Dual self-assembly of supramolecular peptide nanotubes to provide stabilisation in water

Self-assembling peptides have the ability to spontaneously aggregate into large ordered structures. The reversibility of the peptide hydrogen bonded supramolecular assembly make them tunable to a host of different applications, although it leaves them highly dynamic and prone to disassembly at the low concentration needed for biological applications. Here we demonstrate that a secondary hydrophobic interaction, near the peptide core, can stabilise the highly dynamic peptide bonds, without losing the vital solubility of the systems in aqueous conditions. This hierarchical self-assembly process can be used to stabilise a range of different β-sheet hydrogen bonded architectures

Modelling water molecules inside cyclic peptide nanotubes

Cyclic peptide nanotubes occur during the selfassembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(-DAla- L-Ala)4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1 - 2 - 1 - 2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels

Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces

We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with molecular dynamics to handle in a more effective fashion multidimensional reaction coordinates. The proposed approach is anticipated to be particularly useful for reaction coordinates, the components of which are weakly coupled, as illuminated in a mathematical analysis of the long-time convergence of the algorithm. The strength as well as the intrinsic limitation of the method are discussed and illustrated in two realistic test cases

Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties

The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E 0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (-1.014 eV) then for D-FF (-0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (-6.18 eV) and for D-FF (-6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2-3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method. © 2019 Mathematical Biology and Bioinformatics.Part of this work was developed as part of the CICECO-Aveiro Materials Institute project, POCI-01-0145-FEDER-007679 funded from Fundação para a Ciência e a Tecnologia (FCT) Ref. UID/CTM/50011/2013, and funded from national funds through FCT/MEC, and co-funded by FEDER in accordance with the PT2020 Partnership Agreement. P.Z. thanks the project FCT PTDC/QEQ-QAN/6373/2014. S.K. thanks the project FCT PTDC/CTM-CTM/31679/2017

Encapsulation of a chloroform molecule in a peptide nanotube

We determine the encapsulation of a chloroform molecule into a D,L-Ala cyclopeptide nanotube by investigating the interaction energy between the two molecular structures. We employ the Lennard-Jones potential and a continuum approach which assumes that the atoms are evenly distributed over the molecules providing average atomic densities. Our result demonstrates that the encapsulation depends on the size of the molecule and the internal diameter of the peptide nantube. In particular, the on-axis chloroform molecule is only accepted into a peptide nanotube whose internal radius is greater than 5 Å. If located near the edge of the nanotube, then it is unlikely that the chloroform molecule will enter the nanotube. This is due to the energy valley that the molecule will need to overcome to move past the edge into the open end of the nanotube

Synthesis of composite hydrogels incorporating D,L-cyclic peptide nanotubes as a platform for materials engineering

Thesis (S.M.)--Harvard-MIT Program in Health Sciences and Technology, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 27-30).Composite hydrogels find increasing use as biomaterials because the addition of a filler often improves on the material properties of the original matrix, or provides new optical, magnetic, conductive or bioactive functionalities not inherent to the hydrogel. In this work we synthesized nanocomposite gelatin methacrylate (GelMA) hydrogels that incorporate D,L-cyclic peptide nanotubes. These nanotubes are biocompatible, stiff and their physical and chemical properties can be tailored simply by changing the amino acid sequence of the peptide. We show that the nanotubes successfully integrated into the hydrogel matrix and provided some mechanical reinforcement, without affecting hydrogel porosity or hydration characteristics. We will be using this composite system as a platform for engineering hydrogels with unique physical and biological properties to the hydrogel, for application as biological scaffolds.by Pei Kun Richie Tay.S.M