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Item Antimicrobial activity of a natural compound and analogs against multi-drug-resistant Gram-positive pathogens(American Society for Microbiology, 2024) Shah, Kush N.; Shah, Parth N.; Agobe, Francesca O.; Lovato, Kaitlyn; Gao, Hongyin; Ogun, Oluwadara; Hoffman, Cason; Yabe-Gill, Marium; Chen, Qingquan; Sweatt, Jordan; Chirra, Bhagath; Muñoz-Medina, Ricardo; Farmer, Delaney E.; Kürti, László; Cannon, Carolyn L.The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) has sparked global concern due to the dwindling availability of effective antibiotics. To increase our treatment options, researchers have investigated naturally occurring antimicrobial compounds and have identified MC21-A (C58), which has potent antimicrobial activity against MRSA. Recently, we have devised total synthesis schemes for C58 and its chloro-analog, C59. Here, we report that both compounds eradicate 90% of the 39 MRSA isolates tested [MIC90 and minimum bactericidal concentration (MBC90)] at lower or comparable concentrations compared to several standard-of-care (SoC) antimicrobials including daptomycin, vancomycin, and linezolid. Furthermore, a stable, water-soluble sodium salt of C59, C59Na, demonstrates antimicrobial activity comparable to C59. C59, unlike vancomycin, kills stationary-phase MRSA in a dose-dependent manner and completely eradicates MRSA biofilms. In contrast to vancomycin, exposing MRSA to sub-MIC concentrations of C59 does not result in the emergence of spontaneous resistance. Similarly, in a multi-step study, C59 demonstrates a low propensity of resistance acquisition when compared to SoC antimicrobials, such as linezolid and clindamycin. Our findings suggest C58, C59, and C59Na are non-toxic to mammalian cells at concentrations that exert antimicrobial activity; the lethal dose at median cell viability (LD50) is at least fivefold higher than the MBC90 in the two mammalian cell lines tested. A morphological examination of the effects of C59 on a MRSA isolate suggests the inhibition of the cell division process as a mechanism of action. Our results demonstrate the potential of this naturally occurring compound and its analogs as non-toxic next-generation antimicrobials to combat MRSA infectionsItem Oxidation of Hydrogen Sulfide to Polysulfide and Thiosulfate by a Carbon Nanozyme: Therapeutic Implications with an Emphasis on Down Syndrome(Wiley, 2024) Derry, Paul J.; Liopo, Anton V.; Mouli, Karthik; McHugh, Emily A.; Vo, Anh T. T.; McKelvey, Ann; Suva, Larry J.; Wu, Gang; Gao, Yan; Olson, Kenneth R.; Tour, James M.; Kent, Thomas A.; Smalley-Curl Institute; Welch Institute for Advanced Materials; The NanoCarbon CenterHydrogen sulfide (H2S) is a noxious, potentially poisonous, but necessary gas produced from sulfur metabolism in humans. In Down Syndrome (DS), the production of H2S is elevated and associated with degraded mitochondrial function. Therefore, removing H2S from the body as a stable oxide could be an approach to reducing the deleterious effects of H2S in DS. In this report we describe the catalytic oxidation of hydrogen sulfide (H2S) to polysulfides (HS2+n−) and thiosulfate (S2O32−) by poly(ethylene glycol) hydrophilic carbon clusters (PEG-HCCs) and poly(ethylene glycol) oxidized activated charcoal (PEG-OACs), examples of oxidized carbon nanozymes (OCNs). We show that OCNs oxidize H2S to polysulfides and S2O32− in a dose-dependent manner. The reaction is dependent on O2 and the presence of quinone groups on the OCNs. In DS donor lymphocytes we found that OCNs increased polysulfide production, proliferation, and afforded protection against additional toxic levels of H2S compared to untreated DS lymphocytes. Finally, in Dp16 and Ts65DN murine models of DS, we found that OCNs restored osteoclast differentiation. This new action suggests potential facile translation into the clinic for conditions involving excess H2S exemplified by DS.Item Quantum information scrambling and chemical reactions(National Academy of Sciences, 2024) Zhang, Chenghao; Kundu, Sohang; Makri, Nancy; Gruebele, Martin; Wolynes, Peter G.; Center for Theoretical Biological PhysicsThe ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents that characterize classical chaotic motion. Maldacena, Shenker, and Stanford have suggested a