scholarly journals Extended ɛ34 Phage TSP Renatures After Urea-acid Unfolding

2021 ◽  
Author(s):  
Joseph Ayariga ◽  
Logan Gildea ◽  
Robert Villafane
Keyword(s):  
Protein Engineering ◽  
Biofilm Formation ◽  
Antimicrobial Protein ◽  
Hydrophobic Core ◽  
Free Energies ◽  
Pharmacokinetics And Pharmacodynamics ◽  
Native Conformation ◽  
Urea Denaturation ◽  
Tailspike Protein ◽  
Insight Into

In antimicrobial-peptide/protein engineering, understanding the peptide/protein’s adaptability to harsh environmental conditions such as urea, proteases, fluctuating temperatures, high salts provide enormous insight into the pharmacokinetics and pharmacodynamics of the engineered peptide/protein and its ability to survive the harsh internal environment of the human body such as the gut or the harsh external environment to which they are applied. A previous work in our laboratory demonstrated that our cloned Eɛ34 TSP showed potent antimicrobial activity against Salmonella newington, and more so, could prevent biofilm formation on decellularized tissue. In this work, the effects of urea-acid on the Eɛ34 stability is studied, and the results demonstrates that at lower pHs of 3 and 4 with urea the protein was denatured into monomeric species. However, the protein withstood urea denaturation above pH of 5 and thus remained as trimeric protein. The mechanism of denaturation of Eɛ34 TSP seems to show that urea denatures proteins by depleting hydrophobic core of the protein by directly binding to the amide units via hydrogen bonds. The results of our in-silico investigation determined that urea binds with Eɛ34 TSP with relative free energies range of -3.4 to -2.9 kcal/mol at the putative globular head binding domain of the protein. The urea molecules interacts with with the protein’s predicted hydrophobic core, thus, disrupting and exposing the shielded hydrophobic moieties of Eɛ34 TSP to the solvent. We further showed that after the unfolding of Eɛ34 TSP via urea-acid, renaturation of the protein to its native conformation was possible within few hours. This unique characteristic of refolding of Eɛ34 TSP which is similar to that of the P22 phage tailspike protein is of special interest to protein scientists and can also be exploited in antimicrobial-protein engineering.

scholarly journals Superhydrophobic Nanocoatings as Intervention against Biofilm-Associated Bacterial Infections

Nanomaterials ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1046
Author(s):  
Yinghan Chan ◽  
Xun Hui Wu ◽  
Buong Woei Chieng ◽  
Nor Azowa Ibrahim ◽  
Yoon Yee Then
Keyword(s):  
Biofilm Formation ◽  
Bacterial Infections ◽  
Therapeutic Strategies ◽  
Public Healthcare ◽  
Persistent Infections ◽  
Promising Strategy ◽  
Antimicrobial Interventions ◽  
Novel Therapeutic Strategies ◽  
Insight Into ◽  
Microbial Attachment

Biofilm formation represents a significant cause of concern as it has been associated with increased morbidity and mortality, thereby imposing a huge burden on public healthcare system throughout the world. As biofilms are usually resistant to various conventional antimicrobial interventions, they may result in severe and persistent infections, which necessitates the development of novel therapeutic strategies to combat biofilm-based infections. Physicochemical modification of the biomaterials utilized in medical devices to mitigate initial microbial attachment has been proposed as a promising strategy in combating polymicrobial infections, as the adhesion of microorganisms is typically the first step for the formation of biofilms. For instance, superhydrophobic surfaces have been shown to possess substantial anti-biofilm properties attributed to the presence of nanostructures. In this article, we provide an insight into the mechanisms underlying biofilm formation and their composition, as well as the applications of nanomaterials as superhydrophobic nanocoatings for the development of novel anti-biofilm therapies.

scholarly journals Insight into the effect of quinic acid on biofilm formed byStaphylococcus aureus

RSC Advances ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 3938-3945 ◽  
Author(s):  
Jin-Rong Bai ◽  
Yan-Ping Wu ◽  
Grosu Elena ◽  
Kai Zhong ◽  
Hong Gao
Keyword(s):  
Biofilm Formation ◽  
Quinic Acid ◽  
Biofilm Inhibition ◽  
Key Genes ◽  
Insight Into

QA effectively inhibitedS. aureusbiofilm formation. The key genes of biofilm inhibition induced by QA wereagrAandsarA.

