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Model amphipathic peptide

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https://www.readbyqxmd.com/read/29780514/construction-of-histidine-containing-hydrocarbon-stapled-cell-penetrating-peptides-for-in-vitro-and-in-vivo-delivery-of-sirnas
#1
Soonsil Hyun, Yoonhwa Choi, Ha Neul Lee, Changki Lee, Donghoon Oh, Dong-Ki Lee, Changjin Lee, Yan Lee, Jaehoon Yu
A hydrocarbon stapled peptide based strategy was used to develop an optimized cell penetrating peptide for siRNA delivery. Various stapled peptides, having amphipathic Leu- and Lys-rich regions, were prepared and their cell penetrating potentials were evaluated. One peptide, stEK, was found to have high cell penetration and siRNA delivery abilities at low nanomolar concentrations. In order to improve its ability to promote gene silencing, stEK was modified by replacing several Lys residues with His moieties...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29742406/membrane-curvature-sensing-by-amphipathic-helices-insights-from-implicit-membrane-modeling
#2
Binod Nepal, John Leveritt, Themis Lazaridis
Sensing and generation of lipid membrane curvature, mediated by the binding of specific proteins onto the membrane surface, play crucial roles in cell biology. A number of mechanisms have been proposed, but the molecular understanding of these processes is incomplete. All-atom molecular dynamics simulations have offered valuable insights but are extremely demanding computationally. Implicit membrane simulations could provide a viable alternative, but current models apply only to planar membranes. In this work, the implicit membrane model 1 is extended to spherical and tubular membranes...
May 8, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29737852/cooperative-modes-of-action-of-antimicrobial-peptides-characterized-with-atomistic-simulations-a-study-on-cecropin-b
#3
Ya-Wen Hsiao, Magnus Hedström, Valeria Losasso, Sebastian Metz, Jason Crain, Martyn D Winn
Antimicrobial peptides (AMPs) are widely-occurring host defense agents, of interest as one route for addressing the growing problem of multidrug-resistant pathogens. Understanding the mechanisms behind their anti-pathogen activity is instrumental in designing new AMPs. Herein, we present an all-atom molecular dynamics and free energy study on cecropin B (CB), and its constituent domains. We find a cooperative mechanism in which CB inserts into an anionic model membrane with its amphipathic N-terminal segment, supported by the hydrophobic C-terminal segment of a second peptide...
May 8, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29679519/designing-anticancer-peptides-by-constructive-machine-learning
#4
Francesca Grisoni, Claudia Neuhaus, Gisela Gabernet, Alex Müller, Jan Hiss, Gisbert Schneider
Constructive machine learning enables the automated generation of novel chemical structures without the need for explicit molecular design rules. This study presents the experimental application of such a generative model to design membranolytic anticancer peptides (ACPs) de novo. A recurrent neural network with long short-term memory cells was trained on alpha-helical cationic amphipathic peptide sequences and then fine-tuned with 26 known ACPs. This optimized model was used to generate unique and novel amino acid sequences...
April 21, 2018: ChemMedChem
https://www.readbyqxmd.com/read/29670065/biophysical-investigations-elucidating-the-mechanisms-of-action-of-antimicrobial-peptides-and-their-synergism
#5
REVIEW
Arnaud Marquette, Burkhard Bechinger
Biophysical and structural investigations are presented with a focus on the membrane lipid interactions of cationic linear antibiotic peptides such as magainin, PGLa, LL37, and melittin. Observations made with these peptides are distinct as seen from data obtained with the hydrophobic peptide alamethicin. The cationic amphipathic peptides predominantly adopt membrane alignments parallel to the bilayer surface; thus the distribution of polar and non-polar side chains of the amphipathic helices mirror the environmental changes at the membrane interface...