fundamental quantum bound for the rate of information scrambling, which resembles a limit suggested by Herzfeld for chemical reaction rates. Here, we use OTOCs to study model reactions based on a double-well reaction coordinate coupled to anharmonic oscillators or to a continuum oscillator bath. Upon cooling, as one enters the tunneling regime where the reaction rate does not strongly depend on temperature, the quantum Lyapunov exponent can approach the scrambling bound and the effective reaction rate obtained from a population correlation function can approach the Herzfeld limit on reaction rates: Tunneling increases scrambling by expanding the state space available to the system. The coupling of a dissipative continuum bath to the reaction coordinate reduces the scrambling rate obtained from the early-time OTOC, thus making the scrambling bound harder to reach, in the same way that friction is known to lower the temperature at which thermally activated barrier crossing goes over to the low-temperature activationless tunneling regime. Thus, chemical reactions entering the tunneling regime can be information scramblers as powerful as the black holes to which the quantum Lyapunov exponent bound has usually been applied.Item Switching the spin cycloid in BiFeO3 with an electric field(Springer Nature, 2024) Meisenheimer, Peter; Moore, Guy; Zhou, Shiyu; Zhang, Hongrui; Huang, Xiaoxi; Husain, Sajid; Chen, Xianzhe; Martin, Lane W.; Persson, Kristin A.; Griffin, Sinéad; Caretta, Lucas; Stevenson, Paul; Ramesh, Ramamoorthy; Rice Advanced Materials InstituteBismuth ferrite (BiFeO3) is a multiferroic material that exhibits both ferroelectricity and canted antiferromagnetism at room temperature, making it a unique candidate in the development of electric-field controllable magnetic devices. The magnetic moments in BiFeO3 are arranged into a spin cycloid, resulting in unique magnetic properties which are tied to the ferroelectric order. Previous understanding of this coupling has relied on average, mesoscale measurements. Using nitrogen vacancy-based diamond magnetometry, we observe the magnetic spin cycloid structure of BiFeO3 in real space. This structure is magnetoelectrically coupled through symmetry to the ferroelectric polarization and this relationship is maintained through electric field switching. Through a combination of in-plane and out-of-plane electrical switching, coupled with ab initio studies, we have discovered that the epitaxy from the substrate imposes a magnetoelastic anisotropy on the spin cycloid, which establishes preferred cycloid propagation directions. The energy landscape of the cycloid is shaped by both the ferroelectric degree of freedom and strain-induced anisotropy, restricting the spin spiral propagation vector to changes to specific switching events.Item Hydrogen Peroxide Electrosynthesis in a Strong Acidic Environment Using Cationic Surfactants(American Chemical Society, 2024) Adler, Zachary; Zhang, Xiao; Feng, Guangxia; Shi, Yaping; Zhu, Peng; Xia, Yang; Shan, Xiaonan; Wang, HaotianThe two-electron oxygen reduction reaction (2e–-ORR) can be exploited for green production of hydrogen peroxide (H2O2), but it still suffers from low selectivity in an acidic electrolyte when using non-noble metal catalysts. Here, inspired by biology, we demonstrate a strategy that exploits the micellization of surfactant molecules to promote the H2O2 selectivity of a low-cost carbon black catalyst in strong acid electrolytes. The surfactants near the electrode surface increase the oxygen solubility and transportation, and they provide a shielding effect that displaces protons from the electric double layer (EDL). Compared with the case of a pure acidic electrolyte, we find that, when a small number of surfactant molecules were added to the acid, the H2O2 Faradaic efficiency (FE) was improved from 12% to 95% H2O2 under 200 mA cm–2, suggesting an 8-fold improvement. Our in situ surface enhanced Raman spectroscopy (SERS) and optical microscopy (OM) studies suggest that, while the added surfactant reduces the electrode’s hydrophobicity, its micelle formation could promote the O2 gas transport and its hydrophobic tail could displace local protons under applied negative potentials during catalysis, which are responsible for the improved H2O2 selectivity in strong