Pro Vitam Ltd.

Sfântu-Gheorghe, Romania

Pro Vitam Ltd.

Sfântu-Gheorghe, Romania
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Fejer S.N.,University of Szeged | Fejer S.N.,Pro Vitam Ltd. | Chakrabarti D.,University of Birmingham | Kusumaatmaja H.,Durham University | Wales D.J.,University of Cambridge
Nanoscale | Year: 2014

Using the framework of potential energy landscape theory, we describe two in silico designs for self-assembling helical colloidal superstructures based upon dipolar dumbbells and Janus-type building blocks, respectively. Helical superstructures with controllable pitch length are obtained using external magnetic field driven assembly of asymmetric dumbbells involving screened electrostatic as well as magnetic dipolar interactions. The pitch of the helix is tuned by modulating the Debye screening length over an experimentally accessible range. The second design is based on building blocks composed of rigidly linked spheres with short-range anisotropic interactions, which are predicted to self-assemble into Bernal spirals. These spirals are quite flexible, and longer helices undergo rearrangements via cooperative, hinge-like moves, in agreement with experiment. © 2014 the Partner Organisations.

Jakli I.,Eötvös Loránd University | Csizmadia I.G.,Eötvös Loránd University | Csizmadia I.G.,University of Szeged | Csizmadia I.G.,University of Toronto | And 6 more authors.
Chemical Physics Letters | Year: 2013

Structure, stability, cooperativity and molecular packing of two major backbone forms: 310-helix and β-strand are investigated. Long models HCO-(Xxx)n-NH2 Xxx = Gly and (l-)Ala, n ≤ 34, are studied at two levels of theory including the effect of dispersion forces. Structure and folding preferences are established, the length modulated cooperativity and side-chain determined fold compactness is quantified. By monitoring ΔG°β→α rather than the electronic energy, ΔEβ→α, it appears that Ala is a much better helix forming residue than Gly. The achiral Gly forms a more compact 310-helix than any chiral amino acid residue probed here for l-Ala.

Forman C.J.,University of Cambridge | Fejer S.N.,University of Szeged | Fejer S.N.,Pro Vitam Ltd. | Chakrabarti D.,University of Cambridge | And 3 more authors.
Journal of Physical Chemistry B | Year: 2013

Decorative domains force amyloid fibers to adopt spiral ribbon morphologies, as opposed to the more common twisted ribbon. We model the effect of decorating domains as a perturbation to the relative orientation of β strands in a bilayered extended β-sheet. The model consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting ellipsoids. The relative orientation of the ellipsoids dictates the morphology of the resulting assembly. Amyloid structures derived from experiment are consistent with our model, and we use magnets to demonstrate that the frustration principle is scale and system independent. In contrast to other models of amyloid, our model isolates the effect of frustration from the fundamental interactions between building blocks to reveal the frustration rather than dependence of morphology on the physical interactions. Consequently, amyloid is viewed as a discrete molecular version of the more general macroscopic frustrated bilayer that is exemplified by Bauhinia seedpods. The model supports the idea that the interactions arising from an arbitrary peptide sequence can support an amyloid structure if a bilayer can form first, which suggests that supplementary protein sequences, such as chaperones or decorative domains, could play a significant role in stabilizing such bilayers and therefore in selecting morphology during nucleation. Our model provides a foundation for exploring the effects of frustration on higher-order superstructural polymorphic assemblies that may exhibit complex functional behavior. Two outstanding examples are the systematic kinking of decorated fibers and the nested frustration of the Bauhinia seedpod. © 2013 American Chemical Society.

Jojart B.,University of Szeged | Viskolcz B.,University of Szeged | Posa M.,University of Novi Sad | Fejer S.N.,University of Szeged | Fejer S.N.,Pro Vitam Ltd.
Journal of Chemical Physics | Year: 2014

In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers. © 2014 AIP Publishing LLC.

Fejer S.N.,University of Szeged | Fejer S.N.,Pro Vitam Ltd. | Wales D.J.,University of Cambridge
Soft Matter | Year: 2015

We present a simple model of triblock Janus particles based on discoidal building blocks, which can form energetically stabilized Kagome structures. We find 'magic number' global minima in small clusters whenever particle numbers are compatible with a perfect Kagome structure, without constraining the accessible three-dimensional configuration space. The preference for planar structures with two bonds per patch among all other possible minima on the landscape is enhanced when sedimentation forces are included. For the building blocks in question, structures containing three bonds per patch become progressively higher in energy compared to Kagome structures as sedimentation forces increase. Rearrangements between competing structures, as well as ring formation mechanisms are characterised and found to be highly cooperative. This journal is © The Royal Society of Chemistry.

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