Archaeal biofilms: widespread and complex

2013 ◽  
Vol 41 (1) ◽  
pp. 393-398 ◽  
Author(s):  
Sabrina Fröls
Keyword(s):  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Bacterial Species ◽  
Surface Adhesion ◽  
Form Complex ◽  
Abiotic Surfaces ◽  
Archaeal Species ◽  
Physical And Chemical ◽  
Insight Into ◽  
Mixed Communities

Biofilms or multicellular structures become accepted as the dominant microbial lifestyle in Nature, but in the past they were only studied extensively in bacteria. Investigations on archaeal monospecies cultures have shown that many archaeal species are able to adhere on biotic and abiotic surfaces and form complex biofilm structures. Biofilm-forming archaea were identified in a broad range of extreme and moderate environments. Natural biofilms observed are mostly mixed communities composed of archaeal and bacterial species of various abundances. The physiological functions of the archaea identified in such mixed communities suggest a significant impact on the biochemical cycles maintaining the flow and recycling of the nutrients on earth. Therefore it is of high interest to investigate the characteristics and mechanisms underlying the archaeal biofilm formation. In the present review, I summarize and discuss the present investigations of biofilm-forming archaeal species, i.e. their diverse biofilm architectures in monospecies or mixed communities, the identified EPSs (extracellular polymeric substances), archaeal structures mediating surface adhesion or cell–cell connections, and the response to physical and chemical stressors implying that archaeal biofilm formation is an adaptive reaction to changing environmental conditions. A first insight into the molecular differentiation of cells within archaeal biofilms is given.

scholarly journals Computational Insight into the Rope-Skipping Isomerization of Diarylether Cyclophanes

Symmetry ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2127
Author(s):  
Thomas J. Summers ◽  
Hrishikesh Tupkar ◽  
Tyler M. Ozvat ◽  
Zoë Tregillus ◽  
Kenneth A. Miller ◽  
...  
Keyword(s):  
Asymmetric Catalysis ◽  
Room Temperature ◽  
Chemical Bonds ◽  
Chiral Molecules ◽  
Free Energies ◽  
Design And Synthesis ◽  
The Impact ◽  
Rope Skipping ◽  
Temperature Factors ◽  
Insight Into

The restricted rotation of chemical bonds may lead to the formation of stable, conformationally chiral molecules. While the asymmetry in chiral molecules is generally observed in the presence of one or more stereocenters, asymmetry exhibited by conformational chirality in compounds lacking stereocenters, called atropisomerism, depends on structural and temperature factors that are still not fully understood. This atropisomerism is observed in natural diarylether heptanoids where the length of the intramolecular tether constrains the compounds to isolable enantiomers at room temperature. In this work, we examine the impact tether length has on the activation free energies to isomerization of a diarylether cyclophane substructure with a tether ranging from 6 to 14 carbons. Racemization activation energies are observed to decay from 48 kcal/mol for a 7-carbon tether to 9.2 kcal/mol for a 14-carbon tether. Synthetic efforts to experimentally test these constraints are also presented. This work will likely guide the design and synthesis of novel asymmetric cyclophanes that will be of interest in the catalysis community given the importance of atropisomeric ligands in the field of asymmetric catalysis.

scholarly journals Effect of Essential Oils on Growth Inhibition, Biofilm Formation and Membrane Integrity of Escherichia coli and Staphylococcus aureus