acids.Item Reversible dioxygen uptake at [Cu4] clusters(Royal Society of Chemistry, 2024) Osei, Manasseh Kusi; Mirzaei, Saber; Mirzaei, M. Saeed; Valles, Agustin; Sánchez, Raúl HernándezDioxygen binding solely through non-covalent interactions is rare. In living systems, dioxygen transport takes place via iron or copper-containing biological cofactors. Specifically, a reversible covalent interaction is established when O2 binds to the mono or polynuclear metal center. However, O2 stabilization in the absence of covalent bond formation is challenging and rarely observed. Here, we demonstrate a unique example of reversible non-covalent binding of dioxygen within the cavity of a well-defined synthetic all-Cu(I) tetracopper cluster.Item Stimulator of Interferon Genes Pathway Activation through the Controlled Release of STINGel Mediates Analgesia and Anti-Cancer Effects in Oral Squamous Cell Carcinoma(MDPI, 2024) Dong, Minh Phuong; Dharmaraj, Neeraja; Kaminagakura, Estela; Xue, Jianfei; Leach, David G.; Hartgerink, Jeffrey D.; Zhang, Michael; Hanks, Hana-Joy; Ye, Yi; Aouizerat, Bradley E.; Vining, Kyle; Thomas, Carissa M.; Dovat, Sinisa; Young, Simon; Viet, Chi T.Oral squamous cell carcinoma (OSCC) presents significant treatment challenges due to its poor survival and intense pain at the primary cancer site. Cancer pain is debilitating, contributes to diminished quality of life, and causes opioid tolerance. The stimulator of interferon genes (STING) agonism has been investigated as an anti-cancer strategy. We have developed STINGel, an extended-release formulation that prolongs the availability of STING agonists, which has demonstrated an enhanced anti-tumor effect in OSCC compared to STING agonist injection. This study investigates the impact of intra-tumoral STINGel on OSCC-induced pain using two separate OSCC models and nociceptive behavioral assays. Intra-tumoral STINGel significantly reduced mechanical allodynia in the orofacial cancer model and alleviated thermal and mechanical hyperalgesia in the hind paw model. To determine the cellular signaling cascade contributing to the antinociceptive effect, we performed an in-depth analysis of immune cell populations via single-cell RNA-seq. We demonstrated an increase in M1-like macrophages and N1-like neutrophils after STINGel treatment. The identified regulatory pathways controlled immune response activation, myeloid cell differentiation, and cytoplasmic translation. Functional pathway analysis demonstrated the suppression of translation at neuron synapses and the negative regulation of neuron projection development in M2-like macrophages after STINGel treatment. Importantly, STINGel treatment upregulated TGF-β pathway signaling between various cell populations and peripheral nervous system (PNS) macrophages and enhanced TGF-β signaling within the PNS itself. Overall, this study sheds light on the mechanisms underlying STINGel-mediated antinociception and anti-tumorigenic impact.Item Effect of fabrication processes on BaTiO3 capacitor properties(AIP Publishing, 2024) Jiang, Yizhe; Tian, Zishen; Kavle, Pravin; Pan, Hao; Martin, Lane W.; Rice Advanced Materials InstituteThere is an increasing desire to utilize complex functional electronic materials such as ferroelectrics in next-generation microelectronics. As new materials are considered or introduced in this capacity, an understanding of how we can process these materials into those devices must be developed. Here, the effect of different fabrication processes on the ferroelectric and related properties of prototypical metal oxide (SrRuO3)/ferroelectric (BaTiO3)/metal oxide (SrRuO3) heterostructures is explored. Two different types of etching processes are studied, namely, wet etching of the top SrRuO3 using a NaIO4 solution and dry etching using an Ar+-ion beam (i.e., ion milling). Polarization-electric-field hysteresis loops for capacitors produced using both methods are compared. For the ion-milling process, it is found that the Ar+ beam can introduce defects into the SrRuO3/BaTiO3/SrRuO3 devices and that the milling depth strongly influences the defect level and can induce a voltage imprint on the function. Realizing that such processing approaches may be necessary, work is performed to ameliorate the imprint of the hysteresis loops via ex situ “healing” of the