Aspartic acid and glutamic acid repeats in proteins exhibit strong negative charge distribution and they may play special biological roles. From 39 684 unique structural data in the RCSB Protein Data Bank (PDB), 173 structures were found to contain ordered D/E-rich repeat structures, and 57 of them were related to DNA/RNA functions. The frequency of occurrence of glutamic acid (36.90%) was higher than that of aspartic acid (27.02%). Glycine (2.38%), alanine (2.68%), valine (3.54%), leucine (5.57%), and isoleucine (3.34%), but not methionine (0.91%), were the most abundant hydrophobic residues. The available complex structures suggested that D/E-rich proteins might be involved in DNA mimicry, mRNA processing and regulation of the transcription complex. The region surrounding the D/E-rich repeat sequences plays important roles in the binding specificity toward the target proteins. The numbers and composition of aspartic acid and glutamic acid might also affect binding properties. Aspartic acid and glutamic acid are disorder-promoting residues in the intrinsically disorder proteins. Our findings suggest that the D/E-rich repeats are unique components of intrinsically disordered proteins, which are involved in the gene regulation and could serve as potential druggable fragments or drug targets.

Crown ethers are small, cyclic polyethers that have found wide‐spread use in phase‐transfer catalysis and, to a certain degree, in protein chemistry. Crown ethers readily bind metallic and organic cations, including positively charged amino acid side chains. We elucidated the crystal structures of several protein‐crown ether co‐crystals grown in the presence of 18‐crown‐6. We then employed biophysical methods and molecular dynamics simulations to compare these complexes with the corresponding apoproteins and with similar complexes with ring‐shaped low‐molecular‐weight polyethylene glycols. Our studies show that crown ethers can modify protein surface behavior dramatically by stabilizing either intra‐ or intermolecular interactions. Consequently, we propose that crown ethers can be used to modulate a wide variety of protein surface behaviors, such as oligomerization, domain–domain interactions, stabilization in organic solvents, and crystallization.

Undecaprenyl pyrophosphate phosphatase (UppP), an integral membrane protein, catalyzes the dephosphorylation of undecaprenyl pyrophosphate to undecaprenyl phosphate, which is an essential carrier lipid in the bacterial cell wall synthesis. Sequence alignment reveals two consensus regions, containing glutamate-rich (E/Q)XXXE plus PGXSRSXXT motifs and a histidine residue, specific to the bacterial UppP enzymes. The predicted topological model suggests that both of these regions are localized near the aqueous interface of UppP and face the periplasm, implicating that its enzymatic function is on the outer side of the plasma membrane. The mutagenesis analysis demonstrates that most of the mutations (E17A/E21A, H30A, S173A, R174A, and T178A) within the consensus regions are completely inactive, indicating that the catalytic site of UppP is constituted by these two regions. Enzymatic analysis also shows an absolute requirement of magnesium or calcium ions in enzyme activity. The three-dimensional structural model and molecular dynamics simulation studies have shown a plausible structure of the catalytic site of UppP and thus provides insights into the molecular basis of the enzyme-substrate interaction in membrane bilayers.

Structural analysis of a phosphatase-kinase complex defines a role for the PDZ domain in regulating kinase inactivation.

Curcumin is an anti-inflammatory and neuroprotective compound in turmeric. It is a potential ligand of the aryl hydrocarbon receptor (AhR) that mediates anti-inflammatory signaling. However, the AhR-mediated anti-inflammatory effect of curcumin within the brain remains unclear. We investigated the role of AhR on the curcumin effect in inflammatory astrogliosis. Curcumin attenuated lipopolysaccharide (LPS)-induced proinflammatory IL-6 and TNF-α gene expression in primary cultured rat astrocytes. When AhR was knocked down, LPS-induced IL-6 and TNF-α were increased and curcumin-decreased activation of the inflammation mediator NF-κB p65 by LPS was abolished. Although LPS increased AhR and its target gene CYP1B1, curcumin further enhanced LPS-induced CYP1B1 and indoleamine 2,3-dioxygenase (IDO), which metabolizes tryptophan to AhR ligands kynurenine (KYN) and kynurenic acid (KYNA). Potential interactions between curcumin and human AhR analyzed by molecular modeling of ligand–receptor docking. We identified a new ligand binding site on AhR different from the classical 2,3,7,8-tetrachlorodibenzo-p-dioxin site. Curcumin docked onto the classical binding site, whereas KYN and KYNA occupied the novel one. Moreover, curcumin and KYNA collaboratively bound onto AhR during molecular docking, potentially resulting in synergistic effects influencing AhR activation. Curcumin may enhance the inflammation-induced IDO/KYN axis and allosterically regulate endogenous ligand binding to AhR, facilitating AhR activation to regulate inflammatory astrogliosis.