scholarly journals New self-assembling peptide nanotubes of large diameter using δ-amino acids

2018 ◽  
Vol 9 (43) ◽  
pp. 8228-8233 ◽  
Author(s):  
Alejandro Lamas ◽  
Arcadio Guerra ◽  
Manuel Amorín ◽  
Juan R. Granja
Keyword(s):  
Amino Acids ◽  
Building Block ◽  
Cyclic Peptides ◽  
Large Diameter ◽  
Peptide Nanotubes ◽  
Self Assembling ◽  
Aminocyclohexanecarboxylic Acid

Here we show that 4-aminocyclohexanecarboxylic acid is a rigid stretcher building block for the preparation of cyclic peptides that self-assemble to form peptide nanotubes with large diameter and hydrophobic pores.

scholarly journals Transmembrane Self-Assembled Cyclic Peptide Nanotubes Based on α‐Residues and Cyclic δ‐Amino Acids: A Computational Study

2021 ◽  
Vol 9 ◽  
Author(s):  
Alexandre Blanco-González ◽  
Martín Calvelo ◽  
Pablo F. Garrido ◽  
Manuel Amorín ◽  
Juan R. Granja ◽  
...  
Keyword(s):  
Amino Acids ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Computational Study ◽  
Peptide Nanotubes ◽  
Peptide Motifs ◽  
Self Assembling ◽  
Transmembrane Channels ◽  
Dynamics Simulations ◽  
Cyclic Peptide Nanotubes

Self-assembling cyclic peptide nanotubes have been shown to function as synthetic, integral transmembrane channels. The combination of natural and nonnatural aminoacids in the sequence of cyclic peptides enables the control not only of their outer surface but also of the inner cavity behavior and properties, affecting, for instance, their permeability to different molecules including water and ions. Here, a thorough computational study on a new class of self-assembling peptide motifs, in which δ-aminocycloalkanecarboxylic acids are alternated with natural α-amino acids, is presented. The presence of synthetic δ-residues creates hydrophobic regions in these α,δ-SCPNs, which makes them especially attractive for their potential implementation in the design of new drug or diagnostic agent carrier systems. Using molecular dynamics simulations, the behavior of water molecules, different ions (Li+, Na+, K+, Cs+, and Ca2+), and their correspondent counter Cl− anions is extensively investigated in the nanoconfined environment. The structure and dynamics are mutually combined in a diving immersion inside these transmembrane channels to discover a fascinating submarine nanoworld where star-shaped water channels guide the passage of cations and anions therethrough.

scholarly journals Systematic study of the structural parameters affecting the self-assembly of cyclic peptide–poly(ethylene glycol) conjugates

Soft Matter ◽  
2018 ◽  
Vol 14 (30) ◽  
pp. 6320-6326 ◽  
Author(s):  
Edward D. H. Mansfield ◽  
Matthias Hartlieb ◽  
Sylvain Catrouillet ◽  
Julia Y. Rho ◽  
Sophie C. Larnaudie ◽  
...  
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Hydrophobic Interactions ◽  
Structural Parameters ◽  
The Self ◽  
Poly Ethylene Glycol ◽  
Self Assembling ◽  
Poly Ethylene

Self-assembling cyclic peptides (CP) consisting of amino acids with alternating d- and l-chirality form nanotubes by hydrogen bonding, hydrophobic interactions, and π–π stacking in solution.

Molecular dynamics simulations for designing biomimetic pores based on internally functionalized self-assembling α,γ-peptide nanotubes

2015 ◽  
Vol 17 (43) ◽  
pp. 28586-28601 ◽  
Author(s):  
Martín Calvelo ◽  
Saulo Vázquez ◽  
Rebeca García-Fandiño
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Peptide Nanotubes ◽  
Self Assembling ◽  
Self Assembled ◽  
Dynamics Simulations

Internally functionalized peptide nanotubes composed of α- and γ-amino acids self assembled in lipid bilayers are studied using Molecular Dynamics simulations, projecting a promising future for their use as biomimetic channels when properly innerderivatized.

scholarly journals Hypothesis: daptomycin permeabilizes membranes by forming self-assembled nanotubes

2020 ◽  
Vol 7 (1) ◽  
pp. 59-71
Author(s):  
Alexander Zhivich ◽  
Keyword(s):  
Experimental Data ◽  
Clinical Practice ◽  
Mechanism Of Action ◽  
Mode Of Action ◽  
Cyclic Peptides ◽  
Bacterial Membrane ◽  
Peptide Nanotubes ◽  
Self Assembling ◽  
Primary Focus ◽  
Lipopeptide Antibiotic

Daptomycin is the only lipopeptide antibiotic that is widely used in clinical practice. It was discovered by Eli Lilly and then studied and commercialized by Cubist Pharmaceuticals in 2003. Although this antibiotic has been used for 17 years, the debate over its mechanism of action is ongoing. In this paper, we discuss the different hypotheses on the mode of action of this antibiotic with a primary focus on the bacterial membrane permeabilization as the main mechanism of action. By comparing the experimental data on the oligomerization of daptomycin in membranes with properties of self-assembling cyclic peptides, we conclude that the structure of daptomycin oligomer should resemble the structures of peptide nanotubes that serve as ion channels in membranes.

Two one-dimensional arrays of naphthyl and anthryl groups along peptide nanotubes prepared from cyclic peptides comprising α- and β-amino acids

Soft Matter ◽  
2018 ◽  
Vol 14 (37) ◽  
pp. 7597-7604 ◽  
Author(s):  
Yuki Tabata ◽  
Hirotaka Uji ◽  
Tomoya Imai ◽  
Shunsaku Kimura
Keyword(s):  
Amino Acids ◽  
Electronic Properties ◽  
Cyclic Peptides ◽  
Molecular Assembly ◽  
Peptide Nanotubes ◽  
One Dimensional ◽  
Cyclic Hexapeptide

A novel cyclic hexapeptide composed of l-α-naphthylalanine, d-α-anthrylalanine, and four β-alanines (CP6) is synthesized and its molecular assembly into peptide nanotubes (PNTs) and the electronic properties arising from one-dimensional arrays of aromatic groups along the PNTs are investigated.

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

2020 ◽  
Vol 27 (9) ◽  
pp. 923-929
Author(s):  
Gaurav Pandey ◽  
Prem Prakash Das ◽  
Vibin Ramakrishnan
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Light Scattering ◽  
Chain Length ◽  
Self Assembly ◽  
The Self ◽  
Ionic Charge ◽  
Self Assembling ◽  
Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

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