Tatjana Skrbic

Tatjana Skrbic
Università Ca' Foscari Venezia | UNIVE · Department of Molecular Science and Nanosystems

PhD in Physics

About

39
Publications
3,533
Reads
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368
Citations
Additional affiliations
September 2018 - present
University of Oregon
Position
  • Researcher
June 2014 - August 2018
Università Ca' Foscari Venezia
Position
  • PostDoc Position
May 2012 - May 2014
Scuola Internazionale Superiore di Studi Avanzati di Trieste
Position
  • PostDoc Position

Publications

Publications (39)
Article
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow from their native state structures and therefore understanding sequence-structure relationships is of fundamen...
Preprint
Full-text available
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow from their native state structures and therefore understanding sequence-structure relationships is of fundamen...
Article
We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that the mere addition of side spheres results in key modifications of standard polymer behavior. One obtains a marginally compact phase at low temperatures; the structures in...
Article
The native state structures of globular proteins are stable and well packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures—α helices and strands assembled into β sheets—with no adjustable...
Article
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple analytic arguments complemented by extensive computer simulations. We find several striking results: there is...
Preprint
Full-text available
We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that the mere addition of side spheres results in key modifications of standard polymer behavior. One obtains a novel marginally compact phase at low temperatures, the structur...
Preprint
Full-text available
Chain molecules play a key role in the polymer field and in living cells.Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple analytic arguments complemented by extensive computer simulations. We find several striking results: there is a...
Article
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state folds from myriad possible conformations? In order to address these questions, we represe...
Preprint
Full-text available
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state folds from myriad possible conformations? In order to address these questions, we represe...
Preprint
Full-text available
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures, alpha-helices and strands assembled into beta-sheets, with no ad...
Article
Full-text available
The use of glass for pharmaceutical new applications such as high-technology drugs, requires the strictest container inertness. A common theme of paramount importance in glass container integrity preservation is the detailed mechanism driving the sudden failure due the crack propagation. Using a combination of discrete element method (DEM) and fini...
Preprint
Full-text available
Using thermodynamics integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarity, ranging from the most polar water to the most non-polar cyclohexane. The amino acid side chain equivalents are obtained from the 20 natural amino acids by replacing the backbone part with a hydrogen atom,...
Preprint
Full-text available
Using thermodynamics integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarity, ranging from the most polar water to the most non-polar cyclohexane. The amino acid side chain equivalents are obtained from the 20 natural amino acids by replacing the backbone part with a hydrogen atom,...
Article
Using thermodynamic integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarities, ranging from the most polar water to the most non-polar cyclohexane. The amino acid side chain equivalents are obtained from the 20 natural amino acids by replacing the backbone part with a hydrogen atom...
Article
Full-text available
We investigate the self-assembly process of a surfactant with inverted polarity in water and cyclohexane using both all-atom and coarse grained hybrid particle-field molecular dynamics simulations. Unlike conventional surfactants, the molecule under study proposed in a recent experiment (M. Facchin et al., RSC Adv. 2017, 7, 15337–15341) is formed b...
Preprint
Full-text available
The use of glass for pharmaceutical new applications such as high-technology drugs, requires the strictest container inertness. A common theme of paramount importance in glass container integrity preservation is the detailed mechanism driving the sudden failure due the crack propagation. Using a combination of Discrete Element Method (DEM) and Fini...
Preprint
Full-text available
We investigate the self-assembly process of a surfactant with inverted polarity in water and cyclohexane using both all-atom and coarse grained hybrid particle-field molecular dynamics simulations. Unlike conventional surfactants, the molecule under study proposed in a recent experiment (M. Facchin et al., RSC Adv. 2017, 7, 15337–15341) is formed...
Article
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses—one yielding an energy penalty for local bends (energetic stiffness) and the other two forbidding certain classes of chain conformations (entropic sti...
Preprint
Full-text available
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for local bends (energetic stiffness) and the other two forbidding certain classes of chain conformations (entropic...
Preprint
Full-text available
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric constraint that non-consecutive beads cannot overlap, and with a pairwise attractive square well potential acc...
Article
Full-text available