April 18, 2018: Biomolecules
https://www.readbyqxmd.com/read/29652823/molecular-dynamics-simulations-of-human-antimicrobial-peptide-ll-37-in-model-popc-and-popg-lipid-bilayers
#6
Liling Zhao, Zanxia Cao, Yunqiang Bian, Guodong Hu, Jihua Wang, Yaoqi Zhou
Cathelicidins are a large family of cationic antimicrobial peptides (AMPs) found in mammals with broad spectrum antimicrobial activity. LL-37 is the sole amphipathic α-helical AMP from human Cathelicidins family. In addition to its bactericidal capability, LL-37 has antiviral, anti-tumor, and immunoregulatory activity. Despite many experimental studies, its molecular mechanism of action is not yet fully understood. Here, we performed three independent molecular dynamics simulations (600 ns or more) of a LL-37 peptide in the presence of 256 lipid bilayers with 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphoglycerol (POPG) mimicking bacterial and 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) mimicking mammalian membranes...
April 13, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29652473/a-smart-photosensitizer-tumor-triggered-oncotherapy-by-self-assembly-photodynamic-nanodots
#7
Yuhua Jia, Jinyu Li, Jincan Chen, Ping Hu, Longguang Jiang, Xueyuan Chen, Mingdong Huang, Zhuo Chen, Peng Xu
Clinical photosensitizers suffer from the disadvantages of fast photobleaching and high systemic toxicities due to the off-target photodynamic effects. To address these problems, we report a self-assembled pentalysine-phthalocyanine assembly nanodots (PPAN) fabricated by an amphipathic photosensitizer-peptide conjugate. We triggered the PDT effects of photosensitizers by precisely controlling the assembly and disintegration of the nanodots. In physiological aqueous conditions, PPAN exhibited a size-tunable spherical conformation with a highly positive shell of the polypeptides and a hydrophobic core of the π-stacking Pc moieties...
April 13, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29589536/cryptic-antimicrobial-peptides-identification-methods-and-current-knowledge-of-their-immunomodulatory-properties
#8
Elio Pizzo, Valeria Cafaro, Alberto Di Donato, Eugenio Notomista
Cationic antimicrobial peptides (CAMPs), also known as host defence peptides (HDPs), are essential evolutionarily conserved components of innate immunity, constitutively or inducibly expressed in response to invasion by pathogens. In addition to a direct antimicrobial action, they are able to synergistically operate with other defence molecules to combat infection by neutralization of endotoxins, chemokine-like activities, induction of angiogenesis and wound repair. The importance of CAMPs has been highlighted in animal models and supported by observations in patient studies...
March 27, 2018: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/29550289/penetration-in-3d-tumor-spheroids-and-explants-adding-a-further-dimension-to-the-structure-activity-relationship-of-cell-penetrating-peptides
#9
Dirk van den Brand, Cornelia Veelken, Leon Massuger, Roland Brock
Drug delivery into tumors and metastases is a major challenge in the eradication of cancers such as epithelial ovarian carcinoma. Cationic cell-penetrating peptides (CPPs) are a promising group of delivery vehicles to mediate cellular entry of molecules that otherwise poorly enter cells. However, little is known about their penetration behavior in tissues. Here, we investigated penetration of cationic CPPs in 3D ovarian cancer spheroids and patient-derived 3D tumor explants. Penetration kinetics and distribution after long-term incubation were imaged by confocal microscopy...
June 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29541273/protection-efficacy-of-c5a-against-vaginal-and-rectal-hiv-challenges-in-humanized-mice
#10
Philippe A Gallay, Udayan Chatterji, Aaron Kirchhoff, Angel Gandarilla, Richard B Pyles, Marc M Baum, John A Moss
Introduction: In the absence of a vaccine, there is an urgent need for the identification of effective agents that prevent HIV transmission in uninfected individuals. Non-vaccine Biomedical Prevention (nBP) methods, such as topical or systemic pre-exposure prophylaxis (PrEP), are promising strategies to slow down the spread of AIDS. Methods: In this study, we investigated the microbicidal efficacy of the viral membrane-disrupting amphipathic SWLRDIWDWICEVLSDFK peptide called C5A...
