Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 1503.05334

Structuring of counterions around dna double helix: a molecular dynamics study

O. O. Liubysh·A. V. Vlasiuk·S. M. Perepelytsya
View original source ↗Read source document ↗Export metadata ↓

Abstract

Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been simulated. The systems have been considered in the regimes without excess salt and with different salts (0.5 M of NaCl, KCl or CsCl) added. The results have showed that the Na$^{+}$ counterions interact with the phosphate groups directly from outside of the double helix and via water molecules at the top edge of DNA minor groove. The potassium ions are mostly localized in the grooves of the double helix, and the cesium ions penetrate deeply inside the minor groove being bonded directly to the atoms of nucleic bases. Due to the electrostatic repulsion the chlorine ions tend to be localized at large distances from the DNA polyanion, but some Cl$^{-}$ anions have been detected near atomic groups of the double helix forming electrically neutral pairs with counterions already condensed on DNA. The DNA sites, where counterions are incorporated, are characterized by local changes of double helix structure. The lifetime of Na$^{+}$ and K$^{+}$ in complex with DNA atomic groups is less than 0.5 ns, while in the case of the cesium ions it may reach several nanoseconds. In this time scale, the Cs$^{+}$ counterions form a structured system of charges in the DNA minor groove that can be considered as ionic lattice.

Explore related subjects

q-bio.BM

Keep this discovery

BibTeXRIS

O. O. Liubysh, A. V. Vlasiuk, S. M. Perepelytsya. 2015-03-18. Structuring of counterions around dna double helix: a molecular dynamics study. https://arxiv.org/abs/1503.05334

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Sequence-Informed Geometric Evaluation of RNA 3D Structures

Computational RNA structure pipelines generate many candidate conformations for the same sequence. Reliable evaluation therefore requires more than recognising plausible geometry, it requires determining whether that geometry is compatible with the sequence. We introduce SIRGE, a sequence-informed geometric evaluator that conditions structural representations on nucleotide embeddings from a pretrained RNA language model. Early results show that SIRGE outperforms established evaluators in Kendall--$\tau$ alignment, Top-1 selection, and Top-3 ranking. Controlled comparisons further show that sequence conditioning corrects errors made by an otherwise matched geometric model and improves target-level rank structure. These findings provide initial evidence that pretrained sequence representations supply ranking information that complements geometric reasoning.

q-bio.BM↗
arXiv2026

PocketVE: Stable and Property-Guided Structure-Based Drug Design with Variance-Exploding Diffusion

Protein-conditioned 3D molecule generation is a central challenge in structure-based drug design, requiring a balance between pocket compatibility, molecular properties, and physical geometry. We propose \textbf{PocketVE}, a protein-pocket-conditioned variance-exploding (VE) diffusion framework that couples stable coordinate denoising with inference-time property guidance. Specifically, PocketVE combines an EDM-style training and sampling setup for 3D denoising, classifier-free guidance for multi-property steering without external property classifiers, and adaptive protein perturbation as a training-time pocket regularizer. Evaluated on CrossDocked2020 under the GenBench3D protocol, PocketVE improves Valid$_{3\text{D}}$ from 58.6 to 80.6 and reduces strain energy from 457.4 to 127.9 relative to its TAGMol architectural baseline, while retaining competitive docking and molecular-property scores under moderate guidance. A guidance-scale study shows that moderate guidance gives a favorable balance between target-related objectives and geometric quality, whereas stronger guidance can degrade geometry and distributional fidelity. Pocket-permutation and PoseCheck diagnostics further support pocket-specific spatial compatibility with reduced steric conflicts. Overall, the results suggest that geometric stability and inference-time property guidance should be considered as coupled design objectives.

q-bio.BM↗
arXiv2026

Predicting directional flexibility in proteins

Predicting protein dynamics is a long-standing problem in computational structural biology. Often, protein function critically depends on local directed motions, such as hinge movements, catalytic loop rearrangements and domain reorientations, which can be characterized by directional flexibility and correlated structural motions of the protein backbone. While Molecular Dynamics (MD) simulations provide an established but often prohibitively expensive approach, recent deep generative models aim to reduce this cost by directly predicting conformational ensembles, emulating MD. However, due to their large size and the need to generate several states until the derived dynamical properties converge, these models remain expensive. In this work, we propose BackFlip-2: a fast SE(3)-equivariant graph neural network trained to directly predict dynamical descriptors, such as directional backbone flexibility and pairwise dynamic correlations, from an equilibrium structure. In a series of experiments, we show that our model matches the accuracy of substantially larger ensemble generation models while being orders of magnitude faster, and demonstrate that the proposed equivariant architecture is especially well-suited for capturing anisotropic motions in proteins. BackFlip-2 model weights, training and inference code are available at https://github.com/graeter-group/backflip.

q-bio.BM↗