Crystal structure and enantioselectivity of terpene cyclization in SAM-dependent methyltransferase TleD.

TleD is a SAM (S-adenosyl-l-methionine)-dependent methyltransferase and acts as one of the key enzymes in the teleocidin B biosynthesis pathway. Besides methyl transferring, TleD also rearranges the geranyl and indole moieties of the precursor to form a six-membered ring. Moreover, it does not show homologies with any known terpenoid cyclases. In order to elucidate how such a remarkable reaction could be achieved, we determined the complex crystal structures of TleD and the cofactor analogue S-adenosyl-l-homocysteine with or without the substrate teleocidin A1. A domain-swapped pattern via an additional N-terminal α-helix is observed in TleD hexamers. Structural comparison and alignment shows that this additional N-terminal α-helix is the common feature of SAM methyltransferase-like cyclases TleD and SpnF. The residue Tyr21 anchors the additional N-terminal α-helix to a 'core SAM-MT fold' and is a key residue for catalytic activity. Molecular dynamics simulation results suggest that the dihedral angle C23-C24-C25-C26 of teleocidin A1 is preferred to 60-90° in the TleD and substrate complex structure, which tend to adopt a Re-face stereocenter at C25 position after reaction and is according to in vitro enzyme reaction experiments. Our results also demonstrate that methyl transfer can be a new chemical strategy for carbocation formation in the terpene cyclization, which is the key initial step.

Structural transformation of the amyloidogenic core region of TDP-43 protein initiates its aggregation and cytoplasmic inclusion.

TDP-43 (TAR DNA-binding protein of 43 kDa) is a major deposited protein in amyotrophic lateral sclerosis and frontotemporal dementia with ubiquitin. A great number of genetic mutations identified in the flexible C-terminal region are associated with disease pathologies. We investigated the molecular determinants of TDP-43 aggregation and its underlying mechanisms. We identified a hydrophobic patch (residues 318-343) as the amyloidogenic core essential for TDP-43 aggregation. Biophysical studies demonstrated that the homologous peptide formed a helix-turn-helix structure in solution, whereas it underwent structural transformation from an α-helix to a ß-sheet during aggregation. Mutation or deletion of this core region significantly reduced the aggregation and cytoplasmic inclusions of full-length TDP-43 (or TDP-35 fragment) in cells. Thus, structural transformation of the amyloidogenic core initiates the aggregation and cytoplasmic inclusion formation of TDP-43. This particular core region provides a potential therapeutic target to design small-molecule compounds for mitigating TDP-43 proteinopathies.

Cordyceps militaris: A novel mushroom platform for metabolic engineering.

Cordyceps militaris, widely recognized as a medicinal and edible mushroom in East Asia, contains a variety of bioactive compounds, including cordycepin (COR), pentostatin (PTN) and other high-value compounds. This review explores the potential of developing C. militaris as a cell factory for the production of high-value chemicals and nutrients. This review comprehensively summarizes the fermentation advantages, metabolic networks, expression elements, and genome editing tools specific to C. militaris and discusses the challenges and barriers to further research on C. militaris across various fields, including computational biology, existing DNA elements, and genome editing approaches. This review aims to describe specific and promising opportunities for the in-depth study and development of C. militaris as a new chassis cell. Additionally, to increase the practicability of this review, examples of the construction of cell factories are provided, and promising strategies for synthetic biology development are illustrated.

Peptide diffusion and self-assembly in ambient water nanofilm on mica surface.

Ambient water nanofilms confined on solid surfaces usually show properties not seen in bulk and play unique roles in many important processes. Here we report diffusion and self-assembly of peptides in ambient water nanofilms on mica, based on "drying microcontact printing" and ex situ atomic force microscopy imaging. We found that diffusion and self-assembly of several peptides in the water nanofilms on mica resulted in one-dimensional "epitaxial" nanofilaments. The peptide self-assembly process is sensitive to the amount of water on the surface, and different peptides with varied molecular structures show different humidity-dependent behaviors. In addition, some peptides that cannot form nanofilaments on substrates in bulk water can be successfully self-assembled into nanofilaments in the water nanofilm.

Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly.

Subcellular membrane-less organelles consist of proteins with low complexity domains. Many of them, such as hnRNPA1, can assemble into both a polydisperse liquid phase and an ordered solid phase of amyloid fibril. The former mirrors biological granule assembly, while the latter is usually associated with neurodegenerative disease. Here, we observe a reversible amyloid formation of hnRNPA1 that synchronizes with liquid-liquid phase separation, regulates the fluidity and mobility of the liquid-like droplets, and facilitates the recruitment of hnRNPA1 into stress granules. We identify the reversible amyloid-forming cores of hnRNPA1 (named hnRACs). The atomic structures of hnRACs reveal a distinct feature of stacking Asp residues, which contributes to fibril reversibility and explains the irreversible pathological fibril formation caused by the Asp mutations identified in familial ALS. Our work characterizes the structural diversity and heterogeneity of reversible amyloid fibrils and illuminates the biological function of reversible amyloid formation in protein phase separation.

Peptide self-assembly on mica under ethanol-containing atmospheres: effects of ethanol on epitaxial growth of peptide nanofilaments.

Our previous study has shown that the self-assembly of several neurodegenerative-disease-related peptides in ambient water nanofilm condensed on mica is very sensitive to the amount of water on the surface. In this paper, we will demonstrate our hypothesis that the introduction of ethanol into the water nanofilm alters the properties of the interfacial water, resulting in changes of the peptide nanostructures self-assembled on the substrate. The assembly behaviors of peptides under different ethanol-containing atmospheres on mica were investigated by atomic force microscopy. GAV-9a began to form bent nanofilaments under an ethanol-containing atmosphere, and the self-assembled nanofilaments became thicker when a higher ratio of ethanol to water in the vapor was used. Based on these results, we propose a possible mechanism that the peptides adopt a "tilted upright" orientation when ethanol is present in the incubation environment. The effect of the peptide's terminal groups on the self-assembled nanostructures under the ethanol-containing atmosphere was also discussed.

Supramolecular structures of amyloid-related peptides in an ambient water nanofilm.

An ambient water nanofilm condensed on a solid surface provides a good model system to study the self-assembling behaviors of peptides in a confined environment. In this paper, the self-assembly of three short amyloid-related peptides in a water nanofilm confined on a mica substrate was studied using drying microcontact printing (D-µCP) and atomic force microscopy (AFM). The three peptides, which share the same amino acid sequence but have different terminal groups, were placed on mica surfaces by D-µCP. The samples were then incubated in a chamber with a controlled temperature and relative humidity (RH) in which water nanofilms were generated on the sample surfaces. AFM images revealed that the peptides assembled into two kinds of supramolecular structures: nanofilaments and nanosheets. The peptides' terminal groups and the thickness of the water nanofilms determined the self-assembled supramolecular structures in the water nanofilm. Through AFM investigation of the formation and transformation of the peptides' supramolecular structures, we conclude that the peptides' self-assembly process was dominated by weak interactions, such as hydrophobic and electrostatic interactions and hydrogen bonding, between the peptide molecules, the mica substrate, and the water nanofilm. On the basis of these results, a model that describes the peptide arrangement in the confined water nanofilm is proposed. This study reveals the complicated interactions of the peptides at an interface, which may be a general mechanism in vivo because water confinement around biomolecules and membranes is a universal phenomenon.