Monte Carlo simulations of peptide-membrane interactions with the MCPep web server

Gofman, Yana; Haliloğlu, Türkan; Ben‐Tal, Nir

doi:10.1093/nar/gks577

Cited by 29 publications

(33 citation statements)

References 38 publications

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“…The average helical content of the peptides in water or in the membrane and the simulation of the residue distribution on the membrane surface are shown. The prediction was performed by using MCPEP software (43). The orientation of each peptide toward the membrane bilayer additionally is shown in the 3D conformation model.…”

Section: Resultsmentioning

confidence: 99%

“…Secondary structure predictions of the sequence of the YopM34-73 fragment were obtained via the web server PSIPRED (42). The secondary structure propensity in membrane or water environments, as well as the membrane simulation, was obtained for the peptide sequences via the MCPEP web server (43). The helical wheel projection was obtained by using the online tool HeliQuest (44).…”

Section: Methodsmentioning

confidence: 99%

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Bacterium-Derived Cell-Penetrating Peptides Deliver Gentamicin To Kill Intracellular Pathogens

Gomarasca

Martins

Greune

et al. 2017

Antimicrob Agents Chemother

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Commonly used antimicrobials show poor cellular uptake and often have limited access to intracellular targets, resulting in low antimicrobial activity against intracellular pathogens. An efficient delivery system to transport these drugs to the intracellular site of action is needed. Cell-penetrating peptides (CPPs) mediate the internalization of biologically active molecules into the cytoplasm. Here, we characterized two CPPs, ␣1H and ␣2H, derived from the Yersinia enterocolitica YopM effector protein. These CPPs, as well as Tat (trans-activator of transcription) from HIV-1, were used to deliver the antibiotic gentamicin to target intracellular bacteria. The YopM-derived CPPs penetrated different endothelial and epithelial cells to the same extent as Tat. CPPs were covalently conjugated to gentamicin, and CPP-gentamicin conjugates were used to target infected cells to kill multiple intracellular Gram-negative pathogenic bacteria, including Escherichia coli K1, Salmonella enterica serovar Typhimurium, and Shigella flexneri. Taken together, CPPs show great potential as delivery vehicles for antimicrobial agents and may contribute to the generation of new therapeutic tools to treat infectious diseases caused by intracellular pathogens.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Bacterium-Derived Cell-Penetrating Peptides Deliver Gentamicin To Kill Intracellular Pathogens

Gomarasca

Martins

Greune

et al. 2017

Antimicrob Agents Chemother

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“…(B) 3D representation of DENV C protein (PDB1R6R; left) highlighting the region comprising pepM and pepR (blue) and structural localization of both CPP templates, pepM (green) and pepR (orange), at the DENV C protein monomer structure. (C) Sequence, secondary structure propensity prediction in water and lipid bilayers (using MCPEP [22]) and 3D conformation prediction (using I-TASSER [23]) of pepM (green) and pepR (orange). In (B) and (C), the conformational representations were done with PYMOL software [59].…”

Section: Resultsmentioning

confidence: 99%

“…1C), can be assigned to two distinct CPP families [4,5,7]: pepM is highly hydrophobic and contains two Pro residues, which is typical of the hydrophobic/Pro CPP family, and pepR is highly cationic (+12) and fits the requirements of the Arg/Lys-rich CPP family [4,5,7]. MCPEP, a computational tool that estimates the probability of occurrence of secondary structure in peptides (both in aqueous environment and when inserted in lipid bilayers) by Monte Carlo simulation [22], predicts that both peptides acquire a random coil conformation in water. When in membranes, pepM tends to form two a-helices separated by the Pro-rich segment, and pepR tends to form a single long a-helix ( Figs 1C and S1).…”

Section: Resultsmentioning

confidence: 99%

“…For secondary structure propensity prediction, the sequence of DENV C protein [17] (PDB ID 1R6R) was submitted to the web server PSIPRED [19] (http://bioinf.cs.ucl.ac.uk/psipred/), while pepR and pepM sequences were submitted to MCPEP server [22] (http://ben tal.tau.ac.il/MCPep/index.html). Prediction confidence of the algorithm was represented with a bar scale (higher confidence corresponds to larger bars).…”