process-induced defects by annealing the ferroelectric material in a barium-and-oxygen-rich environment via a chemical-vapor-deposition-style process. This work provides a pathway for the nanoscale fabrication of these candidate materials for next-generation memory and logic applications.Item Bridging physical intuition and hardware efficiency for correlated electronic states: the local unitary cluster Jastrow ansatz for electronic structure(Royal Society of Chemistry, 2023) Motta, Mario; Sung, Kevin J.; Whaley, K. Birgitta; Head-Gordon, Martin; Shee, JamesA prominent goal in quantum chemistry is to solve the molecular electronic structure problem for ground state energy with high accuracy. While classical quantum chemistry is a relatively mature field, the accurate and scalable prediction of strongly correlated states found, e.g., in bond breaking and polynuclear transition metal compounds remains an open problem. Within the context of a variational quantum eigensolver, we propose a new family of ansatzes which provides a more physically appropriate description of strongly correlated electrons than a unitary coupled cluster with single and double excitations (qUCCSD), with vastly reduced quantum resource requirements. Specifically, we present a set of local approximations to the unitary cluster Jastrow wavefunction motivated by Hubbard physics. As in the case of qUCCSD, exactly computing the energy scales factorially with system size on classical computers but polynomially on quantum devices. The local unitary cluster Jastrow ansatz removes the need for SWAP gates, can be tailored to arbitrary qubit topologies (e.g., square, hex, and heavy-hex), and is well-suited to take advantage of continuous sets of quantum gates recently realized on superconducting devices with tunable couplers. The proposed family of ansatzes demonstrates that hardware efficiency and physical transparency are not mutually exclusive; indeed, chemical and physical intuition regarding electron correlation can illuminate a useful path towards hardware-friendly quantum circuits.Item Cell behaviors underlying Myxococcus xanthus aggregate dispersal(American Society for Microbiology, 2023) Murphy, Patrick; Comstock, Jessica; Khan, Trosporsha; Zhang, Jiangguo; Welch, Roy; Igoshin, Oleg A.; Center for Theoretical Physical BiologyThe soil bacterium Myxococcus xanthus is a model organism with a set of diverse behaviors. These behaviors include the starvation-induced multicellular development program, in which cells move collectively to assemble multicellular aggregates. After initial aggregates have formed, some will disperse, with smaller aggregates having a higher chance of dispersal. Initial aggregation is driven by two changes in cell behavior: cells slow down inside of aggregates and bias their motion by reversing direction less frequently when moving toward aggregates. However, the cell behaviors that drive dispersal are unknown. Here, we use fluorescent microscopy to quantify changes in cell behavior after initial aggregates have formed. We observe that after initial aggregate formation, cells adjust the bias in reversal timings by initiating reversals more rapidly when approaching unstable aggregates. Using agent-based modeling, we then show dispersal is predominantly generated by this change in bias, which is strong enough to overcome slowdown inside aggregates. Notably, the change in reversal bias is correlated with the nearest aggregate size, connecting cellular activity to previously observed correlations between aggregate size and fate. To determine if this connection is consistent across strains, we analyze a second M. xanthus strain with reduced levels of dispersal. We find that far fewer cells near smaller aggregates modified their bias. This implies that aggregate dispersal is under genetic control, providing a foundation for further investigations into the role it plays in the life cycle of M. xanthus.Item A scientific machine learning framework to understand flash graphene synthesis(Royal Society of Chemistry, 2023) Sattari, Kianoosh; Eddy, Lucas; Beckham, Jacob L.; Wyss, Kevin M.; Byfield, Richard; Qian, Long; Tour, James M.; Lin, Jian; NanoCarbon Center; Welch Institute for Advanced MaterialsFlash Joule heating (FJH) is a far-from-equilibrium (FFE) processing method for converting