pinecone/core-2020-05-10-deduplication huggingface dataset:
Cosolvent, ions, and temperature effects on the structural properties of cecropin A-Magainin 2 hybrid peptide in solutions

Antimicrobial peptides are promising alternative to traditional antibiotics and antitumor drugs for the battle against new antibiotic resistant bacteria strains and cancer maladies. The study of their structural and dynamics properties at physiological conditions can help to understand their stability, delivery mechanisms, and activity in the human body. In this article, we have used molecular dynamics simulations to study the effects of solvent environment, temperature, ions concentration, and peptide concentration on the structural properties of the antimicrobial hybrid peptide Cecropin A–Magainin 2. In TFE/water mixtures, the structure of the peptide retained α-helix contents and an average hinge angle in close agreement with the experimental NMR and CD measurements reported in literature. Compared to the TFE/water mixture, the peptide simulated at the same ionic concentration lost most of its α-helix structure. The increase of peptide concentration at both 300 and 310 K resulted in the peptide aggregation. The peptides in the complex retained the initial N-ter α-helix segment during all the simulation. The α-helix stabilization is further enhanced in the high salt concentration simulations. The peptide aggregation was not observed in TFE/water mixture simulations and, the peptide aggregate, obtained from the water simulation, simulated in the same conditions did dissolve within few tens of nanoseconds. The results of this study provide insights at molecular level on the structural and dynamics properties of the CA-MA peptide at physiological and membrane mimic conditions that can help to better understand its delivery and interaction with biological interfaces. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 1–14, 201
Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in hela cells

Binding of polo-like kinase 1 (Plk1) polo-box domains (PBDs) to phosphothreonine (pThr)/phosphoserine (pSer)-containing sequences is critical for the proper function of Plk1. Although high-affinity synthetic pThr-containing peptides provide starting points for developing PBD-directed inhibitors, to date the efficacy of such peptides in whole cell assays has been poor. This potentially reflects limited cell membrane permeability arising, in part, from the di-anionic nature of the phosphoryl group or its mimetics. In our current article we report the unanticipated on-resin N(τ)-alkylation of histidine residues already bearing a N(π)- alkyl group. This resulted in cationic imidazolium-containing pThr peptides, several of which exhibit single-digit nanomolar PBD-binding affinities in extracellular assays and improved antimitotic efficacies in intact cells. We enhanced the cellular efficacies of these peptides further by applying bio-reversible pivaloyloxymethyl (POM) phosphoryl protection. New structural insights presented in our current study, including the potential utility of intramolecular charge masking, may be useful for the further development of PBD-binding peptides and peptide mimetics.National Institutes of Health (U.S.) (Grants ES015339 and GM104047
Meeting report: SMART timing—principles of single molecule techniques course at the University of Michigan 2014

Four days after the announcement of the 2014 Nobel Prize in Chemistry for “the development of super‐resolved fluorescence microscopy” based on single molecule detection, the Single Molecule Analysis in Real‐Time (SMART) Center at the University of Michigan hosted a “Principles of Single Molecule Techniques 2014” course. Through a combination of plenary lectures and an Open House at the SMART Center, the course took a snapshot of a technology with an especially broad and rapidly expanding range of applications in the biomedical and materials sciences. Highlighting the continued rapid emergence of technical and scientific advances, the course underscored just how brightly the future of the single molecule field shines. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 296–302, 2015
Modification of Daunorubicin-GnRH-III Bioconjugates With Oligoethylene Glycol Derivatives to Improve Solubility and Bioavailability for Targeted Cancer Chemotherapy

