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At least 145 records · Page 8

Structural studies of intrinsically disordered MLL -fusion protein AF9 in complex with peptidomimetic inhibitors

AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL -rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP–AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1–2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein–inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural, functional, and regulatory evaluation of a cysteine post-translationally modified Gcn5-related N -acetyltransferase

Polyamines within the cell are tightly regulated by spermidine/spermine N-acetyltransferase (SSAT) enzymes. While several SSATs have been investigated in different bacterial species, there is still a significant gap in knowledge about which proteins are functional SSATs in many organisms. For example, while it is known that Pseudomonas aeruginosa synthesizes the polyamine spermidine, the SSAT that acetylates this molecule and its importance in regulating intracellular polyamines remains unknown. We previously identified a candidate Gcn5-related N-acetyltransferase (GNAT) protein from P. aeruginosa (PA2271) that could fulfill this role since it acetylates spermidine, but no further studies were conducted. Here, we explored the structure/function relationship of the PA2271 protein by determining its X-ray crystal structure and performing enzyme kinetics assays. We also identified active site residues that are essential for catalysis and substrate binding. As the study progressed, we encountered results that led us to explore the importance of four cysteine residues on enzyme activity and disulfide bond formation or modification of cysteine residues. We found these cysteine residues in PA2271 are important for protein solubility and activity, and there is an interrelationship between cysteine residues that contribute to these effects. Furthermore, we also found disulfide bonds could form between C 121 and C 165 and speculate that these residues may contribute to redox regulation of PA2271 protein activity.

59 BASIC BIOLOGICAL SCIENCES↗

Nanoscale friction of CVD single-layer MoS 2 with controlled defect formation

Two-dimensional (2D) layered nanomaterials such as graphene, molybdenum disulfide (MoS 2 ), or tungsten disulfide offer a promising solution in areas of solid-state lubrication, due to their excellent mechanical properties as well as low friction. However, defects can influence their friction and reduce their superior tribological properties. Thus, it is crucial to understand the effects of defects on sliding behavior in 2D nanomaterials, to foster a functional strategy for utilizing 2D nanomaterials as solid-state tribological films. In this study, frictional effects of defects, grain boundaries, and atomic-scale structural defects were explored on chemical vapor deposition (CVD) grown single layer MoS 2 . Selective patterning of defects into MoS 2 was accomplished via controlled irradiation of helium ions with varying ion doses. The friction of MoS 2 was characterized by friction force microscopy (FFM) and was found that friction depends on the defect formation controlled by helium ion irradiation. This approach offers a correlation between surface topography, defects and friction. Understanding the relative friction of MoS 2 in the presence of different levels of defects is foundational to studying tribological properties of a single layer MoS 2 at both nanoscales and macroscales.

36 MATERIALS SCIENCE↗

Ion-Conducting Dynamic Solid Polymer Electrolyte Adhesives

Cross-linked polymer electrolytes containing structurally dynamic disulfide bonds have been synthesized to investigate their combined ion transport and adhesive properties. Dynamic network polymers of varying cross-link densities are synthesized via thiol oxidation of a bisthiol monomer, 2,2'-(ethylenedioxy)diethanethiol, and tetrathiol cross-linker, pentaerythritol tetrakis(3-mercaptopropionate). At optimal loading of lithium bis(trifluoromethane-sulfonyl-imide) (LiTFSI) salt, the ionic conductivities (σ) at 90 °C are about 1 × 10–4 and 1 × 10–5 S/cm at the lowest and highest cross-linking, respectively. Notably, in comparison to the equivalent nondynamic network, the dynamic network shows a positive deviation in σ above 90 °C, which suggests the enhancement of ion transport occurs from the difference in structural relaxation on account of the dissociation of disulfide bonds. Lap shear adhesion and conductivity tests on ITO-coated glass substrates reveal the dynamic network exhibits a higher adhesive shear strength of 0.2 MPa (vs 0.03 MPa for the nondynamic network) and higher σ after the application of external stimulus (UV light or heat). The adhesive strength and σ are stable over multiple debonding/rebonding cycles and, thus, demonstrating the utility of these structurally dynamic networks as solid polymer electrolyte adhesives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Sulfur: Tuning the Viscoelastic and Surface Properties of Natural Keratin Fibers

