Molecular dynamics simulations in photosynthesis
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments,
lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics …
lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics …
State-dependent lipid interactions with the A2a receptor revealed by MD simulations using in vivo-mimetic membranes
Membranes are known to have modulatory effects on G protein-coupled receptors (GPCRs)
via specific lipid interactions. However, the mechanisms of such modulations in …
via specific lipid interactions. However, the mechanisms of such modulations in …
Insights into the polyhexamethylene biguanide (PHMB) mechanism of action on bacterial membrane and DNA: A molecular dynamics study
S Sowlati-Hashjin, P Carbone… - The Journal of Physical …, 2020 - ACS Publications
Polyhexamethylene biguanide (PHMB) is a cationic polymer with antimicrobial and antiviral
properties. It has been commonly accepted that the antimicrobial activity is due to the ability …
properties. It has been commonly accepted that the antimicrobial activity is due to the ability …
Chemical additives enable native mass spectrometry measurement of membrane protein oligomeric state within intact nanodiscs
Membrane proteins play critical biochemical roles but remain challenging to study. Recently,
native or nondenaturing mass spectrometry (MS) has made great strides in characterizing …
native or nondenaturing mass spectrometry (MS) has made great strides in characterizing …
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
Motivation Glycans play a central role in many essential biological processes. Glycan
Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files …
Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files …
CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an
extension over a traditional additive or pairwise FF and provides a more realistic model of …
extension over a traditional additive or pairwise FF and provides a more realistic model of …
In Situ Analysis of Weakly Bound Proteins Reveals Molecular Basis of Soft Corona Formation
D Sanchez-Guzman, G Giraudon--Colas, L Marichal… - ACS …, 2020 - ACS Publications
Few experimental techniques allow the analysis of the protein corona in situ. As a result,
little is known on the effects of nanoparticles on weakly bound proteins that form the soft …
little is known on the effects of nanoparticles on weakly bound proteins that form the soft …
Computing relative binding affinity of ligands to receptor: An effective hybrid single-dual-topology free-energy perturbation approach in NAMD
An effective hybrid single-dual-topology protocol is designed for the calculation of relative
binding affinities of small ligands to a receptor. The protocol was developed as an extension …
binding affinities of small ligands to a receptor. The protocol was developed as an extension …
PtdIns4P is required for the autophagosomal recruitment of STX17 (syntaxin 17) to promote lysosomal fusion
The autophagosomal SNARE STX17 (syntaxin 17) promotes lysosomal fusion and
degradation, but its autophagosomal recruitment is incompletely understood. Notably …
degradation, but its autophagosomal recruitment is incompletely understood. Notably …
Molecular dynamics simulations of membrane proteins: An overview
K Goossens, H De Winter - Journal of chemical information and …, 2018 - ACS Publications
Simulations of membrane proteins have been rising in popularity in the past decade.
Advancements in technology and force fields made it possible to simulate behavior of …
Advancements in technology and force fields made it possible to simulate behavior of …