low-value carbon-based materials to flash graphene (FG). Despite its promises in scalability and performance, attempts to explore the reaction mechanism have been limited due to the complexities involved in the FFE process. Data-driven machine learning (ML) models effectively account for the complexities, but the model training requires a considerable amount of experimental data. To tackle this challenge, we constructed a scientific ML (SML) framework trained by using both direct processing variables and indirect, physics-informed variables to predict the FG yield. The indirect variables include current-derived features (final current, maximum current, and charge density) predicted from the proxy ML models and reaction temperatures simulated from multi-physics modeling. With the combined indirect features, the final ML model achieves an average R2 score of 0.81 ± 0.05 and an average RMSE of 12.1% ± 2.0% in predicting the FG yield, which is significantly higher than the model trained without them (R2 of 0.73 ± 0.05 and an RMSE of 14.3% ± 2.0%). Feature importance analysis validates the key roles of these indirect features in determining the reaction outcome. These results illustrate the promise of this SML to elucidate FFE material synthesis outcomes, thus paving a new avenue to processing other datasets from the materials systems involving the same or different FFE processes.Item Radical ligand transfer: a general strategy for radical functionalization(Beilstein-Institut, 2023) Jr, David T. Nemoto; Bian, Kang-Jie; Kao, Shih-Chieh; West, Julian G.The place of alkyl radicals in organic chemistry has changed markedly over the last several decades, evolving from challenging-to-generate “uncontrollable” species prone to side reactions to versatile reactive intermediates enabling construction of myriad C–C and C–X bonds. This maturation of free radical chemistry has been enabled by several advances, including the proliferation of efficient radical generation methods, such as hydrogen atom transfer (HAT), alkene addition, and decarboxylation. At least as important has been innovation in radical functionalization methods, including radical–polar crossover (RPC), enabling these intermediates to be engaged in productive and efficient bond-forming steps. However, direct engagement of alkyl radicals remains challenging. Among these functionalization approaches, a bio-inspired mechanistic paradigm known as radical ligand transfer (RLT) has emerged as a particularly promising and versatile means of forming new bonds catalytically to alkyl radicals. This development has been driven by several key features of RLT catalysis, including the ability to form diverse bonds (including C–X, C–N, and C–S), the use of simple earth abundant element catalysts, and the intrinsic compatibility of this approach with varied radical generation methods, including HAT, radical addition, and decarboxylation. Here, we provide an overview of the evolution of RLT catalysis from initial studies to recent advances and provide a conceptual framework we hope will inspire and enable future work using this versatile elementary step.Item Battery metal recycling by flash Joule heating(AAAS, 2023) Chen, Weiyin; Chen, Jinhang; Bets, Ksenia V.; Salvatierra, Rodrigo V.; Wyss, Kevin M.; Gao, Guanhui; Choi, Chi Hun; Deng, Bing; Wang, Xin; Li, John Tianci; Kittrell, Carter; La, Nghi; Eddy, Lucas; Scotland, Phelecia; Cheng, Yi; Xu, Shichen; Li, Bowen; Tomson, Mason B.; Han, Yimo; Yakobson, Boris I.; Tour, James M.; Welch Institute for Advanced Materials; NanoCarbon Center; Applied Physics Program; Smalley-Curl InstituteThe staggering accumulation of end-of-life lithium-ion batteries (LIBs) and the growing scarcity of battery metal sources have triggered an urgent call for an effective recycling strategy. However, it is challenging to reclaim these metals with both high efficiency and low environmental footprint. We use here a pulsed dc flash Joule heating (FJH) strategy that heats the black mass, the combined anode and cathode, to >2100 kelvin within seconds, leading to ~1000-fold increase in subsequent leaching kinetics. There are high recovery yields of all the battery metals, regardless of their chemistries, using even diluted acids like 0.01 M HCl, thereby lessening the secondary waste stream. The ultrafast