A microscopic spin model is proposed for the phenomenological Zimm-Bragg helix-coil transition in biopolymers. This shown to provide same thermophysical properties of original and it allows a very convenient framework compute statistical quantities. Physical origins this are made transparent by an exact mapping into one-dimensional Ising with external field. However, dependence on temperature reduced field turns out differ from standard hence gives rise different properties, despite...

Protein-like systems are studied using models of increasing complexity starting from a tangent-beads chain and gradually adding the possibility overlapping for consecutive beads, as well presence additional smaller beads mimicking side chains, Wang–Landau techniques.

Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. Hydrogen bonds play crucial role in stabilizing three-dimensional structure proteins. Naturally, information about strength hydrogen contained measured DSC profiles. Despite its obvious importance, there no approach that would allow extraction such from capacity measurements. In order connect microscopic properties polypeptide chain, proper model required fit....

Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost forming helical state in one repeating unit; entropic, accounting for decrease entropy due to formation; and geometric, indicating how many units are affected formation state. Depending on their effect transition, solvents or co-solutes classified with respect action these parameters. Solvent interactions that alter entropic helix osmotic affect both stability...

Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order connect measured properties particular protein, model required fit. We discuss here application an exact two-state formula with its approximation process DSC experimental data on protein folding in water. The approximate relies smallness transition interval, which different for each protein. With example set 33 proteins, we show practical validity...

The problem of the helix-coil transition biopolymers in explicit solvents, such as water, with ability for hydrogen bonding a solvent is addressed analytically using suitably modified version Generalized Model Polypeptide Chains. Besides regular transition, an additional coil-helix or reentrant also found at lower temperatures. arises due to competition between polymer-polymer and polymer-water bonds. balance two types can be shifted either direction through changes not only temperature, but...

Abstract By taking into account base–base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one‐dimensional Potts‐like model with many‐particle interactions, GMPC describes helix–coil transition in both polypeptides and polynucleotides. In framework show that correctly introduced nearest‐neighbor against background hydrogen bonding lead to increased stability (melting temperature) and, unexpectedly, decreased cooperativity (maximal correlation...

We analyze the problem of helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms solvent action: action through formation solvent-polymer hydrogen bonds that can compete with intrinsic intra-polymer bonded configurations (competing interactions) and implicit action, where interactions tune biopolymer changing activity (non-competing interactions). The overall spin Hamiltonian is comprised three terms: background \emph{in...

A microscopic Potts-like one-dimensional model with many-particle interactions is developed to construct a statistical mechanical description of the melting heterogeneous sequence duplex DNA. For this model, referred as generalized polypeptide chains (GMPC), closed-form expression for free energy derived. The characteristic equation enables estimates on temperature and transition interval, consistent results obtained from more classical approaches. From temperature-dependent weight parameter...

Motivated by measurements on stretched double-stranded DNA in the presence of multivalent cations, we develop a statistical mechanical model for compaction an insoluble semiflexible polymer under tension. Using mean-field approach, determine order extended-to-compact transition and provide interpretation magnitude interval tensions over which takes place. In simplest thermodynamic limit infinitely long homogeneous polymer, is first-order that occurs at single value For finite length chains...

Dynamic light scattering (DLS) and size exclusion chromatography (SEC), that are among the most popular methods for determining polymer nanoparticle (PNP) sizes, essentially depend on quality of solution.

We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account specificity its primary sequence, as quantified by phase space volume ratio number all accessible states to corresponding helical conformation. The resulting transition diagram is then juxtaposed with unusual behavior secondary structures in Intrinsically Disordered Proteins (IDPs) and similarities are observed, even if protein folding more complex than transition. In fact,...

Abstract Solubility of polysilane macromolecules has so far been a scientific as well technological problem due to lack understanding their proper molecular size and agglomeration/de-agglomeration conditions. Here we show that, in contrary previous reports, the molecules are inherently small enough be, under right conditions, dissolved. We used dynamic light scattering differential scanning calorimetry that even dilute regime polymer agglomerated at room temperature undergo de-agglomeration...

Within the recently developed Hamiltonian formulation of Zimm and Bragg model we re-evaluate several size dependent approximations partition function. Our analysis is based on comparison chain length N with maximal correlation (persistence) ξ helical conformation. For first time re-derive function zipper by taking limits Zimm-Bragg eigenvalues. The critical consideration applicability boundaries for single-sequence (zipper) long has shown a gap in description range experimentally relevant...

Abstract Coarse‐grained chain simulations were used to study fragments of two homologous proteins the peripheral subunit‐binding domain (PSBD) family, Bacillus stearothermophilus PSBD (E3BD) and Escherichia coli 2‐oxo‐glutarate dehydrogenase (BBL). To ascertain a robust rank order folding cooperativity, native‐centric intraprotein interactions modeled by (i) common Gō‐like potential, (ii) potentials with desolvation barriers or (iii) many‐body terms. Homologous can possess substantially...

Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and nucleotides deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) two, a phenomenon related hybridization. We propose Hamiltonian formulation for zipper model that accounts DNA-CNT interactions allows processing experimental data, which has awaited an available theory decade.

The coil to globule transition of the polypeptide chain is physical phenomenon behind folding globular proteins. Globular proteins with a single domain usually consist about 30 100 amino acid residues, and this finite size extends interval coil-globule phase transition. Based on pedantic derivation two-state model, we introduce number residues as parameter in expressions for two cooperativity measures reveal their significance. We conclude that k2 measure, defined ratio van ’t Hoff...

We report on theoretical investigation of interactions different mechanisms and their influence onto DNA cooperativity helix–coil transition (melting). Using the modified version microscopic Potts-like one-dimensional model we showed that increased stacking results in decreased correlation length. The decrease is explained as a result combined hydrogen bonding stacking.

The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised two interacting side-by-side. Hamiltonian takes into account four possible types interactions between repeated units chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when energy Ihh+Icc (h-h, c-c) overwhelms Ihc+Ich mixed (h-c, c-h) interactions, correlation length rises substantially, resulting narrowing interval. In opposite case,...

The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types interactions occurring over different scales. This new scale GMPC applied in several specific cases examine: combined influence stacking or antistacking and hydrogen bonding, spatial restrictions on the length helical segments, cooperativity temperature interval helix-coil transition duplex DNA. For combination with bonding reduces basic uniscale a redefined scaling parameter Delta....