Daunorubicin-GnRH-III bioconjugates have recently been developed as drug delivery systems\ud
with potential applications in targeted cancer chemotherapy. In order to improve their\ud
biochemical properties, several strategies have been pursued: (1) incorporation of an\ud
enzymatic cleavable spacer between the anticancer drug and the peptide-based targeting\ud
moiety, (2) peptide modification by short chain fatty acids or (3) attachment of two anticancer\ud
drugs to the same GnRH-III derivative. Although these modifications led to more potent\ud
bioconjugates, a decrease in their solubility was observed. Here we report on the design,\ud
synthesis and biochemical characterization of daunorubicin-GnRH-III bioconjugates with\ud
increased solubility, which could be achieved by incorporating oligoethylene glycol-based\ud
spacers in their structure. First, we have evaluated the effect of an oligoethylene glycol-based\ud
spacer on the solubility, enzymatic stability/degradation, cellular uptake and in vitro cytostatic\ud
effect of a bioconjugate containing only one daunorubicin attached through a GFLG\ud
tetrapeptide spacer to the GnRH-III targeting moiety. Thereafter, more complex compounds\ud
containing two copies of daunorubicin, GFLG spacers as well as Lys(nBu) in position 4 of\ud
GnRH-III were synthesized and biochemically characterized. Our results indicated that all\ud
synthesized oligoethylene glycol-containing bioconjugates had higher solubility in cell culture\ud
medium than the unmodified analogs. They were degraded in the presence of rat liver\ud
lysosomal homogenate leading to the formation of small drug containing metabolites. In the\ud
case of bioconjugates containing two copies of daunorubicin, the incorporation of\ud
oligoethylene glycol-based spacers led to increased in vitro cytostatic effect on MCF-7 human\ud
breast cancer cells
Neighbor-directed histidine N (τ)-alkylation: A route to imidazolium-containing phosphopeptide macrocycles

Our recently discovered, selective, on-resin route to N(τ)-alkylated imidazolium-containing histidine residues affords new strategies for peptide mimetic design. In this, we demonstrate the use of this chemistry to prepare a series of macrocyclic phosphopeptides, in which imidazolium groups serve as ring-forming junctions. Interestingly, these cationic moieties subsequently serve to charge-mask the phosphoamino acid group that directed their formation. Neighbor-directed histidine N(τ)-alkylation opens the door to new families of phosphopeptidomimetics for use in a range of chemical biology contexts.National Institutes of Health (U.S.) (Grants ES015339 and GM104047
Effects of linker sequence modifications on the structure, stability and biological activity of a cyclic α-conotoxin

The cyclic conotoxin analogue cVc1.1 is a promising lead molecule for the development of new treatments for neuropathic and chronic pain. The design of this peptide includes a linker sequence that joins the N and C termini together, improving peptide stability while maintaining the structure and activity of the original linear Vc1.1. The effect of linker length on the structure, activity and stability of cyclised conotoxins has been studied previously but the effect of altering the composition of the linker sequence has not been investigated. In this study, we designed three analogues of cVc1.1 with linker sequences that varied in charge, hydrophobicity and hydrogen bonding capacity and examined the effect on structure, stability, membrane permeability and biological activity. The three designed peptides were successfully synthesized using solid phase peptide synthesis approaches and had similar structures and stability compared with cVc1.1. Despite modifications in charge, hydrophobicity and hydrogen bonding potential, which are all factors that can affect membrane permeability, no changes in the ability of the peptides to pass through membranes in either PAMPA or Caco-2 cell assay were observed. Surprisingly, modification of the linker sequence was deleterious to biological activity. These results suggest the linker sequence might be a useful part of the molecule for optimization of bioactivity and not just the physiochemical properties of cVc1.1
Cyclic peptide oral bioavailability: lessons from the past

Achieving high oral bioavailability for drugs is a key design objective in drug development. It is not surprising then that with the growing expectation of peptides as future drugs, there has also been an increasing interest in developing oral peptide therapeutics. Brought to the fore are questions such as what makes peptides orally bioavailable and how this can be achieved; questions which have inspired research into the area for decades. Early research in the area focused on linear peptides with more recent literature focusing on cyclic peptides, motivated in part by cyclic peptides like cyclosporine A that have demonstrated drug-like oral bioavailability. In this review, we take a look at research on the oral bioavailability of peptides, focusing on factors that affect passive permeability
Discovery, isolation and structural characterization of cyclotides from Viola sumatrana miq