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1474
Author(s):  
Andrés Martínez ◽  
Marcela Manrique-Moreno ◽  
Maria C. Klaiss-Luna ◽  
Elena Stashenko ◽  
German Zafra ◽  
...  
Keyword(s):  
Essential Oils ◽  
Lipid Bilayers ◽  
Biofilm Formation ◽  
Method Development ◽  
Membrane Integrity ◽  
Thymus Vulgaris ◽  
Hydrophobic Core ◽  
Synthetic Membranes ◽  
E Coli ◽  
Microdilution Method

Biofilm as a cellular conformation confers survival properties to microbial populations and favors microbial resistance. Here, we investigated the antimicrobial, antibiofilm, antimotility, antihemolytic activity, and the interaction with synthetic membranes of 15 essential oils (EOs) on E. coli ATCC 25922 and S. aureus ATCC 29213. Antimicrobial activity of EOs was determined through microdilution method; development of the biofilm was assessed using the crystal violet assay and SEM microscopy. Results indicate that Lippia origanoides thymol–carvacrol II chemotype (LTC II) and Thymus vulgaris (TV) exhibited a significant antibacterial activity, with MIC values of 0.45 and 0.75 mg/mL, respectively. The percentage of biofilm formation inhibition was greater than 70% at subinhibitory concentrations (MIC50) for LTC II EO. The results demonstrate that these two oils had significantly reduced the hemolytic effect of S. aureus by 54% and 32%, respectively, and the mobility capacity by swimming in E. coli with percentages of decrease of 55% and 47%, respectively. The results show that LTC II and TV EOs can interact with the hydrophobic core of lipid bilayers and alter the physicochemical properties of membranes. The findings suggest that LTC II and TV oils may potentially be used to aid in the treatment of S. aureus and E. coli infections.

scholarly journals Biofilm formation by group A Streptococcus: a role for the streptococcal regulator of virulence (Srv) and streptococcal cysteine protease (SpeB)

Microbiology ◽  
2009 ◽  
Vol 155 (1) ◽  
pp. 46-52 ◽  
Author(s):  
Christopher D. Doern ◽  
Amity L. Roberts ◽  
Wenzhou Hong ◽  
Jessica Nelson ◽  
Slawomir Lukomski ◽  
...  
Keyword(s):  
Cysteine Protease ◽  
Biofilm Formation ◽  
Group A Streptococcus ◽  
Immunoblot Analysis ◽  
Wild Type ◽  
Flow Conditions ◽  
Group A ◽  
Streptococcus A ◽  
Insight Into ◽  
Western Immunoblot Analysis

Recently, biofilms have become a topic of interest in the study of the human pathogen group A Streptococcus (GAS). In this study, we sought to learn more about the make-up of these structures and gain insight into biofilm regulation. Enzymic studies indicated that biofilm formation by GAS strain MGAS5005 required an extracellular protein and DNA component(s). Previous results indicated that inactivation of the transcriptional regulator Srv in MGAS5005 resulted in a significant decrease in virulence. Here, inactivation of Srv also resulted in a significant decrease in biofilm formation under both static and flow conditions. Given that production of the extracellular cysteine protease SpeB is increased in the srv mutant, we tested the hypothesis that increased levels of active SpeB may be responsible for the reduction in biofilm formation. Western immunoblot analysis indicated that SpeB was absent from MGAS5005 biofilms. Complementation of MGAS5005Δsrv restored the biofilm phenotype and eliminated the overproduction of active SpeB. Inhibition of SpeB with E64 also restored the MGAS5005Δsrv biofilm to wild-type levels.

scholarly journals Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA

2019 ◽  
Vol 47 (21) ◽  
pp. 11069-11076 ◽  
Author(s):  
Jocelyne Vreede ◽  
Alberto Pérez de Alba Ortíz ◽  
Peter G Bolhuis ◽  
David W H Swenson
Keyword(s):  
Double Helix ◽  
Path Sampling ◽  
Important Process ◽  
Free Energies ◽  
Transition Path ◽  
Base Pairs ◽  
Transition Path Sampling ◽  
Insight Into ◽  
Adenine Base ◽  
Transition Interface

