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Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations.
This study of lipid-mediated interactions between proteins is based on a theory recently developed by the authors for describing the structure of the hydrocarbon chains in the neighborhood of aExpand
TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance.
TLDR
Comparison of MD-derived order parameters with those obtained from model-free analysis of nuclear magnetic resonance (NMR) relaxation data shows high agreement for N-H moieties within alpha- and beta-secondary structures, but significant deviation for those in loops. Expand
Lipid-mediated interactions between intrinsic membrane proteins: dependence on protein size and lipid composition.
TLDR
The results indicate that the packing of the hydrocarbon chains around protein inclusions in LBMs gives rise to a generic (i.e., nonspecific) lipid-mediated interaction which favors the association of two alpha-helices and depends on the lipid composition of the membrane. Expand
Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids.
TLDR
An extension of the classical surfactant theory of Israelachvili based on shapes is proposed to introduce the concept of a "dynamically induced shape" of the membrane lipids by the peptide. Expand
Ligand Binding to Truncated Hemoglobin N from Mycobacterium tuberculosis Is Strongly Modulated by the Interplay between the Distal Heme Pocket Residues and Internal Water*
TLDR
Molecular dynamics simulations, performed with trHbN and its distal mutants, indicated that in the absence of a distal water molecule, ligand access to the heme iron is not hindered and that a water molecule is stabilized next to theHeme iron through hydrogen-bonding with Tyr(B10) and Gln(E11). Expand
Structural characterization of the tunnels of Mycobacterium tuberculosis truncated hemoglobin N from molecular dynamics simulations
TLDR
Tunnel dynamics in trHbN was found to be controlled by the side‐chain conformation of the Tyr33(B10), Gln58(E11), and Phe62(E15) residues, and it is proposed that the EH and the long tunnels are used for apolar ligands storage. Expand
Quinazoline‐4‐piperidine sulfamides are specific inhibitors of human NPP1 and prevent pathological mineralization of valve interstitial cells
TLDR
Quinazoline‐4‐piperidine sulfamides (QPS) have been described as potent inhibitors of NPP1, but their mode of inhibition as well as their selectivity and capacity to modify biological processes have not been investigated. Expand
Molecular model of hemoglobin N from Mycobacterium tuberculosis bound to lipid bilayers: a combined spectroscopic and computational study.
TLDR
The interactions between hemoglobin N (HbN), a group I 2-on-2 hemoglobin from the pathogenic Mycobacterium tuberculosis (Mtb), and biological membranes using both experimental techniques and MD simulations indicated that HbN is a peripheral protein, and the association with the membranes occurred via the pre-A, G, and H helices. Expand
Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida.
TLDR
The hypothesis that A. salmonicida is a considerable reservoir for mobile genetic elements such as plasmids is confirmed, reinforced by the discovery of an isolate of this bacterium bearing an additional unidentified small plasmid. Expand
Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces
A straightforward method that accounts for the long-range Lennard-Jones (LJ) terms in constant pressure molecular dynamics simulations is presented. This long-range correction (LRC) consists of anExpand
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