Abstract
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.
Highlights
The translocation of different species between the compartmentalized inner regions of living cells and their environment plays a core role on their viability and probability of survival
The original self-assembling cyclic peptide nanotubes (SCPNs) were comprised of D- and L-α-amino acids that adopted a flat conformation in which the amide groups (NH and CO) lie perpendicular to the plane of the ring (Figure 1A). (De Santis et al, 1974; Bong et al, 2001) This special arrangement allows the formation of hydrogen bonds (H-bonds) between contiguous cyclic peptides (CPs) owing to the complementarity between H-bond donor and acceptor groups on both sides of each disc structure
This study aims to explore in detail the internal properties of transmembrane α,δ-SCPN channels, evaluating and carefully investigating the structural and dynamical behavior of water, LiCl, KCl, NaCl, CsCl, and CaCl2 inside this type of nanotubes
Summary
The translocation of different species between the compartmentalized inner regions of living cells and their environment plays a core role on their viability and probability of survival. One of the main advantages of these rod-shaped peptide materials is the simplicity with which their inner and outer properties can be modulated upon appropriate selection of the CP sequence; while the number and type of amino acids determine the internal diameter of the nanotube, the characteristics of its outer surface depend on the properties of the side chains of the amino acids In this sense, the design of SCPNs that interact with the hydrophobic part of biomembranes has been carried out through the appropriate selection of amino acids in the basic peptide subunit (Ghadiri et al, 1994)
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