arXiv subjects

Elena A. Zubova

Publications and source records attributed to Elena A. Zubova.

5 recordsLinked to original sources

arXiv2025

Cation-DNA outer sphere coordination in DNA polymorphism

There are two approaches to describing DNA-ions interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry approach is a search for modes of direct binding of ions to ionophores of DNA. We study both the inner and outer sphere coordination of ions by ionophores of the A and C forms of DNA in molecular dynamics simulations in two low-polarity solvents: in ethanol-water and methanol-water mixtures. We show that the counterion-DNA outer sphere coordination plays a key role in the experimentally observed conformational polymorphism of the DNA molecule: a transition to the A form in ethanol and to the C form in methanol. We identify the ionophores responsible for the existence of the A- and C-complexes. In both the complexes, the ions' inner sphere ligands are mostly water molecules, the ions reside in water clusters. In ethanol-water mixture, the water clusters are large, the major groove of the A-DNA is filled with water, and all ionophores are accessible to ions. In methanol-water mixture, the water clusters are small, and a large number of methanol clusters are present near DNA surface. They interfere with the coordination of ions in one of the ionophores of the major groove, and also with other ionophores near phosphates. Therefore, in methanol, the interaction energy of counterions with A-DNA cannot compensate for the repulsion between closely located phosphates. Therefore, the ions fill more accessible ionophores of the C-complex, converting DNA into the C form.

q-bio.BM↗

arXiv2022

C-A test of DNA force fields

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.

physics.comp-ph↗

arXiv2019

Shear induced martensitic transformations in crystalline polyethylene: direct MD simulation

For the first time, we carry out molecular dynamics (MD) simulation of shear-induced martensitic phase transitions between the orthorhombic and non-orthorhombic (triclinic and monoclinic) phases of crystalline polyethylene (PE) in the framework of a realistic all atom model of the polymer. We show that the variation of the shear rate allows observing on a nano-sample both a strongly nonequilibrium phase transition occurring by random nucleation and irregular growth of a new phase ('civilian' way, for rapid deformations) and the coherent, or 'military', kinetics (generally considered as usual for martensitic transformations). We induce transitions from the orthorhombic to the triclinic phase according to two transformation modes observed in experiment on PE single crystals. Rapid deformation favors the transition directly to the triclinic phase, slow deformation - first to the intermediate monoclinic, and only then - to the triclinic phase. The second way corresponds to the experiment on extended chain PE. We explain this result and analyze the competition between different transformation and plastic deformation modes. Rotations of PE chains around their axes necessary for the transition between the orthorhombic and non-orthorhombic phases are executed by short twist defects diffusing along the chains. The transition between the monoclinic and triclinic phases occurs through half-chain-period translations of the chains along their axes, mostly collectively, as crystallographic slips.

cond-mat.mtrl-sci↗

arXiv2016

The "sugar" coarse-grained DNA model

More than twenty coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (6 per nucleotide) needed for the "sugar" GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up" approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions.

physics.chem-ph↗

arXiv2011

The simplest model of polymer crystal exhibiting polymorphism

Almost all the polymer crystals have several polymorphic modifications. Their structure and existence conditions, as well as transitions between them are not understood even in the case of the 'model' polymer polyethylene (PE). For analysis of polymorphism in polymer crystals, we consider the simplest possible model of polymer chain: an extended flat zigzag made of 'united' atoms (replacing CH2-groups in PE chain); the united atoms belonging to different zigzags interact via Lennard-Jones potential. Analysis of potential of interaction between such zigzags allowed to predict the structure of five possible equilibrium lattices in polymer crystal built out of such zigzags. Molecular dynamics simulation of the crystal built out of flexible zigzags showed that, depending on model parameters (dimensions of the zigzag and equilibrium distance of Lennard-Jones potential), one to three of these lattices are stable in bulk at low temperatures. We have determined the model parameters at which the existing stable lattices are analogous to the ones observed in real PE and linear alkanes. The triclinic lattice has the lowest potential energy, then follows the monoclinic lattice, and the orthorhombic lattice has the highest energy, exactly as in full atomic (with hydrogens) molecular dynamics models.

cond-mat.mtrl-sci↗