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric constraint that non-consecutive beads cannot overlap, and with a pairwise attractive square well potential acc...
Article
Full-text available
A phase of matter is a familiar notion for inanimate physical matter. The nature of a phase of matter transcends the microscopic material properties. For example, materials in the liquid phase have certain common properties independent of the chemistry of the constituents: liquids take the shape of the container; they flow; and they can be poured ‐...
Preprint
Full-text available
A phase of matter is a familiar notion for inanimate physical matter. The nature of a phase of matter transcends the microscopic material properties. For example, materials in the liquid phase have certain common properties independent of the chemistry of the constituents: liquids take the shape of the container; they flow; and they can be poured -...
Article
We investigate the effects of solvent specificities on the stability of the native structure (NS) of a protein on the basis of our free-energy function (FEF). We use CPB-bromodomain (CBP-BD) and apoplastocyanin (apoPC) as representatives of the protein universe and water, methanol, ethanol, and cyclohexane as solvents. The NSs of CBP-BD and apoPC c...
Preprint
Full-text available
We investigate the effects of solvent specificities on the stability of the native structure (NS) of a protein on the basis of our free-energy function (FEF). We use CPB-bromodomain (CBP-BD) and apoplastocyanin (apoPC) as representatives of the protein universe and water, methanol, ethanol, and cyclohexane as solvents. The NSs of CBP-BD and apoPC c...
Article
Predicting the binding affinity between protein monomers is of paramount importance for the understanding of thermodynamical and structural factors that guide the formation of a complex. Several numerical techniques have been developed for the calculation of binding affinities with different levels of accuracy. Approaches such as thermodynamic inte...
Article
Taking protein G with 56 residues for a case study, we investigate the mechanism of protein folding. In addition to its native structure possessing α-helix and β-sheet contents of 27% and 39%, respectively, we construct a number of misfolded decoys with a wide variety of α-helix and β-sheet contents. We then consider a hierarchy of 8 different mode...
Article
Full-text available
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential repres...
Article
Full-text available
We study the equilibrium properties of a flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To this aim, we use both replica exchange canonical simulations and micro-canonical Wang-Landau techniques. We per...
Article
Full-text available
Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the t...
Article
Full-text available
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we...
Article
Full-text available
For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical m...
Article
Full-text available
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase)...
Article
Full-text available
We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways approach. We find evidence for the existence of two folding pathways, which differ by the order of formation of the two hairpins. This result is consistent with the analysis of the experimental data on the f...
Article
Full-text available
MD simulations of protein folding using parallel or distributed computing can at most assess small chains with folding times in the μs range. The Dominant Reaction Pathways (DRP) approach now allows to simulate the folding of medium-sized proteins on just few tens of CPUs. We discuss the results of the DRP simulations of the folding of two proteins...
Article
In recent years, symmetry-adapted imaginary-time correlation functions have been extensively used to study the rotational spectrum of doped ^4He clusters within the frame of the reptation quantum Monte Carlo method. The success of this approach relies on the choice of suitable correlation functions, whose spectral resolution is dominated by few, we...
Article
We discuss the use of generalized, symmetry-adapted, imaginary-time correlation functions to study the rotational spectrum of doped helium clusters within the frame of the reptation quantum Monte Carlo method. Analysis of these correlation functions allows one to enhance the computational efficiency in the calculation of weak spectral features, as...
Article
The rotational excitation spectrum, including the vibrational shift of the rotational band, of several CO isotopomers solvated in He clusters has been calculated. Reptation quantum Monte Carlo simulations are used in conjunction with an accurate He-CO potential energy surface, which quantitatively describes the rovibrational spectrum of the binary...
Article
Recent measurements of infrared spectra of Carbon dioxide molecules embedded in Helium droplets reveal a weak satellite band (SB) accompanying a sharp R(0) rovibrational line. By re-analyzing previous quantum Monte Carlo calculations of the rotational dynamics of various dopant molecules in Helium clusters, we find indeed evidence for rotational ex...

Questions

Question (1)
Question
When conducting calculations in Gromacs v5 in order to compute free energy of solvation of aminoacid analogs in cyclohexane, the calculations decouple not just the solute molecule from the solvent, but also the solvent molecules between themselves. It seems that the problem is that somehow Gromacs do not understand that cyclohexane has the role of the solvent, while in the case of the water everything works. Which is the correct way to conduct this simulation? Thank you very much in advance!

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