative‐like effect in animals in both sleeping and FST studies. QR (50 mg/kg) exhibited a similar pattern of activity as SCL. However, its effects were more prominent than those of SCL groups. SCL (10 mg/kg) altered the DZP‐3‐mediated effects. SCL‐10 co‐treated with QR‐50 significantly (p < 0.05) increased the latency and decreased sleep time and immobility time, suggesting possible synergistic antidepressant‐like effects. In silico studies revealed that SCL and QR demonstrated better binding affinities with GABAA receptor, especially α2, α3, and α5 subunits. Both compounds also exhibited good ADMET and drug‐like properties. In animal studies, the both compounds worked synergistically to provide antidepressant‐like effects in a slightly different fashion. As a conclusion, the combined administration of SCL and QR may be used in upcoming neurological clinical trials, according to in vivo and in silico findings. However, additional investigation is necessary to verify this behavior and clarify the potential mechanism of action.

show abstract

Comparative homology ofPleurotus ostreatuslaccase enzyme: Swiss model or Modeller?

Cited by 7 publications

References 93 publications

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis

Molecularly Imprinted Polymer-Based Electrochemical Sensing in Protein Detection

Quercetin increases the antidepressant‐like effects of sclareol and antagonizes diazepam in thiopental sodium‐induced sleeping mice: A possible GABAergic transmission intervention

Contact Info

Product

Resources

About