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Clusters of hydrophobic residues are known to promote structured protein stability and drive protein aggregation. Recent work has shown that identifying contiguous hydrophobic residue clusters (termed “blobs”) has proven useful in both intrinsically disordered protein (IDP) simulation and human genome studies. However, a graphical interface was unavailable. Here, we present the blobulator: an interactive and intuitive web interface to detect intrinsic modularity in any protein sequence based on hydrophobicity. We demonstrate three use cases of the blobulator and show how identifying blobs with biologically relevant parameters provides useful information about a globular protein, two orthologous membrane proteins, and an IDP. Other potential applications are discussed, including: predicting protein segments with critical roles in tertiary interactions, providing a definition of local order and disorder with clear edges, and aiding in predicting protein features from sequence. The blobulator GUI can be found atwww.blobulator.branniganlab.org, and the source code with pip installable command line tool can be found on GitHub at www.GitHub.com/BranniganLab/blobulator. 

Water adsorption on transition metal dichalcogenides and other 2D materials is generally governed by weak van der Waals interactions. This results in a hydrophobic character of the basal planes, and defects may play a significant role in water adsorption and water cluster nucleation. However, there is a lack of detailed experimental investigations on water adsorption on defective 2D materials. Here, by combining low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations, we study in that context the well-defined mirror twin boundary (MTB) networks separating mirror-grains in 2D MoSe 2 . These MTBs are dangling bond-free extended crystal modifications with metallic electronic states embedded in the 2D semiconducting matrix of MoSe 2 . Our DFT calculations indicate that molecular water also interacts similarly weak with these MTBs as with the defect-free basal plane of MoSe 2 . However, in low temperature STM experiments, nanoscopic water structures are observed that selectively decorate the MTB network. This localized adsorption of water is facilitated by functionalization of the MTBs by hydroxyls formed by dissociated water. Hydroxyls may form by dissociating of water at undercoordinated defects or adsorbing of radicals from the gas phase in the UHV chamber. Our DFT analysis indicates that the metallic MTBs adsorb these radicals much stronger than on the basal plane due to charge transfer from the metallic states into the molecular orbitals of the OH groups. Once the MTBs are functionalized with hydroxyls, molecular water can attach to them, forming water channels along the MTBs. This study demonstrates the role metallic defect states play in the adsorption of water even in the absence of unsaturated bonds that have been so far considered to be crucial for adsorption of hydroxyls or water. 

Abstract Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinialigand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site. 

The tnaC regulatory gene from the tna operon of Escherichia coli controls the transcription of its own operon through an attenuation mechanism relying on the accumulation of arrested ribosomes during inhibition of its own translation termination. This free L-Trp dependent mechanism of inhibition of translation termination remains unclear. Here, we analyzed the inhibitory effects of L-Trp on the function of two known E. coli translation termination factors, RF1 and RF2. Using a series of reporter genes, we found that the in vivo L-Trp sensitivity of tnaC gene expression is influenced by the identity of its stop codon, with the UGA stop codon producing higher expression efficiency of the tnaA-lacZ gene construct than the UAG stop codon. in vitro TnaC-peptidyl-tRNA accumulation and toeprinting assays confirmed that in the presence of L-Trp, the UGA stop codon generates higher accumulation of both TnaC-peptidyl-tRNA and arrested ribosomes than does the UAG stop codon. RF-mediated hydrolysis assays corroborated that L-Trp blocks RF2 function more than that of RF1. Mutational analyses disclosed that amino acids substitutions at the 246 and 256 residue positions surrounding the RF2-GGQ functional motif reduce L-Trp dependent expression of the tnaC(UGA) tnaA-lacZ construct and the ability of L-Trp to inhibit RF2-mediated cleavage of the TnaC-peptidyl-tRNA. Altogether, our results indicate that L-Trp preferentially blocks RF2 activity during translation termination of the tnaC gene. This inhibition depends on the identities of amino acid residues surrounding the RF2-GGQ functional motif. 

Abstract Edges and point defects in layered dichalcogenides are important for tuning their electronic and magnetic properties. By combining scanning tunneling microscopy (STM) with density functional theory (DFT), the electronic structure of edges and point defects in 2D‐PtSe₂are investigated where the 1.8 eV bandgap of monolayer PtSe₂facilitates the detailed characterization of defect‐induced gap states by STM. The stoichiometric zigzag edge terminations are found to be energetically favored. STM and DFT show that these edges exhibit metallic 1D states with spin polarized bands. Various native point defects in PtSe₂are also characterized by STM. A comparison of the experiment with simulated images enables identification of Se‐vacancies, Pt‐vacancies, and Se‐antisites as the dominant defects in PtSe₂. In contrast to Se‐ or Pt‐vacancies, the Se‐antisites are almost devoid of gap states. Pt‐vacancies exhibit defect induced states that are spin polarized, emphasizing their importance for inducing magnetism in PtSe₂. The atomic‐scale insights into defect‐induced electronic states in monolayer PtSe₂provide the fundamental underpinning for defect engineering of PtSe₂‐monolayers and the newly identified spin‐polarized edge states offer prospects for engineering magnetic properties in PtSe₂nanoribbons.