2018: Open Virology Journal
https://www.readbyqxmd.com/read/29537020/characterization-of-the-structural-ensembles-of-p53-tad2-by-molecular-dynamics-simulations-with-different-force-fields
#11
Yanhua Ouyang, Likun Zhao, Zhuqing Zhang
Intrinsically disordered regions (IDRs) or proteins (IDPs), which play crucial biological functions in essential biological processes of life, do not have well-defined secondary or tertiary structures when isolated in solution. The highly dynamic properties and conformational heterogeneity of IDPs make them challenging to study with traditional experimental techniques. As a powerful complementary tool for experiments, all-atom molecular dynamics simulation can obtain detailed conformational information on IDPs, but the limitation of force field accuracy is a challenge for reproducing IDP conformers...
March 28, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29501607/the-n-terminal-amphipathic-helix-of-pex11p-self-interacts-to-induce-membrane-remodelling-during-peroxisome-fission
#12
Juanjuan Su, Ann S Thomas, Tanja Grabietz, Christiane Landgraf, Rudolf Volkmer, Siewert J Marrink, Chris Williams, Manuel N Melo
Pex11p plays a crucial role in peroxisome fission. Previously, it was shown that a conserved N-terminal amphipathic helix in Pex11p, termed Pex11-Amph, was necessary for peroxisomal fission in vivo while in vitro studies revealed that this region alone was sufficient to bring about tubulation of liposomes with a lipid consistency resembling the peroxisomal membrane. However, molecular details of how Pex11-Amph remodels the peroxisomal membrane remain unknown. Here we have combined in silico, in vitro and in vivo approaches to gain insights into the molecular mechanisms underlying Pex11-Amph activity...
June 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29393934/the-interfacial-electrostatic-potential-modulates-the-insertion-of-cell-penetrating-peptides-into-lipid-bilayers
#13
Matías A Via, Joaquín Klug, Natalia Wilke, Luis S Mayorga, M G Del Pópolo
Cell-penetrating peptides (CPP) are short sequences of cationic amino-acids that show a surprising ability to traverse lipid bilayers. CPP are considered to be some of the most effective vectors to introduce membrane-impermeable cargos into cells, but the molecular basis of the membrane translocation mechanisms and its dependence on relevant membrane physicochemical properties have yet to be fully determined. In this paper we resort to Molecular Dynamics simulations and experiments to investigate how the electrostatic potential across the lipid/water interface affects the insertion of hydrophilic and amphipathic CPP into two-dimensional lipid structures...
February 14, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29388242/large-scale-ab-initio-modeling-of-structurally-uncharacterized-antimicrobial-peptides-reveals-known-and-novel-folds
#14
Mara Kozic, Stephen J Fox, Jens M Thomas, Chandra S Verma, Daniel J Rigden
Antimicrobial resistance within a wide range of infectious agents is a severe and growing public health threat. Antimicrobial peptides (AMPs) are among the leading alternatives to current antibiotics, exhibiting broad spectrum activity. Their activity is determined by numerous properties such as cationic charge, amphipathicity, size, and amino acid composition. Currently, only around 10% of known AMP sequences have experimentally solved structures. To improve our understanding of the AMP structural universe we have carried out large scale ab initio 3D modeling of structurally uncharacterized AMPs that revealed similarities between predicted folds of the modeled sequences and structures of characterized AMPs...
May 2018: Proteins
https://www.readbyqxmd.com/read/29355319/recurrent-neural-network-model-for-constructive-peptide-design
#15
Alex T Müller, Jan A Hiss, Gisbert Schneider
We present a generative long short-term memory (LSTM) recurrent neural network (RNN) for combinatorial de novo peptide design. RNN models capture patterns in sequential data and generate new data instances from the learned context. Amino acid sequences represent a suitable input for these machine-learning models. Generative models trained on peptide sequences could therefore facilitate the design of bespoke peptide libraries. We trained RNNs with LSTM units on pattern recognition of helical antimicrobial peptides and used the resulting model for de novo sequence generation...
