Computational and theoretical advances in studies of intrinsically disordered proteins

RB Best - Current opinion in structural biology, 2017 - Elsevier
Highlights•Improvements in all-atom simulations and implicit solvent models now allow IDP
simulations with realistic dimensions to be performed.•Native-centric coarse-grained …

Toward an understanding of biochemical equilibria within living cells

G Rivas, AP Minton - Biophysical reviews, 2018 - Springer
Four types of environmental effects that can affect macromolecular reactions in a living cell
are defined: nonspecific intermolecular interactions, side reactions, partitioning between …

A Kirkwood-Buff derived force field for aqueous alkali halides

MB Gee, NR Cox, Y Jiao, N Bentenitis… - Journal of chemical …, 2011 - ACS Publications
A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide
solutions (MX), where M= Li+, Na+, K+, Rb+, and Cs+ and X= F–, Cl–, Br–, and I–, and their …

Compositional influence of synthesized magnetic nanoparticles on epoxy composites: dielectric, magnetic, and optical characteristics

P Sharma, DV Shah, S Thakor… - … Science, Part B, 2024 - Taylor & Francis
Epoxy nano-magnetic composites exhibit remarkable and promising properties by
synergistically combining the properties of epoxy resin and magnetic nanofillers. The current …

Evolution of all-atom protein force fields to improve local and global properties

GH Zerze, W Zheng, RB Best… - The journal of physical …, 2019 - ACS Publications
Experimental studies on intrinsically disordered and unfolded proteins have shown that in
isolation they typically have low populations of secondary structure and exhibit distance …

Kirkwood–Buff approach rescues overcollapse of a disordered protein in canonical protein force fields

D Mercadante, S Milles, G Fuertes… - The journal of …, 2015 - ACS Publications
Understanding the function of intrinsically disordered proteins is intimately related to our
capacity to correctly sample their conformational dynamics. So far, a gap between …

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties

S Boothroyd, OC Madin, DL Mobley… - Journal of chemical …, 2022 - ACS Publications
Developing a sufficiently accurate classical force field representation of molecules is key to
realizing the full potential of molecular simulations as a route to gaining a fundamental …

Characterization of a Bacillus megaterium strain with metal bioremediation potential and in silico discovery of novel cadmium binding motifs in the regulator, CadC

WMNH Kumari, S Thiruchittampalam… - Applied microbiology …, 2021 - Springer
Bioremediation of toxic metal ions using bacterial strains is a promising tool. Metal binding
motifs in microbial proteins are involved in the regulation and transport of such toxic metals …

Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins

JJ Alston, A Soranno, AS Holehouse - Methods, 2021 - Elsevier
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have
emerged from a niche corner of biophysics to be recognized as essential drivers of cellular …

Linking trehalose self-association with binary aqueous solution equation of state

L Sapir, D Harries - The Journal of Physical Chemistry B, 2011 - ACS Publications
In aqueous solutions, trehalose possesses a high propensity to form hydrogen bonds with
water as well as other trehalose molecules. This hydrogen bonding not only affects water …