Biomedical subjects

Piotr Romiszowski

Publications and source records attributed to Piotr Romiszowski.

12 recordsLinked to original sources

PubMed2006

Computer simulation of polypeptides in a confinement.

A coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied. The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms-hydrophobic and hydrophilic. The positions of the united atoms were restricted to the vertices of a [310] lattice. The force field consisted of a rigorous excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions. Monte-Carlo simulations were carried out using the algorithm based on the chain's local changes of conformation and employing the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system.

Computer Simulation↗

PubMed2006

Motion of a branched polymer chain in confinement: a Monte Carlo study.

The aim of the study was a theoretical investigation of the polymer molecules located between two parallel and impenetrable surfaces which were also attractive for polymer segments. The chains were constructed of identical segments and were restricted to knots of a simple cubic lattice. Since the chains were at good solvent conditions the only interactions between the segments of the chain were the excluded volume. The properties of the model chains were determined by means of Monte Carlo simulations with a sampling algorithm based on the chain's local changes of conformation. The differences and similarities in the structure for different adsorption regimes and the size of the slit were shown and discussed. It was observed that at certain conditions the polymer chain was adsorbed at one of the confining surfaces, and then after a certain period of time it detached from this surface and approached the opposite wall; this switch was repeated many times. The influence of the strength of the adsorption, the size of the slit, and the chain's length on the frequency of these jumps were determined. The mechanism of the chain's motion during the switch was also shown.

Journal Article↗

PubMed2005

Star-branched polymers in an adsorbing slit: a Monte Carlo study.

A coarse-grained model of star-branched polymer chains confined in a slit was studied. The slit was formed by two parallel impenetrable surfaces, which were attractive for polymer beads. The polymer chains were flexible homopolymers built of identical united atoms whose positions in space were restricted to the vertices of a simple cubic lattice. The chains were regular star polymers consisted of f = 3 branches of equal length. The chains were modeled in good solvent conditions and, thus, there were no long-range specific interactions between the polymer beads-only the excluded volume was present. Monte Carlo simulations were carried out using the algorithm based on a chain's local changes of conformation. The influence of the chain length, the distances between the confining surfaces, and the strength of the adsorption on the properties of the star-branched polymers was studied. It was shown that the universal behavior found previously for the dimension of chains was not valid for some dynamic properties. The strongly adsorbed chains can change their position so that they swap between both surfaces with frequency depending on the size of the slit and on the temperature only.

Journal Article↗

PubMed2005

Properties of star-branched and linear chains in confined space. A Monte-Carlo study.

We have studied the properties of simple models of linear and star-branched polymer chains confined in a slit formed by two parallel impenetrable walls. The polymer chains consisted of identical united atoms (homopolymers) and were restricted to a simple cubic lattice. Two macromolecular architectures of the chain: linear and regular stars with three branches of equal length, were studied. The excluded volume was the only potential introduced into the model and thus the system was athermal. Monte-Carlo simulations with the sampling algorithm based on the chain's local changes of conformation were carried out for chains with different lengths as well as for different distances between the confining surfaces. We found that the properties of model chains differ for both macromolecular architectures but a universal behavior for both kinds of chains was also found. Investigation of the frequency of chain-wall contacts shows that the ends of the chains are much more mobile than the rest of the chain, especially in the vicinity of the branching point in star polymers. [Figure: see text]. The scheme of a star-branched (left) and a linear (right) chain located between two parallel impenetrable surfaces.

Algorithms↗

PubMed2005

Computer simulation of polypeptide translocation through a nanopore.

A simplified model of polypeptide chains was designed and studied by means of computer simulations. Chains were represented by a sequence of united atoms located at the positions of the alpha-carbons. A further assumption was the lattice approximation for the chains. We used a (310) lattice, which was found useful for studying properties of proteins. The force field used consisted of a long-range contact potential between amino-acid residues and a local preference for forming alpha-helical states. The chain consisted of two kinds of residues: hydrophilic (P) and hydrophobic (H) ones forming model helical septets--HHPPHPP--in a sequence. The chains were placed near an impenetrable surface with a square hole in it. The size of the hole was comparable or smaller than the size of a chain. The properties of these model chains were determined using the Monte-Carlo simulation method. During the simulations, translocation of the chain through the hole in the wall was observed. The influence of the chain length, the temperature differences on both sides of the wall and the force field on the chain properties were investigated. It was shown that the translocation time scales as N(2.2) and it was found that the presence of the local helical potential significantly slows down the process of translocation. [Figure: see text]. The snapshots of typical chain's conformation obtained during the simulation for chain consisted of N = 60. The values of the local potential epsilon(loc) = -8.

Computer Simulation↗

PubMed2004

Properties of branched confined polymers.

A model of star-branched polymer chains confined in a slit formed by two parallel surfaces was studied. The chains were embedded to a simple cubic lattice and consisted of f=3 branches of equal length. The macromolecules had the excluded volume and the confining surfaces were impenetrable for polymer segments. No attractive interactions between polymer segments and then between polymer segments and the surfaces were assumed and therefore the system was a thermal. Monte Carlo simulations were carried out employing the sampling algorithm based on chain's local changes of conformation. Lateral diffusion of star-branched chains was studied. Dynamic properties of star-branched chains between the walls with impenetrable rod-like obstacles were also studied and compared to the previous case. The density profiles of polymer segments on the slit were determined. The analysis of contacts between the polymer chain and the surfaces was also carried out.