Natural keratin fibers, such as wool, possess a complex hierarchical structure that governs their mechanical properties and surface energy. However, the extent to which these characteristics are influenced by combined contributions of structural variations (e.g., fiber diameter, intermediate filament (IF) packing) and chemical composition (e.g., disulfide bond density) remains poorly understood. In this study, we investigate wool fibers from five sheep breeds (Merino, Polwarth, Cheviot, Eider, and Devon) to elucidate how these factors influence viscoelasticity and surface interactions. Using a multimodal approach integrating interfacial and bulk characterization methods, including inverse gas chromatography (IGC), atomic force microscopy-infrared spectroscopy (AFM-IR), X-ray photoelectron spectroscopy (XPS), uniaxial tensile testing, and synchrotron small-angle X-ray scattering (SAXS), we show that the nanometer-thick 18-methyleicosanoic acid (18-MEA) layer is consistently present across all wool types and plays a key role in governing hydrophobicity and surface heterogeneity. A controlled isothermal treatment at 200 °C, designed to cleave disulfide bonds, results in a nearly 40% reduction in specific surface area across all fiber types, accompanied by a significant decrease in tensile strength and 80% reduction in elongation at break for Merino and Devon wool, but limited influence on the mechanical properties of Eider fibers. Furthermore, rate-dependent tensile testing within the elastic regime reveals distinct viscoelastic responses among the fiber types, suggesting that the sulfur-rich protein matrix surrounding IFs and its structure contribute actively to stress partitioning. Altogether, when combined with conclusions from SAXS measurements of IF spacing, our work offers compelling insights into the role of the keratin-associated protein (KAP) matrix in shaping wool fiber mechanics. Differences in mechanical behavior among wool types, despite similar IF spacing or sulfur content, highlight the importance of matrix composition and cross-linking density, suggesting that the molecular architecture of the KAP network may be a dominant factor in determining fiber performance.

X-ray scattering↗

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗

Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes

The three-finger proteins are a collection of disulfide bond rich proteins of great biomedical interests. Scalable recombinant expression and purification of bioactive three-finger proteins is quite difficult. We introduce a working pipeline for expression, purification and validation of disulfide-bond rich three-finger proteins using E. coli as the expression host. With this pipeline, we have successfully obtained highly purified and bioactive recombinant α-Βungarotoxin, k-Bungarotoxin, Hannalgesin, Mambalgin-1, α-Cobratoxin, MTα, Slurp1, Pate B etc. Milligrams to hundreds of milligrams of recombinant three finger proteins were obtained within weeks in the lab. The recombinant proteins showed specificity in binding assay and six of them were crystallized and structurally validated using X-ray diffraction protein crystallography. Our pipeline allows refolding and purifying recombinant three finger proteins under optimized conditions and can be scaled up for massive production of three finger proteins. As many three finger proteins have attractive therapeutic or research interests and due to the extremely high quality of the recombinant three finger proteins we obtained, our method provides a competitive alternative to either their native counterparts or chemically synthetic ones and should facilitate related research and applications.

59 BASIC BIOLOGICAL SCIENCES↗

Expanding the Scope of Pnictogen‐Assisted Cyclophane Self‐Assembly

Cyclophanes are a fundamentally interesting class of compounds that host a wide range of unique and emergent properties. Furthermore, synthesis of complex and/or functionalized cyclophanes can often suffer from harsh reaction conditions, long reaction times, and sometimes low yields using stepwise methods. We have previously reported an efficient, high-yielding, metalloid-directed self-assembly method to prepare disulfide, thioether, and hydrocarbon cyclophanes and cages that feature mercaptomethyl-arenes as starting materials. Herein, we report the synthesis of 21 new disulfide and thioether assemblies that expand this high yielding self-assembly method to a wide breadth of macrocycles and cages with diverse structures. Remarkably, the high-yielding, efficient syntheses still proceed under dynamic covalent control using electron-deficient, heteroaryl, cycloalkyl, spiro, and even short alkenyl/alkynyl substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins

Abstract Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Harnessing Machine Learning to Predict MoS 2 Solid Lubricant Performance

Physical vapor deposited (PVD) molybdenum disulfide (MoS 2 ) solid lubricant coatings are an exemplar material system for machine learning methods due to small changes in process variables often causing large variations in microstructure and mechanical/tribological properties. Here, in this work, a gradient boosted regression tree machine learning method is applied to an existing experimental data set containing process, microstructure, and property information to create deeper insights into the process-structure–property relationships for molybdenum disulfide (MoS 2 ) solid lubricant coatings. The optimized and cross-validated models show good predictive capabilities for density, reduced modulus, hardness, wear rate, and initial coefficients of friction. The contribution of individual deposition variables (i.e., argon pressure, deposition power, target conditioning) on coating properties is highlighted through feature importance. The process-property relationships established herein show linear and non-linear relationships and highlight the influence of uncontrolled deposition variables (i.e., target conditioning) on the tribological performance.