high temperature achieves thermal decomposition of the passivated solid electrolyte interphase and valence state reduction of the hard-to-dissolve metal compounds while mitigating diffusional loss of volatile metals. Life cycle analysis versus present recycling methods shows that FJH significantly reduces the environmental footprint of spent LIB processing while turning it into an economically attractive process.Item MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange(Springer Nature, 2023) Abualrous, Esam T.; Stolzenberg, Sebastian; Sticht, Jana; Wieczorek, Marek; Roske, Yvette; Günther, Matthias; Dähn, Steffen; Boesen, Benedikt B.; Calvo, Marcos Martínez; Biese, Charlotte; Kuppler, Frank; Medina-García, Álvaro; Álvaro-Benito, Miguel; Höfer, Thomas; Noé, Frank; Freund, ChristianPresentation of antigenic peptides by major histocompatibility complex class II (MHC-II) proteins determines T helper cell reactivity. The MHC-II genetic locus displays a large degree of allelic polymorphism influencing the peptide repertoire presented by the resulting MHC-II protein allotypes. During antigen processing, the human leukocyte antigen (HLA) molecule HLA-DM (DM) encounters these distinct allotypes and catalyzes exchange of the placeholder peptide CLIP by exploiting dynamic features of MHC-II. Here, we investigate 12 highly abundant CLIP-bound HLA-DRB1 allotypes and correlate dynamics to catalysis by DM. Despite large differences in thermodynamic stability, peptide exchange rates fall into a target range that maintains DM responsiveness. A DM-susceptible conformation is conserved in MHC-II molecules, and allosteric coupling between polymorphic sites affects dynamic states that influence DM catalysis. As exemplified for rheumatoid arthritis, we postulate that intrinsic dynamic features of peptide–MHC-II complexes contribute to the association of individual MHC-II allotypes with autoimmune disease.Item Engineering chirality at wafer scale with ordered carbon nanotube architectures(Springer Nature, 2023) Doumani, Jacques; Lou, Minhan; Dewey, Oliver; Hong, Nina; Fan, Jichao; Baydin, Andrey; Zahn, Keshav; Yomogida, Yohei; Yanagi, Kazuhiro; Pasquali, Matteo; Saito, Riichiro; Kono, Junichiro; Gao, Weilu; Carbon Hub; Smalley-Curl InstituteCreating artificial matter with controllable chirality in a simple and scalable manner brings new opportunities to diverse areas. Here we show two such methods based on controlled vacuum filtration - twist stacking and mechanical rotation - for fabricating wafer-scale chiral architectures of ordered carbon nanotubes (CNTs) with tunable and large circular dichroism (CD). By controlling the stacking angle and handedness in the twist-stacking approach, we maximize the CD response and achieve a high deep-ultraviolet ellipticity of 40 ± 1 mdeg nm−1. Our theoretical simulations using the transfer matrix method reproduce the experimentally observed CD spectra and further predict that an optimized film of twist-stacked CNTs can exhibit an ellipticity as high as 150 mdeg nm−1, corresponding to a g factor of 0.22. Furthermore, the mechanical rotation method not only accelerates the fabrication of twisted structures but also produces both chiralities simultaneously in a single sample, in a single run, and in a controllable manner. The created wafer-scale objects represent an alternative type of synthetic chiral matter consisting of ordered quantum wires whose macroscopic properties are governed by nanoscopic electronic signatures and can be used to explore chiral phenomena and develop chiral photonic and optoelectronic devices.Item High-temperature electrothermal remediation of multi-pollutants in soil(Springer Nature, 2023) Deng, Bing; Carter, Robert A.; Cheng, Yi; Liu, Yuan; Eddy, Lucas; Wyss, Kevin M.; Ucak-Astarlioglu, Mine G.; Luong, Duy Xuan; Gao, Xiaodong; JeBailey, Khalil; Kittrell, Carter; Xu, Shichen; Jana, Debadrita; Torres, Mark Albert; Braam, Janet; Tour, James M.; NanoCarbon Center and the Rice Advanced Materials Institute; Smalley-Curl InstituteSoil contamination is an environmental issue due to increasing anthropogenic activities. Existing processes for soil remediation suffer from long treatment time and lack generality because of different sources, occurrences, and properties of pollutants. Here, we report a high-temperature