Ligand migration in myoglobin: a combined study of computer simulation and x-ray crystallography

A ligand-migration mechanism of myoglobin was studied by a multidisciplinary approach that used x-ray crystallography and molecular dynamics simulation. The former revealed the structural changes of the protein along with the ligand migration, and the latter provided the statistical ensemble of protein conformations around the thermal average. We developed a novel computational method, homogeneous ensemble displacement, and generated the conformational ensemble of ligand-detached species from that of ligand-bound species. The thermally averaged ligand-protein interaction was illustrated in terms of the potential of mean force. Although the structural changes were small, the presence of the ligand molecule in the protein matrix significantly affected the 3D scalar field of the potential of mean force, in accordance with the self-opening model proposed in the previous x-ray study.     

Finite termination of the proximal point algorithm in Banach spaces

In this paper, we show that the convex optimization problem can be solved by the proximal point algorithm in a finite number of steps under the assumption that the solution set is a set of weak sharp minima.     

Structural basis for the phase switching of bisaminecopper(II) cations at the thermal limits of lattice stability

The structural grounds of the decrease of point and lattice symmetries coupled with switching of the exchange interaction in single crystals of a highly strained, coordinationally unsaturated bisdiaminecopper(II) cation are described. The combined magnetic susceptibility and X-ray diffraction results indicate that the interplay between the inherent vibronic instability and ligand-field strain imposed by moderately flexible, coordinationally shielding ligands enables effective switching of the pseudo-Jahn-Teller d9 centers between states with different exchange interaction in the low-temperature regime and valence orbital orientation and coordination geometry in the high-temperature regime. Within the low-temperature hysteresis region, the phase transition can also be induced by excitation of the ligand-to-metal charge-transfer bands, resulting in overall shrinkage of the lattice. The compound is a prototype of weakly electronically coupled one-dimensional Jahn-Teller systems, which can undergo phase transitions induced by light, in addition to heating, cooling, and change of pressure, and it represents a prospective basis for the design of switching materials capable of multimode external control.     

An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides

The incorporation of non-proteinogenic amino acids (NPAAs) enriches the structural diversity of nonribosomal peptides. Recently, four NPAA-containing cyclic hexapeptides, longicatenamides A−D, were isolated using a combined-culture strategy. Based on in silico analysis, we discovered their putative biosynthetic gene cluster (lon) and proposed a possible biosynthetic mechanism. Surprisingly, the lon22 gene encodes an atypical arginine dihydrolase, which can also catalyze the hydrolysis of citrulline to ornithine. Phylogenetic analysis showed that Lon22-like proteins form a novel clade that is separated from other guanidine-modifying enzymes. After rational design, the catalytic efficiencies of a Lon22 Y80F mutant for arginine and citrulline substrates were 2.31- and 4.70-fold that of the wild-type (WT), respectively. In addition, characterization of the Lon20-A4 adenylation domain suggested that it can incorporate both ornithine and lysine into the final products.     

Carrier Protein Mediated Formation of the Dihydropyridazinone Ring in Actinopyridazinone Biosynthesis

Heterocycles with nitrogen-nitrogen (N−N) bonds are privileged building blocks of synthetic drugs. They are also found in natural products, although the biosynthetic logic behind them is poorly understood. Actinopyridazinones produced by Streptomyces sp. MSD090630SC-05 possess unique dihydropyridazinone rings that have been studied as core nuclei in several approved synthetic therapeutics. Herein, we performed gene knockouts and in vitro biochemical experiments to elucidate the major steps in actinopyridazinone biosynthesis, including the unprecedented carrier protein mediated machinery for dihydropyridazinone formation.