MoS2↗

Insights into Copper Sulfide Formation from Cu and S K edge XAS and DFT studies

An understanding of the fundamentals of the reaction between CuO with trace amounts of H 2 S to form CuS products is critical for the optimal utilization of this process in sulfur removal applications. Unfortunately, CuS is a complex material, featuring various Cu 2-x S compounds (with 0 ≤ x ≤ 1), distorted crystal phases, and varying electronic structures and coordination environments of Cu and S ions. In this work, we combine ex situ and in situ X-ray absorption spectroscopy (XAS) at S and Cu K edges, fixed bed sorption experiments, DFT simulations, and other characterization techniques to speciate the CuS products formed at different temperatures (298–383 K) and from CuO sorbents with different crystallite sizes (2.8–40 nm). The results of our analysis identify the formation of a distorted CuS layer at the surface of CuO crystals with disulfide groups with shorter Cu–S bonds and higher delocalization of the positive charge of the Cu center into (S 1– )2. This distorted CuS layer dominates the XAS signal at lower temperatures (298–323 K) and at the initial stages of sulfidation at higher temperatures (353 and 383 K) where conversion is low (<40%). First-principles atomistic simulations confirm the thermodynamic favorability of the formation of surface (S 1– )2 on both CuO (111) and ($\bar{1}11$) surfaces, providing further support for our experimental observations. Furthermore, these simulations reveal that the presence of disulfide bonds stabilized surface hydroxyl groups, leading to lower Gibbs Free Energies of their surface migration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ATCUN-like Copper Site in βB2-Crystallin Plays a Protective Role in Cataract-Associated Aggregation

Cataract is the leading cause of blindness worldwide, and it is caused by crystallin damage and aggregation. Senile cataractous lenses have relatively high levels of metals, while some metal ions can directly induce the aggregation of human γ-crystallins. Here, for this work, we evaluated the impact of divalent metal ions in the aggregation of human βB2-crystallin, one of the most abundant crystallins in the lens. Turbidity assays showed that Pb 2+ , Hg 2+ , Cu 2+ , and Zn 2+ ions induce the aggregation of βB2-crystallin. Metal-induced aggregation is partially reverted by a chelating agent, indicating the formation of metal-bridged species. Our study focused on the mechanism of copper-induced aggregation of βB2-crystallin, finding that it involves metal-bridging, disulfide-bridging, and loss of protein stability. Circular dichroism and electron paramagnetic resonance (EPR) revealed the presence of at least three Cu 2+ binding sites in βB2-crystallin, one of them with spectroscopic features typical for Cu 2+ bound to an amino-terminal copper and nickel (ATCUN) binding motif, which is found in Cu transport proteins. The ATCUN-like Cu binding site is located at the unstructured N-terminus of βB2-crystallin, and it could be modeled by a peptide with the first six residues in the protein sequence (NH 2 -ASDHQF-). Isothermal titration calorimetry indicates a nanomolar Cu 2+ binding affinity for the ATCUN-like site. An N-truncated form of βB2-crystallin is more susceptible to Cu-induced aggregation and is less thermally stable, indicating a protective role for the ATCUN-like site. EPR and X-ray absorption spectroscopy studies reveal the presence of a copper redox active site in βB2-crystallin that is associated with metal-induced aggregation and formation of disulfide-bridged oligomers. Our study demonstrates metal-induced aggregation of βB2-crystallin and the presence of putative copper binding sites in the protein. Whether the copper-transport ATCUN-like site in βB2-crystallin plays a functional/protective role or constitutes a vestige from its evolution as a lens structural protein remains to be elucidated.

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Surfactant-Mediated Growth and Patterning of Atomically Thin Transition Metal Dichalcogenides

The role of additives in facilitating the growth of conventional semiconducting thin films is well-established. Apparently, their presence is also decisive in the growth of two-dimensional transition metal dichalcogenides (TMDs), yet their role remains ambiguous. In this work, we show that the use of sodium bromide enables synthesis of TMD monolayers via a surfactant-mediated growth mechanism, without introducing liquefaction of metal oxide precursors. We discovered that sodium ions provided by sodium bromide chemically passivate edges of growing molybdenum disulfide crystals, relaxing in-plane strains to suppress 3D islanding and promote monolayer growth. To exploit this growth model, molybdenum disulfide monolayers were directly grown into desired patterns using predeposited sodium bromide as a removable template. In conclusion, the surfactant-mediated growth not only extends the families of metal oxide precursors but also offers a way for lithography-free patterning of TMD monolayers on various surfaces to facilitate fabrication of atomically thin electronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