Section: Peptide Computational Analysismentioning

confidence: 99%

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Nucleic acid delivery by cell penetrating peptides derived from dengue virus capsid protein: design and mechanism of action

et al. 2013

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Cell penetrating peptides (CPPs) can be used as drug delivery systems for different therapeutic molecules. In this work two novel CPPs, pepR and pepM, designed from two domains of the dengue virus (DENV) capsid protein, were studied for their ability to deliver nucleic acids into cells as non-covalently bound cargo. Translocation studies were performed by confocal microscopy in HepG2, BHK and HEK cell lineages, astrocytes and peripheral blood mononuclear cells. Combined studies in HepG2 cells, astrocytes and BHK cells, at 4 and 37°C or using specific endocytosis inhibitors, revealed that pepR and pepM use distinct internalization routes: pepM translocates lipid membranes directly, while pepR uses an endocytic pathway. To confirm these results, a methodology was developed to monitor the translocation kinetics of both peptides by real-time flow cytometry. Kinetic constants were determined, and the amount of nucleic acids delivered was estimated. Additional studies were performed in order to understand the molecular bases of the peptide-mediated translocation. Peptide-nucleic acid and peptide-lipid membrane interactions were studied quantitatively based on the intrinsic fluorescence of the peptides. pepR and pepM bound ssDNA to the same extent. Partition studies revealed that both peptides bind preferentially to anionic lipid membranes, adopting an a-helical conformation. However, fluorescence quenching studies suggest that pepM is deeply inserted into the lipid bilayer, in contrast with pepR. Moreover, only pepM is able to promote the fusion and aggregation of vesicles composed of zwitterionic lipids. Altogether, the results show that DENV capsid protein derived peptides serve as good templates for novel CPP-based nucleic acid delivery strategies, defining different routes for cell entry.

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Secondary structure of cell‐penetrating peptides during interaction with fungal cells

2018

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Cell-penetrating peptides (CPPs) are peptides that cross cell membranes, either alone or while carrying molecular cargo. Although their interactions with mammalian cells have been widely studied, much less is known about their interactions with fungal cells, particularly at the biophysical level. We analyzed the interactions of seven CPPs (penetratin, Pep-1, MPG, pVEC, TP-10, MAP, and cecropin B) with the fungal pathogen Candida albicans using experiments and molecular simulations. Circular dichroism (CD) of the peptides revealed a structural transition from a random coil or weak helix to an α-helix occurs for all peptides when the solvent is changed from aqueous to hydrophobic. However, CD performed in the presence of C. albicans cells showed that proximity to the cell membrane is not necessarily sufficient to induce this structural transition, as penetratin, Pep-1, and MPG did not display a structural shift in the presence of cells. Monte Carlo simulations were performed to further probe the molecular-level interaction with the cell membrane, and these simulations suggested that pVEC, TP-10, MAP, and cecropin B strongly penetrate into the hydrophobic domain of the membrane lipid bilayer, inducing a transition to an α-helical conformation. In contrast, penetratin, Pep-1 and MPG remained in the hydrophilic region without a shift in conformation. The experimental data and MC simulations combine to explain how peptide structure affects their interaction with cells and their mechanism of translocation into cells (direct translocation vs. endocytosis). Our work also highlights the utility of combining biophysical experiments, biological experiments, and molecular modeling to understand biological phenomena.

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Monte Carlo simulations of peptide-membrane interactions with the MCPep web server

Cited by 29 publications

References 38 publications

Bacterium-Derived Cell-Penetrating Peptides Deliver Gentamicin To Kill Intracellular Pathogens

Bacterium-Derived Cell-Penetrating Peptides Deliver Gentamicin To Kill Intracellular Pathogens

Nucleic acid delivery by cell penetrating peptides derived from dengue virus capsid protein: design and mechanism of action

Secondary structure of cell‐penetrating peptides during interaction with fungal cells

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