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.

SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces.

Curvature is an intrinsic feature of biological membranes underlying vital cellular processes such as endocytosis, membrane fusion-fission, trafficking, and remodeling. The continuous expansion of the spatiotemporal scales accessible to computational simulations nowadays makes possible quasi-atomistic molecular dynamics simulations of these processes. In despite of that, computation of the shapes and curvatures associated with the dynamics of biological membranes remains challenging.

Hydration, ionic valence and cross-linking propensities of cations determine the stability of lipopolysaccharide (LPS) membranes.

The supra-molecular structure of LPS aggregates governs outer membrane permeability and activation of the host immune response during Gram-negative bacterial infections. Molecular dynamics simulations unveil at atomic resolution the subtle balance between cation hydration and cross-linking ability in modulating phase transitions of LPS membranes.

The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View.

Lipopolysaccharides (LPS) are the main constituent of the outer bacterial membrane of Gram-negative bacteria. Lipid-A is the structural region of LPS that interacts with the innate immune system and induces inflammatory responses. It is formed by a phosphorylated β-d-glucosaminyl-(1→6)-α-N-glucosamine disaccharide backbone containing ester-linked and amide-linked long-chain fatty acids, which may vary in length and number depending on the bacterial strains and the environment.

The patterns of base sequences in the nucleic acids of prokaryotes and eukaryotes reflect features of their abiotic past.

The base sequences of the nucleic acids corresponding to ten proteins (aconitase, alcohol dehydrogenase, enolase, fumarase, isocitrate dehydrogenase, lactate dehydrogenase, phosphofructokinase, phosphoglycerate mutase, pyruvate kinase and succinate dehydrogenase) belonging to a total of 154 species, ranging from prokaryotes to vertebrates, were compared with the base sequences of oligoribotides whose growth rates were calculated by a chemical kinetics model. It was shown that oligoribotides grown according to the kinetics model have a fraction of repetitive bases larger than expected from random processes. The base sequences of nucleic acids of prokaryotes and eukaryotes retain, in decreasing proportions, this feature of their abiotic past.

Do older taxa have older proteins?

We have confirmed through an enlarged set of 728 species with 10,000 or more compiled codons, and a subset of 237 species with at least 50,000 compiled codons, that the mean values of a previously described index phi [the mean value of the ratio between the relative (G, C) content of Class II and Class I codons, where G and C are guanine and cytosine] decrease monotonically across five large taxa, viz archaea, bacteria, eukaryotes (excluding metazoa), metazoa (excluding vertebrates) and vertebrates. It is proposed that these main taxa diverge successively from an ancestral progenome along lines which have persisted over long periods of time, leading to a primordial non-symmetrical phylogenetic tree. Further divergence, i.