One-Step Transfer of Symmetric and Asymmetric Contacts for Large-Scale 2D Electronics and Optoelectronics

Two-dimensional (2D) semiconductors are highly promising candidates for thin-film transistor applications due to their scalability, transferability, atomic thickness, and relatively high carrier mobility. However, a substantial performance gap remains between individual devices based on single-crystalline 2D films and wafer-scale integrated circuits, primarily due to defects introduced during conventional fabrication processes. Here, we report a diamond-assisted electrode transfer technique for the van der Waals integration of wafer-scale prefabricated electrode arrays onto 2D materials, enabling scalable electronics and optoelectronics. Implemented on metal–organic chemical vapor deposition-grown monolayer molybdenum disulfide, this method forms ultraclean metal–semiconductor interfaces, yielding field-effect transistors with excellent ohmic contacts, a low contact resistance of 400 Ω·μm, and a Schottky barrier height of only 9 meV. Furthermore, we demonstrate a scalable transistor array on monolayer molybdenum disulfide with excellent device performance uniformity, achieving an average field-effect mobility of 30 cm 2 V –1 s –1 and an on/off current ratio exceeding 105. Additionally, high photocurrent and responsivity were demonstrated in the array devices, showing their potential for excellent image detection. We further demonstrate the versatility of this technique by fabricating a Schottky diode array through a single-step transfer of asymmetric electrodes─low work function aluminum and high work function gold─onto monolayer tungsten diselenide. This approach provides a clean, effective solution for contact engineering in 2D materials, offering a viable pathway toward wafer-scale, high-performance 2D electronics, optoelectronics, and integrated circuits.

2D electronics↗

Nickel–Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F 430 . The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C–S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni–thiol interaction between Ni(II)–MCR and inhibitor CoMSH, a Ni(I)–thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)–disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)–sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)–N/O complex, not Ni(I)–S. These studies rule out direct Ni(I)–sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)–sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism

Mitochondrial metabolism requires the chaperoned import of disulfide-stabilized proteins via CHCHD4/MIA40 and its enigmatic interaction with oxidoreductase Apoptosis-inducing factor (AIF). By crystallizing human CHCHD4’s AIF-interaction domain with an activated AIF dimer, we uncover how NADH allosterically configures AIF to anchor CHCHD4’s β-hairpin and histidine-helix motifs to the inner mitochondrial membrane. The structure further reveals a similarity between the AIF-interaction domain and recognition sequences of CHCHD4 substrates. NMR and X-ray scattering (SAXS) solution measurements, mutational analyses, and biochemistry show that the substrate-mimicking AIF-interaction domain shields CHCHD4’s redox-sensitive active site. Disrupting this shield critically activates CHCHD4 substrate affinity and chaperone activity. Regulatory-domain sequestration by NADH-activated AIF directly stimulates chaperone binding and folding, revealing how AIF mediates CHCHD4 mitochondrial import. These results establish AIF as an integral component of the metazoan disulfide relay and point to NADH-activated dimeric AIF as an organizational import center for CHCHD4 and its substrates. Importantly, AIF regulation of CHCHD4 directly links AIF’s cellular NAD(H) sensing to CHCHD4 chaperone function, suggesting a mechanism to balance tissue-specific oxidative phosphorylation (OXPHOS) capacity with NADH availability.

Brosey, Chris A↗

Insights into the extraction of photogenerated holes from CdSe/CdS nanorods for oxidative organic catalysis

Using aerobic oxidative coupling of thiophenol in organic media as a model reaction, we show that photogenerated holes in CdSe/CdS core–shell nanorods can be efficiently extracted. As a result, CdSe/CdS nanorods can serve as an efficient visible-light photocatalyst at a very low concentration (~1.5 × 10 -4 mol%). We show that primary amines play an important role in the transformation of thiols into disulfides by forming a soluble thiolate in nonpolar solvent. Using time-resolved optical spectroscopy and electron paramagnetic resonance spectroscopy, we show that thiolate can efficiently extract the photogenerated holes from CdSe/CdS nanorods and transform into disulfide in organic solvent. Overall, our data indicate that there are two reaction pathways responsible for S–S coupling of thiolate upon illumination of CdSe/CdS nanorods. We demonstrate that instead of scavenging of photogenerated holes by sacrificial species for prevention of photo corrosion of CdSe/CdS nanorods, the photogenerated holes can be efficiently used for oxidative organic synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