electrothermal process for rapid, water-free remediation of multiple pollutants in soil. The temperature of contaminated soil with carbon additives ramps up to 1000 to 3000 °C as needed within seconds via pulsed direct current input, enabling the vaporization of heavy metals like Cd, Hg, Pb, Co, Ni, and Cu, and graphitization of persistent organic pollutants like polycyclic aromatic hydrocarbons. The rapid treatment retains soil mineral constituents while increases infiltration rate and exchangeable nutrient supply, leading to soil fertilization and improved germination rates. We propose strategies for upscaling and field applications. Techno-economic analysis indicates the process holds the potential for being more energy-efficient and cost-effective compared to soil washing or thermal desorption.Item Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam(Springer Nature, 2023) Malla, Tek Narsingh; Zielinski, Kara; Aldama, Luis; Bajt, Sasa; Feliz, Denisse; Hayes, Brendon; Hunter, Mark; Kupitz, Christopher; Lisova, Stella; Knoska, Juraj; Martin-Garcia, Jose Manuel; Mariani, Valerio; Pandey, Suraj; Poudyal, Ishwor; Sierra, Raymond G.; Tolstikova, Alexandra; Yefanov, Oleksandr; Yoon, Chung Hong; Ourmazd, Abbas; Fromme, Petra; Schwander, Peter; Barty, Anton; Chapman, Henry N.; Stojkovic, Emina A.; Batyuk, Alexander; Boutet, Sébastien; Phillips, George N.; Pollack, Lois; Schmidt, MariusFor decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.Item Machine learning coarse-grained potentials of protein thermodynamics(Springer Nature, 2023) Majewski, Maciej; Pérez, Adrià; Thölke, Philipp; Doerr, Stefan; Charron, Nicholas E.; Giorgino, Toni; Husic, Brooke E.; Clementi, Cecilia; Noé, Frank; De Fabritiis, Gianni; Center for Theoretical Biological PhysicsA generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.Item Protein target highlights in CASP15: Analysis of models by structure providers(Wiley, 2023) Alexander, Leila T.; Durairaj, Janani; Kryshtafovych, Andriy; Abriata, Luciano A.; Bayo, Yusupha; Bhabha, Gira; Breyton, Cécile; Caulton, Simon G.; Chen, James; Degroux, Séraphine; Ekiert, Damian C.; Erlandsen, Benedikte S.; Freddolino, Peter L.; Gilzer, Dominic; Greening, Chris; Grimes, Jonathan M.; Grinter, Rhys; Gurusaran, Manickam; Hartmann, Marcus D.; Hitchman, Charlie J.; Keown, Jeremy R.; Kropp, Ashleigh; Kursula, Petri; Lovering, Andrew L.; Lemaitre, Bruno; Lia, Andrea; Liu, Shiheng; Logotheti, Maria; Lu, Shuze; Markússon, Sigurbjörn; Miller, Mitchell D.; Minasov, George; Niemann, Hartmut H.; Opazo, Felipe; Phillips Jr, George N.; Davies, Owen R.; Rommelaere, Samuel; Rosas-Lemus, Monica; Roversi, Pietro; Satchell, Karla; Smith, Nathan; Wilson, Mark A.; Wu, Kuan-Lin; Xia, Xian; Xiao, Han; Zhang, Wenhua; Zhou, Z. Hong; Fidelis, Krzysztof; Topf, Maya; Moult, John; Schwede, TorstenWe present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.Item Niobium Oxide Photocatalytically Oxidizes Ammonia in Water at Ambient Conditions(SciELO, 2024) Elias, Welman; Clark, Chelsea; Heck, Kimberly; Arredondo, Jacob; Wang, Bo; Toro, Andras; Kürtib, László; Wong, Michael; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water TreatmentAmmonia contamination in water is a significant environmental issue since it is toxic and leads to eutrophication. Photocatalysis has been investigated as a strategy for ammonia degradation but can potentially form toxic nitrite (NO2–) and nitrate (NO3–) byproducts. This work reports on the ability of niobium oxide (Nb2O5) to photocatalytically oxidize aqueous-phase ammonia (NH3). Whereas as-synthesized Nb2O5 showed little catalytic activity (< 1% NH3 conversion after 6 h of UV-C irradiation, at room temperature and atmospheric pressure, and under O2 headspace), Nb2O5 treated in basic solution (OH-Nb2O5) was able to photocatalytically degrade NH3 at ca. 9% conversion after six hours, with ca. 70% selectivity to the desired N2, with a first-order rate constant of ca. 12 times higher than the as synthesize catalyst (1.6 × 10–3 min–1 vs. 2.0 × 10–2 min–1). Raman spectroscopic analysis indicated the presence of terminal Nb=O species after base treatment of Nb2O5, implicating them as catalytically active sites. These results underscore how a simple structural modification can significantly affect photocatalytic activity for aqueous ammonia oxidation.