Mechanism of Peroxynitrite Interaction with Ferric Nitrobindin: A Computational Study.

Nitrobindins (Nbs) are all-β-barrel heme proteins present along the evolutionary ladder. They display a highly solvent-exposed ferric heme group with the iron atom being coordinated by the proximal His residue and a water molecule at the distal position. Ferric nitrobindins (Nb(III)) play a role in the conversion of toxic peroxynitrite (ONOO) to harmless nitrate, with the value of the second-order rate constant being similar to those of most heme proteins.

Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation.

Nitrobindins (Nbs) represent an evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom, coordinated by a proximal His residue. Interestingly, even if the distal side is exposed to the solvent, the value of the second order rate constants for ligand binding to the ferrous derivative is almost one order of magnitude lower than those reported for myoglobins (Mbs). Noteworthy, nitric oxide binding to the sixth coordination position of the heme-Fe(II)-atom causes the cleavage or the severe weakening of the proximal His-Fe(II) bond.

Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field.

Cysteine is a common amino acid with a thiol group that plays a pivotal role in a variety of scenarios in redox biochemistry. In contrast, selenocysteine, the 21st amino acid, is only present in 25 human proteins. Classical force-field parameters for cysteine and selenocysteine are still scarce.

Assessing the impact of valence asymmetry in ionic solutions and its consequences on the performance of supercapacitors.

Molecular dynamics simulations were performed to describe the properties of hypothetical salt electrolytic solutions. The main focus of this work is the valence asymmetry, which in recent years has been considered an important aspect in the physical chemistry of aqueous electrolytes. In general, our results show that the structural, energetic, and dynamic properties respond differently to the asymmetry of ionic solutions, but in all cases, appreciable changes were observed.

Salt-in-water and water-in-salt electrolytes: the effects of the asymmetry in cation and anion valence on their properties.

We investigated the structural, dynamic, energetic, and electrostatic properties of electrolytes based on the ion pairs LiCl and LiSO. Atomistic molecular dynamics simulations were used to simulate these aqueous electrolytic solutions at two different concentrations 2 M (normal) and 21 M (superconcentrated, WiSE). The effects of the valence asymmetry of the LiSO electrolyte were also discussed for both salt concentrations.

The tug of war between Al and Na for order-disorder transitions in lipid-A membranes.

Cations play a critical role in the stability and morphology of lipid-A aggregates by neutralizing, hydrating and cross-linking these glycolipid molecules. Monophosphorylated lipid-A is the major immunostimulatory principle in commercially available adjuvants containing Al3+ such as adjuvant system 04 (AS04). The antagonist/agonist immunomodulatory properties of lipid-A are associated with chemical variations (e.

Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers.

Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling the prediction of experimental observables for a variety of chemical systems and processes and majorly impacting the study of biological membranes. However, the chemical diversity of complex lipids beyond phospholipids brings new challenges to well-established protocols used in MD simulations of soft matter and requires continuous assessment to ensure simulation reproducibility and minimize unphysical behavior. Lipopolysaccharides (LPS) are highly charged glycolipids whose aggregation in a lamellar arrangement requires the binding of numerous cations to oppositely charged groups deep inside the membrane.