Water dynamics in the hydration shells of biomolecules

D Laage, T Elsaesser, JT Hynes - Chemical Reviews, 2017 - ACS Publications
The structure and function of biomolecules are strongly influenced by their hydration shells.
Structural fluctuations and molecular excitations of hydrating water molecules cover a broad …

Understanding nucleic acid–ion interactions

J Lipfert, S Doniach, R Das… - Annual review of …, 2014 - annualreviews.org
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the
folding and dynamics of RNA and DNA and their complexes with proteins and with each …

Magnesium ion–water coordination and exchange in biomolecular simulations

O Allnér, L Nilsson, A Villa - Journal of chemical theory and …, 2012 - ACS Publications
Magnesium ions have an important role in the structure and folding mechanism of
ribonucleic acid systems. To properly simulate these biophysical processes, the applied …

Multivalent ions and biomolecules: Attempting a comprehensive perspective

O Matsarskaia, F Roosen‐Runge… - ChemPhysChem, 2020 - Wiley Online Library
Ions are ubiquitous in nature. They play a key role for many biological processes on the
molecular scale, from molecular interactions, to mechanical properties, to folding, to self …

[HTML][HTML] Small-angle scattering techniques for peptide and peptide hybrid nanostructures and peptide-based biomaterials

IW Hamley, V Castelletto - Advances in Colloid and Interface Science, 2023 - Elsevier
The use of small-angle scattering (SAS) in the study of self-assembly of peptides and
peptide conjugates (lipopeptides, polymer-peptide conjugates and others) is reviewed …

Sensitivity of the RNA structure to ion conditions as probed by molecular dynamics simulations of common canonical RNA duplexes

P Kuhrova, V Mlynsky, M Otyepka… - Journal of Chemical …, 2023 - ACS Publications
RNA molecules play a key role in countless biochemical processes. RNA interactions, which
are of highly diverse nature, are determined by the fact that RNA is a highly negatively …

[HTML][HTML] Ion counting from explicit-solvent simulations and 3D-RISM

GM Giambaşu, T Luchko, D Herschlag, DM York… - Biophysical journal, 2014 - cell.com
The ionic atmosphere around nucleic acids remains only partially understood at atomic-level
detail. Ion counting (IC) experiments provide a quantitative measure of the ionic atmosphere …

Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable …

A Savelyev, AD MacKerell Jr - The Journal of Physical Chemistry …, 2015 - ACS Publications
In the present study we report on interactions of and competition between monovalent ions
for two DNA sequences in MD simulations. Efforts included the development and validation …

Quantitative Determination of Metal Ion Adsorption on Cellulose Nanocrystals Surfaces

HR Paul, MK Bera, N Macke, SJ Rowan, MV Tirrell - ACS nano, 2024 - ACS Publications
Nanocellulose is a bio-based material that holds significant potential in the field of water
purification. Of particular interest is their potential use as a key sorbent material for the …

Ion counting demonstrates a high electrostatic field generated by the nucleosome

M Gebala, SL Johnson, GJ Narlikar, D Herschlag - Elife, 2019 - elifesciences.org
In eukaryotes, a first step towards the nuclear DNA compaction process is the formation of a
nucleosome, which is comprised of negatively charged DNA wrapped around a positively …