Journal Article↗

PubMed2003

Thermodynamical properties of simple models of protein-like heteropolymers.

The lattice approximation of a heteropolymer chain as a model of a single polypeptide was used in the computer simulation. The residues of a model polypeptide were represented by the chain of alpha-carbons located on a very flexible [310] lattice. The force field that mimic the intramolecular interactions contained the long-range contact potential between the residues and the local preferences in forming helical structures. The chain consisted of two types of residues that had different hydrophobicity. The simulations were performed by means of the Replica Exchange Monte Carlo method combined with the Histogram method. The series of simulations were carried out to investigate the influence of both components of the force field on the transition temperature and the characteristics of the coil-to-globule transition. The properties of low-temperature ordered structures were determined. The thermodynamical description of the model chain was also given. The phase transition was found to be sharp and cooperative for longer chains and strong helical potential. The collapsed globule contained the strongly hydrophobic residues inside the globule while the remaining residues were mainly located close to the globule surface.

Asparagine↗

PubMed2003

Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model.

Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to experiment. The models semiquantitatively reproduce the approximate order of events of unfolding as well as subtle mutation effects and effects resulting from differences in sequences of similar folds. The short-time mobility of particular residues, observed in simulations, correlates with the crystallographic temperature factor. The main factor controlling unfolding is the native state topology, with sequence playing a less important role. The correlation with various experiments, especially for sequence-specific effects, strongly suggests that properly designed reduced models of proteins can be used for qualitative studies (or prediction) of protein unfolding pathways.

Apoproteins↗

PubMedDate not supplied

Properties of grafted amphiphilic chains. A computer simulation study.

The model of a heteropolymer film formed by polypeptide chains was used for theoretical considerations. The linear chains consisting of amino acid residues were approximated by alpha carbon chains. Each chain was constructed on a very flexible [310] lattice. The inter- and intramolecular interactions consisted of the long-range contact potential between residues. The chains were built of hydrophilic and hydrophobic residues. Chains were terminally attached to an impenetrable surface with lateral motions possible. The Monte Carlo simulations of this model were carried out by using the Metropolis algorithm. The influence of the grafting density, the sequence of the amino acid residues, and the temperature on the static properties of the formed layer were studied and discussed. It was shown that homopolymer chains collapsed at higher temperature than the heteropolymers. The size of the polymers forming brush was smaller for homopolymers than for heteropolymers. The structure of the resulting polymer film and of its external surface was determined. The block copolymers formed well defined hydrophobic and hydrophilic layers, while for the amphiphilic case the composition of the brush layers changed continuously at high temperature. It was observed that the latter effect vanished at the collapsed amphiphilic copolymer.

Journal Article↗

PubMedDate not supplied

Properties of star-branched polymer brushes.

A simple model of a polymer brush was constructed. The star polymers with three arms were terminally attached with one arm (the stem) to an impenetrable surface with the other two arms (branches) free. The excluded volume effect was included into the model as the only interaction. Therefore, the system was studied in good solvent conditions. The simulations were carried out by means of the dynamic Monte Carlo method using the local changes of chain conformations to sample efficiently the conformational space. The influence of both the number of chains (the grafting density) and the length of chains on the static properties of the polymer brush was studied. The internal and local structure of a formed polymer layer was determined. It was shown that the size of the stems increased rapidly with the increase of the grafting density, while the size of the branches diminished. The changes of the spatial orientations of the stems and the branches for different grafting densities were shown and discussed.

Journal Article↗

PubMedDate not supplied

Formation of secondary structures in polypetides. A Monte Carlo simulation.

The lattice approximation of a polypetide chain was used in the computer simulation. The residues of a model polypetide were represented by the chain of a-carbons located on a very flexible [310] lattice. The force field contained the long-range contact potential between the residues as well as the local preferences in forming helical structures. The chain consisted of two types of residues: hydrophillic (P) and hydrophobic (H), forming a typical repeatable helical septet -HHPPHPP-. The simulations were performed by means of the Replica Exchange Monte Carlo method combined with th e Histogram method. A series of simulations were performed enabling one to investigate the influence of both components of the force field on the transition temperature and the characteristics of the coil-to-globule transition. The properties of low-temperature ordered structures were determined. The thermodynamical description of the mod el polypeptide was also given. The phase transition was found to be sharp and cooperative for longer chains and strong helical potential.

Algorithms↗

PubMedDate not supplied

Computer simulation of the receptor-ligand system.

A series of Monte Carlo simulations were carried out for receptor-ligand systems taken from the Protein Data Bank. The models of both objects were based on a simplified low-resolution model. The model chains consisted of alpha carbons and side groups represented by united atoms. The excluded volume effect and specific pairwise contact potential were introduced into the model. The process of docking was simulated step-by-step by random translations and reorientations of the ligand. The stability of complexes formed was investigated for a simple statistical potential between amino acid side groups. The feasibility of the model for finding the binding site on the receptor surface and the proper orientation of docked ligand were also studied.

Algorithms↗