Cyclotides are cyclic peptides from plants in the Violaceae, Rubiaceae, Fabaceae, Cucurbitaceae, and Solanaceae families. They are sparsely distributed in most of these families, but appear to be ubiquitous in the Violaceae, having been found in every plant so far screened from this family. However, not all geographic regions have been examined and here we report the discovery of cyclotides from a Viola species from South-East Asia. Two novel cyclotides (Visu 1 and Visu 2) and two known cyclotides (kalata S and kalata B1) were identified in V. sumatrana. NMR studies revealed that kalata S and kalata B1 had similar secondary structures. Their biological activities were determined in cytotoxicity assays; both had similar cytotoxic activity and were more toxic to U87 cells compared with other cell lines. Overall, the study strongly supports the ubiquity of cyclotides in the Violaceae and adds to our understanding of their distribution and cytotoxic activity
Ocellatin-PT antimicrobial peptides: high-resolution microscopy studies in antileishmania models and interactions with mimetic membrane systems

Although the mechanism of action of antimicrobial peptides (AMPs) is not clear, they can interact electrostatically with the cell membranes of microorganisms. New ocellatin-PT peptides were recently isolated from the skin secretion of Leptodactylus pustulatus. The secondary structure of these AMPs and their effect on Leishmania infantum cells, and on different lipid surface models was characterized in this work. The results showed that all ocellatin-PT peptides have an -helix structure and five of them (PT3, PT4, PT6 to PT8) have leishmanicidal activity; PT1 and PT2 affected the cellular morphology of the parasites and showed greater affinity for leishmania and bacteria-mimicking lipid membranes than for those of mammals. The results show selectivity of ocellatin-PTs to the membranes of microorganisms and the applicability of biophysical methods to clarify the interaction of AMPs with cell membranes.This work was partially supported by grants from INCT Nanobiotecnologia and PVE Project (MCT/CNPq), the Consejo Nacional de Investigaciones Cientiﬁcas y Técnicas (CONICET), and the Agencia Nacional de Promocion Cientíﬁca y Tecnologica (ANPCyT). M.M.M.is a researcher at CONICET. This work has also been supported through project UID/MULTI/04378/2013-POCI/01/0145/FEDER/007728 with ﬁnancial support from FCT/MEC through national funds and co-ﬁnanced by FEDER, under the Partnership Agreement PT2020. Scanning electron microscopy was carried out at Centro de Materiais da Universidade do Porto, CEMUP. Peter Eaton is supported by a Ciência sem Fronteiras grant via CNPq, and his lab work is supported by ﬁnancial support from FCT/MEC through national funds and co-ﬁnanced by FEDER, under the partnership agreement PT2020. Alexandra Pl acido and Ana Georgina Gomes-Alves are grateful to FCT for their grants SFRH/BD/97995/2013 and SFRH/BD/93766/2013, ﬁnanced by POPH–QREN–Tipologia 4.1–Formação Avançada, subsidized by Fundo Social Europeu and Ministério da Ciência, Tecnologia e Ensino Superior. Nuno Vale thanks Programa Operacional Regional do Norte (ON.2) and Faculdade de Ciências da Universidade do Porto (FCUP) for co-funding refurbishment of the Porto Peptide Synthesis Facility (POPUP) through operation NORTE-07-0162-FEDER000111. NV thanks Fundação para a Ciência e Tecnologia (FCT, Portugal) and FEDER (European Union) for funding through project grant IF/00092/2014. Work in AMT laboratory was supported by Project “NORTE-07-0124-FEDER-000002-Host-Pathogen Interactions” cofunded by Programa Operacional Regional do Norte under QREN, through FEDER and FCT. None of the funding bodies were involved in study design, in the collection, analysis and interpretation of data; in the writing of the report; or in the decision to submit the article for publication
Log D versus HPLC derived hydrophobicity : the development of predictive tools to aid in the rational design of bioactive peptoids.

Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP-HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. By comparing log D and average hydrophobicities we highlight the potential advantage of employing the former as a predictive tool in the rational design of biologically active peptoids. This article is protected by copyright
Activity of synthetic peptides against Chlamydia

The in vitro activity of six synthetic peptides against 36 strains of Chlamydia from different origins was investigated. Clavanin MO proved to be the most active peptide, reducing the inclusion number of all Chlamydia strains from 8 different species tested by ≥50% at 10 μg.ml-1. Mastoparan L showed an equal activity against C. trachomatis, C. pneumoniae, C. suis and C. muridarum, but did not exert any inhibitory effect against C. psittaci, C. pecorum, C. abortus and C. avium even at 80 μg.ml-1. These data suggest that clavanin MO could be a promising compound in the prevention and treatment of chlamydial infections
Thermal melt circular dichroism spectroscopic studies for identifying stabilising amphipathic molecules for the voltage-gated sodium channel NavMs

Purified integral membrane proteins require amphipathic molecules to maintain their solubility in aqueous solutions. These complexes, in turn, are used in studies to characterise the protein structures by a variety of biophysical and structural techniques, including spectroscopy, crystallography, and cryo‐electron microscopy. Typically the amphilphiles used have been detergent molecules, but more recently they have included amphipols, which are polymers of different sizes and compositions designed to create smaller, more well‐defined solubilised forms of the membrane proteins. In this study we used circular dichroism spectroscopy to compare the secondary structures and thermal stabilities of the NavMs voltage‐gated sodium channel in different amphipols and detergents as a means of identifying amphipathic environments that maximally maintain the protein structure whilst providing a stabilising environment. These types of characterisations also have potential as means of screening for sample types that may be more suitable for crystallisation and/or cryo‐electron microscopy structure determinations
Physicochemical characterization and antimicrobial properties of rhamnolipids produced by Pseudomonas aeruginosa 47T2 NCBIM 40044

7 pages, 2 figures, 3 tables.-- PMID: 12474254 [PubMed].-- Available online Dec 3, 2002.Pseudomonas aeruginosa 47T2, grown in submerged culture with waste frying oil as a carbon source, produced a mixture of rhamnolipids with surface activity. Up to 11 rhamnolipid homologs (Rha-Rha-C8-C10; Rha-C10-C8/Rha-C8-C10;Rha-Rha-C8-C12:1; Rha-Rha-C10-C10; Rha-Rha-C10-C12:1; Rha-C10-C10; Rha-Rha-C10-C12/Rha-Rha-C12-C10; Rha-C10-C12:1/Rha-C12:1-C10; Rha-Rha-C12:1-C12; Rha-Rha-C10-C14:1; Rha-C10-C12/Rha-C12-C10) were isolated from cultures of P. aeruginosa 47T2 from waste frying oil and identified by HPLC-MS analysis. This article deals with the production, isolation, and chemical characterization of the rhamnolipid mixture RL47T2. The physicochemical and biological properties of RL47T2 as a new product were also studied. Its surface tension decreased to 32.8 mN/m; and the interfacial tension against kerosene to 1 mN/m. The critical micellar concentration for RL47T2 was 108.8 mg/mL. The product showed excellent antimicrobial properties. Antimicrobial activity was evaluated according to the minimum inhibitory concentration (MIC), the lowest concentration of an antimicrobial agent that inhibits development of visible microbial growth. Low MIC values were found for bacteria Serratia marcescens (4 g/mL), Enterobacter aerogenes (8 g/mL), Klebsiella pneumoniae (0.5 g/mL), Staphylococcus aureus and Staphylococcus epidermidis (32 g/mL), Bacillus subtilis (16 g/mL), and phytopathogenic fungal species: Chaetonium globosum (64 g/mL), Penicillium funiculosum (16 g/mL), Gliocadium virens (32 g/mL) and Fusarium solani (75 g/mL).Finnancial support by the CIRIT and CICYT; Grant Number: 199956R 00024, PPQ-2000-0105-P4-03, REN 2001-3224.Peer reviewe
Combined In-Fermenter Extraction and Cross-Flow Microfiltration for Improved Inclusion Body Processing

