Electrostatic interactions in protein structure, folding, binding, and condensation
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …
specific electrostatic interactions, impart important properties to proteins. Modulation of the …
[HTML][HTML] A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization
E Duboue-Dijon, M Javanainen, P Delcroix… - The Journal of …, 2020 - pubs.aip.org
Molecular simulations can elucidate atomistic-level mechanisms of key biological
processes, which are often hardly accessible to experiment. However, the results of the …
processes, which are often hardly accessible to experiment. However, the results of the …
Enhanced-sampling simulations for the estimation of ligand binding kinetics: current status and perspective
The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …
parameter of fundamental importance in drug design. Here we review recent major …
Further along the road less traveled: AMBER ff15ipq, an original protein force field built on a self-consistent physical model
KT Debiec, DS Cerutti, LR Baker… - Journal of chemical …, 2016 - ACS Publications
We present the AMBER ff15ipq force field for proteins, the second-generation force field
developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized …
developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized …
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding
Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …
play an important role in cellular signaling. However, it is challenging to simulate both …
Mechanism of tripeptide trimming of amyloid β-peptide 49 by γ-secretase
The membrane-embedded γ-secretase complex processively cleaves within the
transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue …
transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue …
Ligand modulation of sidechain dynamics in a wild-type human GPCR
GPCRs regulate all aspects of human physiology, and biophysical studies have deepened
our understanding of GPCR conformational regulation by different ligands. Yet there is no …
our understanding of GPCR conformational regulation by different ligands. Yet there is no …
Histone H4 tails in nucleosomes: a fuzzy interaction with DNA
SO Rabdano, MD Shannon, SA Izmailov… - Angewandte …, 2021 - Wiley Online Library
The interaction of positively charged N‐terminal histone tails with nucleosomal DNA plays
an important role in chromatin assembly and regulation, modulating their susceptibility to …
an important role in chromatin assembly and regulation, modulating their susceptibility to …
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals
V Kurauskas, SA Izmailov, ON Rogacheva… - Nature …, 2017 - nature.com
Proteins perform their functions in solution but their structures are most frequently studied
inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using …
inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using …
Rapid quantification of protein-ligand binding via 19F NMR lineshape analysis
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of
fluorine into proteins and fragment libraries for drug discovery has become increasingly …
fluorine into proteins and fragment libraries for drug discovery has become increasingly …