We use on-the-fly finite temperature string method in collective variables to study the transition from a normal to an amyloidogenic conformation of β2-microglobulin. We show that the protonation state of two histidine residues is of key importance, and that under acidic (protonating) conditions, the transition to the amyloidgenic form is facilitated by both displacement of N-terminal residues to disrupt a hydrophobic pocket and by side-chain/side-chain electrostatic attraction, both of which facilitate a cis-trans prolyl isomerization. The free energy barriers for the normal-to-amyloidogenic isomerization are found to be 14.9 and 7.1 kcal/mol for the neutral and protonated cases, respectively, consistent with enhanced amyloidgenesis at low pH observed both in vitro and in hemodialysis-associated amyloidosis, and somewhat lower than experimentally determined barriers for bare prolyl cis-trans isomerization. We suggest specific mutagenesis experiments which could be used to further validate the mechanism observed.

12-Hydroxystearic acid (12HSA) is a well-known organogelator, and its metal salts and derivatives find roles in many important applications. The structures of aggregates of 12-hydroxysteric acid and its salts depend sensitively on cation type, but a fundamental understanding of this phenomenon is lacking. In this study, molecular dynamics simulations were conducted on the microsecond long time scales for (1) 12HSA and (2) its lithium salt, each at 12.5 wt % in explicit hexane solvent. Self-assembly was accelerated by using a modified potential to prohibit alkane chain dihedral gauche states (all-trans-12HSA) and then verified by continuation using standard force-field parameters. In three independent simulation, acceleration using "gauche-less" potentials resulted in self-assembled pseudocrystalline aggregates through formation of polarized five- and six-membered rings between inter-12-hydroxyl groups and head-to-head carboxylic acid dimerization. When subjected to the unmodified dihedral potential, two of the three structures remained stable after 1 μs of MD. Stable structures exhibited a "ring-of-rings" motif, composed of two six-membered acetic acid-dimerized ring bundles with six satellite rings, while the unstable structure did not. In strong contrast, the lithium salt produced a network of fibrils that spanned the volume of the sample. When lithium ions were substituted for carboxylic acid protons in the stable acid structures, they remained intact but lost their chiral nature. Both the acid and lithium structures displayed scattering peaks that agreed with experiment. Taken together, our results suggest that this ring-of-rings structure could be a primary feature of the self-assembly of 12HSA in organic solvents.

Molecular dynamics simulations modeled the aramid poly(p-phenylene terephthalamide) (PPTA) and a related aromatic-aliphatic polyamide derived from a five-carbon aliphatic diacid (PAP5) with nine different reactive and non-reactive force fields. The force fields were evaluated based on crystal structures as well as intermolecular Hbonding and π-molecular interactions. The optimum force field was then used to simulate stress-strain behavior in the chain and transverse-to-chain directions. In the chain direction, PAP5 had higher ultimate stress and failure strain than PPTA; however, the stiffness of PAP5 was lower than PPTA at low strain (0-2%) while the reverse was observed at high strain (last 5% before failure). This contrast, and differences in the transverse direction properties, were explained by the methylene segments of PAP5 that confer conformational freedom, enabling accommodation of low strain without stretching covalent bonds. The simulation approach demonstrated here for two poly-1 Macromolecules 2021 10.1021/acs.macromol.1c00974 mers with distinct chemistry but similar atomic interactions may be extended to other polyamides.

12-Hydroxystearic acid (12HSA) and its derivatives are well-known organogelators, and they play critical roles in a variety of applications. The overall aggregate structure of 12HSA is sensitive to the chirality at the 12th carbon, but a fundamental understanding of this dependence is lacking. In this study, molecular dynamics simulations were conducted on microsecond long time scales for (1) (R)-12HSA, (2) (S)-12HSA, and (3) a 50/50 racemic mixture, each solvated at 12.5 wt % in explicit hexane. Self-assembly was accelerated by turning off alkyl chain dihedral gauche states and forcing the molecules to adopt an all-trans conformation. The stability of the resulting aggregates was tested by quenching them with access to gauche states restored. Ordered aggregates produced from optically pure (R)- and (S)-12HSA remained stable for at least 1 μs. The characteristic ordered structure observed is termed a "ring-of-rings" motif, and it contains two twisted six-membered ringlike bundles connected through acetic acid dimerization and surrounded by six satellite bundles. The chirality at the 12th carbon dictates the overall twist of the rings and thereby the handedness of the aggregates. Racemic mixtures did not produce stable ordered aggregates likely due to insufficient enantiomerically pure ring formation. The most prevalent finite-size effect observed was the stochastic formation of percolating aggregates, which were later avoided by using solvent-permeable, solute-impermeable, confining walls. The resulting ordered aggregates were in all important ways identical to those produced in unconfined systems. The combination of cycling off and on gauche states and the semipermeable walls may be an important new way to study the self-assembly underlying aggregation at industrially relevant concentrations of surfactants in organic solvents.

The serotonin 5-HT(3) receptor (5-HT(3)R) is a member of the Cys-loop ligand-gated ion channel family. We used a combination of site-directed mutagenesis, homology modeling, and ligand-docking simulations to analyze antagonist-receptor interactions. Mutation of E236, which is near loop C of the binding site, to aspartate prevents expression of the receptor on the cell surface, and no specific ligand binding can be detected. On the other hand, mutation to glutamine, asparagine, or alanine produces receptors that are expressed on the cell surface, but decreases receptor affinity for the competitive antagonist d-tubocurarine (dTC) 5-35-fold. The results of a double-mutant cycle analysis employing a panel of dTC analogs to identify specific points of interactions between the dTC analogs and E236 are consistent with E236 making a direct physical interaction with the 12 -OH of dTC. dTC is a rigid molecule of known three-dimensional structure. Together with previous studies linking other regions of dTC to specific residues in the binding site, these data allow us to define the relative spatial arrangement of three different residues in the ligand-binding site: R92 (loop D), N128 (loop A), and E236 (near loop C). Molecular modeling employing these distance constraints followed by molecular-dynamics simulations produced a dTC/receptor complex consistent with the experimental data. The use of the rigid ligands as molecular rulers in conjunction with double-mutant cycle analysis provides a means of mapping the relative positions of various residues in the ligand-binding site of any ligand-receptor complex, and thus is a useful tool for delineating the architecture of the binding site.