February 26, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29329747/antibacterial-properties-of-latarcin-1-derived-cell-penetrating-peptides
#16
Deepthi Poornima Budagavi, Archana Chugh
Cell-penetrating peptides (CPPs) and antimicrobial peptides (AMPs) share certain physicochemical parameters such as amphipathicity, hydrophobicity, cationicity and pI, due to which these two groups of peptides also exhibit overlapping functional characteristics. In our current work, we have evaluated antimicrobial properties of cell-penetrating peptides derived from Latarcin1. Latarcin derived peptide (LDP) exhibited antimicrobial activity against representative microorganisms tested and bactericidal effect against methicillin resistant Staphylococcus aureus (MRSA), which was used as model organism of study in the present work...
March 30, 2018: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29306631/peptide-retention-time-prediction-in-hydrophilic-interaction-liquid-chromatography-comparison-of-separation-selectivity-between-bare-silica-and-bonded-stationary-phases
#17
Victor Spicer, Oleg V Krokhin
Peptide separation selectivity of four different HILIC sorbents was compared through the development of sequence-specific retention prediction algorithms for the datasets of 36-40 thousands peptides each. Hydrophilicity of these sorbents at pH 4.5 (peptide retention under acetonitrile:water gradients) increases in the following order: Luna HILIC < XBridge Amide < Atlantis Silica ∼ Luna HILIC Silica. Bare silica phases are characterized by higher retention coefficients for basic residues (Arg, Lys, His), while interactions with neutral HILIC phases is driven by interaction with the charged residues (Asp, Glu, Arg, Lys, His)...
January 26, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29273750/elimination-of-antibiotic-resistant-surgical-implant-biofilms-using-an-engineered-cationic-amphipathic-peptide-wlbu2
#18
Jonathan B Mandell, Berthony Deslouches, Ronald C Montelaro, Robert M Q Shanks, Yohei Doi, Kenneth L Urish
Antibiotics are unable to remove biofilms from surgical implants. This high antibiotic tolerance is related to bacterial persisters, a sub-population of bacteria phenotypically tolerant to antibiotics secondary to a reduced metabolic state. WLBU2 is an engineered cationic amphipathic peptide designed to maximize antimicrobial activity with minimal mammalian cell toxicity. The objective of this study was to test the ability of WLBU2 to remove Staphylococcus aureus surgical implant biofilms. WLBU2 effectively treated S...
December 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29212939/the-heptad-repeat-c-domain-of-the-respiratory-syncytial-virus-fusion-protein-plays-a-key-role-in-membrane-fusion
#19
Imogen M Bermingham, Keith J Chappell, Daniel Watterson, Paul R Young
Respiratory syncytial virus (RSV) mediates host cell entry through the fusion (F) protein, which undergoes a conformational change to facilitate the merger of viral and host lipid membrane envelopes. The RSV F protein comprises a trimer of disulfide-bonded F1 and F2 subunits that is present on the virion surface in a metastable prefusion state. This prefusion form is readily triggered to undergo refolding to bring two heptad repeats (heptad repeat A [HRA] and HRB) into close proximity to form a six-helix bundle that stabilizes the postfusion form and provides the free energy required for membrane fusion...
February 15, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29090725/arginine-modification-of-lycosin-i-to-improve-inhibitory-activity-against-cancer-cells
#20
Peng Zhang, Jing Ma, Yujie Yan, Bo Chen, Bobo Liu, Cui Jian, Baode Zhu, Songping Liang, Youlin Zeng, Zhonghua Liu
Lycosin-I is a linear amphipathic α-helical anticancer peptide (ACP) extracted from the spider Lycosa singoriensis, which can activate the mitochondrial death pathway to induce apoptosis in tumor cells and up-regulate p27 to inhibit cell proliferation. However, the applicability of lycosin-I as a novel anticancer drug is limited by its low cellular entry and efficacy in solid tumors. Amino acid substitution presents an effective and modest strategy to improve the anticancer activity and bioavailability of ACPs...
November 15, 2017: Organic & Biomolecular Chemistry
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