Binding of the plant-derived toxin simplexin to bovine protein kinase C: insights from molecular dynamics.

Pimelea poisoning of cattle is toxicologically linked to the activation of bovine protein kinase C (PKC) by the plant-derived toxin simplexin. To understand the affinity of PKC for simplexin, we performed molecular dynamics (MD) studies of simplexin, simplexin analogues, and several other activators of PKC. Binding enthalpy calculations indicated that simplexin had the strongest affinity for PKCα-C1B among the activators studied. Key to simplexin's affinity is its ability to form more hydrogen bonds to PKC, compared to the other activators. The C-3 carbonyl group and C-20 hydroxyl group of simplexin were identified as especially important for stabilizing the PKC binding interaction. The hydrophobic alkyl chain of simplexin induces deep membrane embedding of the PKC-simplexin complex, enhancing the protein-ligand hydrogen bonding. Our findings align with previous experiments on structure-activity relationships (SAR) for simplexin analogues, and provide insights that may guide the development of interventions or treatments for Pimelea poisoning.

Molecular dynamics simulations support a preference of cyclotide kalata B1 for phosphatidylethanolamine phospholipids.

Kalata B1 (kB1), a naturally occurring cyclotide has been shown experimentally to bind lipid membranes that contain phosphatidylethanolamine (PE) phospholipids. Here, molecular dynamics simulations were used to explore its interaction with two phospholipids, palmitoyloleoylphosphatidylethanolamine (POPE), palmitoyloleoylphosphatidylcholine (POPC), and a heterogeneous membrane comprising POPC/POPE (90:10), to understand the basis for the selectivity of kB1 towards PE phospholipids. The simulations showed that in the presence of only 10 % POPE lipid, kB1 forms a stable binding complex with membrane bilayers. An ionic interaction between the E7 carboxylate group of kB1 and the ammonium group of PE headgroups consistently initiates binding of kB1 to the membrane. Additionally, stable noncovalent interactions such as hydrogen bonding (E7, T8, V10, G11, T13 and N15), cation-π (W23), and CH-π (W23) interactions between specific residues of kB1 and the lipid membrane play an important role in stabilizing the binding. These findings are consistent with a structure-activity relationship study on kB1 where lysine mutagenesis on the bioactive and hydrophobic faces of the peptide abolished membrane-dependent bioactivities. In summary, our simulations suggest the importance of residue E7 (in the bioactive face) in enabling kB1 to recognize and bind selectively to PE-containing phospholipids bilayers through ionic and hydrogen bonding interactions, and of W23 (in the hydrophobic face) for the association and insertion of kB1 into the lipid bilayer through cation-π and CH-π interactions. Overall, this work enhances our understanding of the molecular basis of the membrane binding and bioactivity of this prototypic cyclotide.

Endo Selectivity in the (4 + 3) Cycloaddition of Oxidopyridinium Ions.

The (4 + 3) cycloaddition of 2-trialkylsilyl-4-alkylbutadienes with an N-methyloxidopyridinium ion affords cycloadducts with high regioselectivity and excellent endo selectivity.

How does cross-conjugation influence thiol additions to enones? A computational study of thiol trapping by the naturally occurring divinyl ketones zerumbone and α-santonin.

Density functional theory calculations are reported which explore how the kinetics and thermodynamics of thiol additions to enones are affected by the incorporation of the enone into a cross-conjugated divinyl ketone moiety. Computations with ωB97X-D//M06-2X indicate that in the parent acyclic system (1,4-pentadien-3-one), cross-conjugation has a small stabilizing effect on the thiol adduct, making the ΔG for the addition slightly more negative, and a larger stabilizing effect on the transition state, lowering ΔG‡. By contrast, in the parent six-membered cyclic system (2,5-cyclohexadien-1-one), cross-conjugation makes ΔG significantly less negative while causing only a small increase in ΔG‡. Both scenarios correspond to a more reversible addition. Thiol additions to two naturally occurring divinyl ketones, zerumbone and α-santonin, are examined. Previous NMR-based assays had shown that zerumbone forms mono- and bis-thiol adducts while α-santonin showed no detectable adduct formation. Computations reveal that the eleven-membered ring structure of zerumbone accelerates thiol trapping, relative to an analogous acyclic model. For α-santonin, the computations reveal that thiol addition is actually also rather facile, and it likely does occur, but the adduct is unstable and rapidly eliminates the thiol. These results illustrate that the inability to detect a thiol adduct in an experimental assay does not necessarily imply that the adduct does not form; instead it may simply be a manifestation of a rapid addition/elimination equilibrium in which the adduct concentration is below the limits of detectability.

Origin of the Excited-State Absorption Spectrum of Polythiophene.

The excited states of conjugated polymers play a central role in their applications in organic solar photovoltaics. The delocalized excited states of conjugated polymers are short-lived (τ < 40 fs) but are imperative in the photovoltaic properties of these materials. Photoexcitation of poly(3-hexylthiophene) (P3HT) induces an excited-state absorption band, but the transitions that are involved are not well understood. In this work, calculations have been performed on P3HT analogues using nonlinear response time-dependent density functional theory to show that an increase in the oligomer length correlates with the dominance of the S1 → S3 transition. Furthermore, the predicted transition energy shows an excellent agreement with experiment. The calculations also yielded results on intramolecular charge transfer in P3HT due to the S1 → S3 transition, providing insight into the mechanism of exciton dissociation to form charge carriers.