Abstract DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are difficult to investigate experimentally because they occur quickly, but only rarely. To gain insight into the mechanisms for this process, we performed transition path sampling simulations on a model nucleotide sequence in which an AT pair changes from WC to HG. This transition can occur in two ways, both starting with loss of hydrogen bonds in the base pair, followed by rotation around the glycosidic bond. In one route the adenine base converts from WC to HG geometry while remaining entirely within the double helix. The other route involves the adenine leaving the confines of the double helix and interacting with water. Our results indicate that this outside route is more probable. We used transition interface sampling to compute rate constants and relative free energies for the transitions between WC and HG. Our results agree with experiments, and provide highly detailed insights into the mechanisms of this important process.

The SagS sensory protein modulates biofilm formation and c-di-GMP levels by Pseudomonas aeruginosa in response to glucose-6-phosphate.

2020 ◽  
Author(s):  
Soyoung Park ◽  
Jozef Dingemans ◽  
Madison Gowett ◽  
Karin Sauer
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genetic Analysis ◽  
Signaling Pathway ◽  
Biofilm Formation ◽  
Phosphate Concentration ◽  
Dependent Manner ◽  
Diguanylate Cyclase ◽  
Swarming Motility ◽  
Two Component ◽  
Insight Into

<p>In <em>Pseudomonas aeruginosa</em>, the orphan two-component sensor SagS contributes to both, the transition to biofilm formation and to biofilm cells gaining their heightened tolerance to antimicrobials. However, little is known about the identity of the signals or conditions sensed by SagS to induce the switch to the sessile, drug tolerant mode of growth. Using a modified Biolog phenotype assay to screen for compounds that modulate attachment in a SagS-dependent manner, we identified glucose-6-phosphate to enhance attachment in a manner dependent on the glucose-6-phosphate concentration and SagS. The stimulatory effect was not limited to the attachment as glucose-6-phosphate likewise enhanced biofilm formation. We show that exposure to glucose-6-phosphate results in decreased swarming motility but increased cellular c-di-GMP levels in biofilms. Genetic analysis indicated that the diguanylate cyclase NicD is an activator of biofilm formation and is not only required for enhanced biofilm formation in response to glucose-6-phosphate but also interacts with SagS. Our findings indicate glucose-6-phosphate to likely mimic a signal or conditions sensed by SagS to activate its motile-sessile switch function. Additionally, our findings provide new insight into the interfaces between the ligand-mediated TCS signaling pathway and c-di-GMP levels.</p>

scholarly journals Lessons in Fundamental Mechanisms and Diverse Adaptations from the 2015 Bacterial Locomotion and Signal Transduction Meeting

2015 ◽  
Vol 197 (19) ◽  
pp. 3028-3040 ◽  
Author(s):  
Birgit M. Prüβ ◽  
Jun Liu ◽  
Penelope I. Higgs ◽  
Lynmarie K. Thompson
Keyword(s):  
Signal Transduction ◽  
Biofilm Formation ◽  
Cell Biology ◽  
Bacterial Species ◽  
Interacting Proteins ◽  
Mathematical Methods ◽  
Detailed Understanding ◽  
Rapid Changes ◽  
Functional Mechanisms ◽  
Insight Into

In response to rapid changes in their environment, bacteria control a number of processes, including motility, cell division, biofilm formation, and virulence. Research presented in January 2015 at the biennial Bacterial Locomotion and Signal Transduction (BLAST) meeting in Tucson, AZ, illustrates the elegant complexity of the nanoarrays, nanomachines, and networks of interacting proteins that mediate such processes. Studies employing an array of biophysical, genetic, cell biology, and mathematical methods are providing an increasingly detailed understanding of the mechanisms of these systems within well-studied bacteria. Furthermore, comparisons of these processes in diverse bacterial species are providing insight into novel regulatory and functional mechanisms. This review summarizes research presented at the BLAST meeting on these fundamental mechanisms and diverse adaptations, including findings of importance for applications involving bacteria of medical or agricultural relevance.

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