Significance of Zn2+ in RyR1 for Structural Integrity and Ligand Binding: Insight from Molecular Dynamics.

Ryanodine receptor type 1 (RyR1) is a Ca2+-release channel central to skeletal muscle excitation-contraction (EC) coupling. RyR1's cryo-EM structures reveal a zinc-finger motif positioned within the cytoplasmic C-terminal domain (CTD). Yet, owing to limitations in cryo-EM resolution, RyR1 structures lack precision in detailing the metal coordination structure, prompting the need for an accurate model. In this study, we employed molecular dynamics (MD) simulations and the density functional theory (DFT) method to refine the binding characteristics of Zn2+ in the zinc-finger site of the RyR1 channel. Our findings also highlight substantial conformational changes in simulations conducted in the absence of Zn2+. Notably, we observed a loss of contact at the interface between protein domains proximal to the zinc-finger site, indicating a crucial role of Zn2+ in maintaining structural integrity and interdomain interactions within RyR1. Furthermore, this study provides valuable insights into the modulation of ATP, Ca2+, and caffeine binding, shedding light on the intricate relationship between Zn2+ coordination and the dynamic behavior of RyR1. Our integrative approach combining MD simulations and DFT calculations enhances our understanding of the molecular mechanisms governing ligand binding in RyR1.

Conformation, flexibility and hydration of hyaluronic acid by molecular dynamics simulations.

Hyaluronic acid (HA) is a biopolymer of disaccharide with two alternate glycosidic bonds, ß(1,3) and ß(1,4). A molecular dynamics study presented here unveiled conformational variability in association with the flexibility of the glycosidic linkers, which depends on the number of disaccharide units. HA chain maintains a rigid rod-like conformation with short chain lengths. Crossover from a rod-like to a random-coil conformation is observed with increasing the chain length. The conformation with the ß(1,4) linkage is more flexible than that with the ß(1,3) linkage. Variation of the radius of gyration and conformational fluctuation showed that the ß(1,4) linkers along with the HA chain length enhance the overall conformational flexibility and therefore elastic response of the polymer chain. Besides the inter-saccharide hydrogen bonding, Na+ binds preferably at the ß(1,4) site. The hydration number of HA increases as an increase in the chain length. The hydration per disaccharide unit remains constant with the chain length.

Furofuran lignans as a new series of antidiabetic agents exerting α-glucosidase inhibition and radical scarvenging: Semisynthesis, kinetic study and molecular modeling.

A new series of furofuran lignans containing catechol moiety were prepared from the reactions between lignans and a variety of phenolics. All 22 products obtained were evaluated against three different α-glucosidases (maltase, sucrase and Baker's yeast glucosidase) and DPPH radical. Of furofuran lignans evaluated, ß-14, having two catechol moieties and one acetoxy group, was the most potent inhibitor against Baker's yeast, maltase, and sucrase with IC50 values of 5.3, 25.7, and 12.9 µM, respectively. Of interest, its inhibitory potency toward Baker's yeast was 28 times greater than standard drug, acarbose and its DPPH radical scavenging (SC50 11.2 µM) was 130 times higher than commercial antioxidant BHT. Subsequent investigation on mechanism underlying the inhibitory effect of ß-14 revealed that it blocked Baker's yeast and sucrase functions by mixed-type inhibition while it exerted non-competitive inhibition toward maltase. Molecular dynamics simulation of the most potent furofuran lignans (4, α-8b, α-14, and ß-14) with the homology rat intestinal maltase at the binding site revealed that the hydrogen bond interactions from catechol, acetoxy, and quinone moieties of furofuran lignans were the key interaction to bind tightly to α-glucosidase. The results indicated that ß-14 possessed promising antidiabetic activity through simultaneously inhibiting α-glucosidases and free radicals.