Repozitorij Univerze v Novi Gorici

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11.
In silico generation of peptides by replica exchange Monte Carlo: Docking-based optimization of maltose-binding-protein ligands
Anna Russo, Pasqualina Liana Scognamiglio, Rolando Pablo Hong Enriquez, Carlo Santambrogio, Rita Grandori, Daniela Marasco, Antonio Giordano, Giacinto Scoles, Sara Fortuna, 2015, izvirni znanstveni članek

Opis: Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
Ključne besede: peptides, docking, optimisation, computation, maltose binding protein, probe, ligand
Objavljeno v RUNG: 12.10.2016; Ogledov: 3921; Prenosov: 140
.pdf Celotno besedilo (4,27 MB)

12.
Chelating effect in short polymers for the design of bidentate binders of increased affinity and selectivity
Sara Fortuna, Federico Fogolari, Giacinto Scoles, 2015, izvirni znanstveni članek

Opis: The design of new strong and selective binders is a key step towards the development of new sensing devices and effective drugs. Both affinity and selectivity can be increased through chelation and here we theoretically explore the possibility of coupling two binders through a flexible linker. We prove the enhanced ability of double binders of keeping their target with a simple model where a polymer composed by hard spheres interacts with a spherical macromolecule, such as a protein, through two sticky spots. By Monte Carlo simulations and thermodynamic integration we show the chelating effect to hold for coupling polymers whose radius of gyration is comparable to size of the chelated particle. We show the binding free energy of flexible double binders to be higher than that of two single binders and to be maximized when the binding sites are at distances comparable to the mean free polymer end-to-end distance. The affinity of two coupled binders is therefore predicted to increase non linearly and in turn, by targeting two non-equivalent binding sites, this will lead to higher selectivity.
Ključne besede: chelation, polymer, multivalency, bidentate, free energy, thermodynamic integration, Monte Carlo
Objavljeno v RUNG: 11.10.2016; Ogledov: 3981; Prenosov: 151
.pdf Celotno besedilo (1,68 MB)

13.
Accurate estimation of the entropy of rotation-translation probability distributions
Federico Fogolari, Cedrix Jurgal Dongmo Foumthuim, Sara Fortuna, Miguel Angel Soler, Alessandra Corazza, Gennaro Esposito, 2016, izvirni znanstveni članek

Opis: The estimation of rotational and translational entropies in the context of ligand binding has been the subject of long-time investigations. The high dimensionality (six) of the problem and the limited amount of sampling often prevent the required resolution to provide accurate estimates by the histogram method. Recently, the nearest-neighbor distance method has been applied to the problem, but the solutions provided either address rotation and translation separately, therefore lacking correlations, or use a heuristic approach. Here we address rotational–translational entropy estimation in the context of nearest-neighbor-based entropy estimation, solve the problem numerically, and provide an exact and an approximate method to estimate the full rotational–translational entropy.
Ključne besede: entropy, probability distribution, molecular dynamics, nearest-neighbor
Objavljeno v RUNG: 11.10.2016; Ogledov: 4321; Prenosov: 0
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14.
Phase behaviour of self-assembled monolayers controlled by tuning physisorbed and chemisorbed states: a lattice-model view
Sara Fortuna, David L. Cheung, Karen Johnston, 2016, izvirni znanstveni članek

Opis: The self-assembly of molecules on surfaces into 2D structures is important for the bottom-up fabrication of functional nanomaterials, and the self-assembledstructure depends on the interplay between molecule-molecule interactions and molecule-surface interactions. Halogenated benzene derivatives on platinum have been shown to have two distinct adsorption states: a physisorbed state and a chemisorbed state, and the interplay between the two can be expected to have a profound effect on the self-assembly and phase behaviour of these systems. We developed a lattice model that explicitly includes both adsorption states, with representative interactions parameterised using density functional theory calculations. This model was used in Monte Carlo simulations to investigate pattern formation of hexahalogenated benzene molecules on the platinumsurface. Molecules that prefer the physisorbed state were found to self-assemble with ease, depending on the interactions between physisorbed molecules. In contrast, molecules that preferentially chemisorb tend to get arrested in disordered phases. However, changing the interactions between chemisorbed and physisorbed molecules affects the phase behaviour. We propose functionalising molecules in order to tune their adsorption states, as an innovative way to control monolayer structure, leading to a promising avenue for directed assembly of novel 2D structures.
Ključne besede: lattice model, hexagonal lattice, Monte Carlo, DFT, density functional theory, benzene, physisorption, chemisorption, halogenated
Objavljeno v RUNG: 11.10.2016; Ogledov: 4475; Prenosov: 0
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15.
Molecule-Driven Substrate Reconstruction in the Two-Dimensional Self-Organization of Fe-Phthalocyanines on Au(110)
Sara Fortuna, Pierluigi Gargiani, Maria Grazia Betti, Carlo Mariani, Arrigo Calzolari, Silvio Modesti, Stefano Fabris, 2012, izvirni znanstveni članek