In this study we demonstrate a new in-fermenter chemical extraction procedure that degrades the cell wall of Escherichia coli and releases inclusion bodies (IBs) into the fermentation medium. We then prove that cross-flow microfiltration can be used to remove 91% of soluble contaminants from the released IBs. The extraction protocol, based on a combination of Triton X-100, EDTA, and intracellular T7 lysozyme, effectively released most of the intracellular soluble content without solubilising the IBs. Cross-flow microfiltration using a 0.2 m ceramic membrane successfully recovered the granulocyte macrophage-colony stimulating factor (GM-CSF) IBs with removal of 91% of the soluble contaminants and virtually no loss of IBs to the permeate. The filtration efficiency, in terms of both flux and transmission, was significantly enhanced by in-fermenter BenzonaseÂ® digestion of nucleic acids following chemical extraction. Both the extraction and filtration methods exerted their efficacy directly on a crude fermentation broth, eliminating the need for cell recovery and resuspension in buffer. The processes demonstrated here can all be performed using just a fermenter and a single cross-flow filtration unit, demonstrating a high level of process intensification. Furthermore, there is considerable scope to also use the microfiltration system to subsequently solubilise the IBs, to separate the denatured protein from cell debris, and to refold the protein using diafiltration. In this way refolded protein can potentially be obtained, in a relatively pure state, using only two unit operations
Pediocin production by Pediococcus acidilactici in solid state culture on a waste medium: Process simulation and experimental results

7 páginas, 6 figurasThe production of pediocin by Pediococcus acidilactici was comparatively studied in submerged and solid-state culture, using polyurethane foam particles soaked in commercial (MRS) and waste media with various supplements, where product concentrations were 15 times higher in MRS medium. For the solid state analysis, cultures were treated by successive compression and refilling of tubular minireactors equipped with a piston, without the need for reinoculation. This method was found to be simple, reproducible, and easily controllable, allowing culture productivity to be maintained for long periods of time without alterations in the basic properties of the system. In addition, yields were found to be superior compared to those from submerged culture. The system kinetics were modeled on the basis of widely accepted assumptions with a good fit to the experimental results and observed biomass fluctuations less evident than those predicted by the kinetic modelPeer reviewe
Haloalkane hydrolysis by Rhodococcus erythropolis cells: Comparison of conventional aqueous phase dehalogenation and nonconventional gas phase dehalogenation

Biofiltration of air polluted by volatile organic compounds is now recognized by the industrial and research communities as an effective and viable alternative to standard environmental technologies. Whereas many studies have focused on solid/liquid/gas biofilters, there have been fewer reports on waste air treatment using other biological processes, especially in a solid/gas biofilter. In this study, a comparison was made of the hydrolysis of\ud
halogenated compounds (such as 1-chlorobutane) by lyophilized Rhodococcus erythropolis cells in a novel solid/\ud
gas biofilter and in the aqueous phase. We first determined\ud
the culture conditions for the production of R. erythropolis\ud
cells with a strong dehalogenase activity. Four different\ud
media were studied and the amount of 1-chlorobutane\ud
was optimized. Next, we report the possibility to use\ud
R. erythropolis cells in a solid/gas biofilter in order to\ud
transform halogenated compounds in corresponding alcohols.\ud
The effect of experimental parameters (total flow into\ud
the biofilter, thermodynamic activity of the substrates,\ud
temperature, carbon chain length of halogenated substrates)\ud
on the activity and stability of lyophilized cells in\ud
the gas phase was determined. A critical water thermodynamic\ud
activity (aw) of 0.4 is necessary for the enzyme to\ud
become active and optimal dehalogenase activity for the\ud
lyophilized cells is obtained for an aw of 0.9. A temperature\ud
of reaction of 40jC represents the best compromise\ud
between stability and activity. Activation energy of the\ud
reaction was determined and found equal to 59.5 KJ/mol.\ud
The pH effect on the dehalogenase activity of R. erythropolis cells was also studied in the gas phase and in the aqueous phase. It was observed that pH 9.0 provided the best activity in both systems. We observed that in the aqueous phase R. erythropolis cells were less sensitive to\ud
the variation in pH than R. erythropolis cells in the gas\ud
phase. Finally, the addition of volatile Lewis base (triethylamine) in the gaseous phase and the action of the lysozyme in order to permeabilize the cells was found to be highly beneficial to the effectiveness of the biofilter