Opis: The structural patterns formed by molecular self-assembly at surfaces are usually controlled by the relative strengths of the intermolecular and molecule–substrate interactions. An additional steering effect is present when the substrate can easily reconstruct upon molecular adsorption, which therefore drives a self-templating effect on the metal support. This is here demonstrated for the model case of Fe-phthalocyanine molecules adsorbed on the Au(110) surface. Scanning tunneling microscopy shows that molecular adsorption promotes a local (1 × 5) surface reconstruction, which drives the assembly of molecular chains along the [11̅0] direction. The order and periodicity of the molecular assemblies are determined with low energy electron diffraction patterns. Density functional theory calculations reveal the energetic origins of the molecule-driven substrate reconstruction. Since the function of molecular overlayers at surfaces is strongly correlated to their structure, these results have implications in the design of new metal/molecular interfaces.
Ključne besede: self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction
Objavljeno v RUNG: 11.10.2016; Ogledov: 4587; Prenosov: 0
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16.
Polymer Vesicles with a Colloidal Armor of Nanoparticles
Rong Chen, Daniel J. G. Pearce, Sara Fortuna, David L. Cheung, Stefan A. F. Bon, 2011, izvirni znanstveni članek

Opis: The fabrication of polymer vesicles with a colloidal armor made from a variety of nanoparticles is demonstrated. In addition, it is shown that the armored supracolloidal structure can be postmodified through film-formation of soft polymer latex particles on the surface of the polymersome, hereby effectively wrapping the polymersome in a plastic bag, as well as through formation of a hydrogel by disintegrating an assembled polymer latex made from poly(ethyl acrylate-co-methacrylic acid) upon increasing the pH. Furthermore, ordering and packing patterns are briefly addressed with the aid of Monte Carlo simulations, including patterns observed when polymersomes are exposed to a binary mixture of colloids of different size.
Ključne besede: Pickering emultion, self-assemblt, Monte Carlo, simulation, nanoparticle, packing, pattern garnd canonical, colloids
Objavljeno v RUNG: 11.10.2016; Ogledov: 4700; Prenosov: 0
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17.
Oxalic acid adsorption states on the clean Cu(110) surface
Sara Fortuna, 2016, izvirni znanstveni članek

Opis: Carboxylic acids are known to assume a variety of configurations on metallic surfaces. In particular oxalic acid on the Cu(110) surface has been proposed to assume a number of upright configurations. Here we explore with DFT calculations the possible structures that oxalic acid can form on copper 110 at different protonation states, with particular attention at the possibility of forming structures composed of vertically standing molecules. In its fully protonated form it is capable of anchoring itself on the surface thanks to one of its hydrogen-free oxygens. We show the monodeprotonated upright molecule with two oxygens anchoring it on the surface to be the lowest energy conformation of a single oxalic molecules on the Cu(110) surface. We further show that it is possible for this configuration to form dense hexagonally arranged patterns in the unlikely scenario in which adatoms are not involved.
Ključne besede: oxalic acid, oxalate, cu(110), copper, surface, adsorption, density functional theory, DFT
Objavljeno v RUNG: 11.10.2016; Ogledov: 4441; Prenosov: 0
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18.
Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Miguel Soler, Ario De Marco, Sara Fortuna, 2016, izvirni znanstveni članek

Opis: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules
Ključne besede: nanobodies, molecular dynamics, modeling, antibody solubility
Objavljeno v RUNG: 11.10.2016; Ogledov: 4614; Prenosov: 244
.pdf Celotno besedilo (1,95 MB)

19.
Agent based modelling for the 2D molecular self-organization of realistic molecules
Sara Fortuna, Alessandro Troisi, 2010, izvirni znanstveni članek

Opis: We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.
Ključne besede: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram
Objavljeno v RUNG: 11.10.2016; Ogledov: 4763; Prenosov: 0
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20.
Hexagonal lattice model of the patterns formed by hydrogen-bonded molecules on the surface
Sara Fortuna, David L. Cheung, Alessandro Troisi, 2010, izvirni znanstveni članek

Opis: We model the two-dimensional self-assembly of planar molecules capable of complementary interactions (like hydrogen bonding) as a set of hexagonal tiles on a hexagonal lattice. We use Monte Carlo simulations to study the phase diagrams of three model systems. The phases are characterized using a variety of order parameters, and they are studied as a function of the strength of the complementary interaction energy. This simplified model is proven to be capable of reproducing the phases encountered in real systems, unifying within the same framework most of the structures encountered experimentally.
Ključne besede: self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice
Objavljeno v RUNG: 10.10.2016; Ogledov: 4758; Prenosov: 0
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