Now showing items 1-20 of 588

    • Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography 

      Pandey, S.; Calvey, G.; Katz, A. M.; Malla, T. N.; Koua, F. H. M.; (2021)
      Single-millisecond mix-and-inject experiments are presented on ligand binding to an enzyme performed at the European Free-Electron Laser with high X-ray repetition rates.
    • Surface-facilitated trapping by active sites: From catalysts to viruses 

      Misiura, Mikita M.; Berezhkovskii, Alexander M.; Bezrukov, Sergey M.; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physic (2021)
      Trapping by active sites on surfaces plays important roles in various chemical and biological processes, including catalysis, enzymatic reactions, and viral entry into host cells. However, the mechanisms of these processes remain not well understood, mostly because the existing theoretical descriptions are not fully accounting for the role of the ...
    • Steady-State Dynamics of Exclusion Process with Local Reversible Association of Particles 

      Jindal, Akriti; Kolomeisky, A.B.; Gupta, Arvind Kumar (2021)
      Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these observations, we developed a theoretical model for collective dynamics of biological molecular motors that accounts ...
    • JP-8 Desulfurization by CuNa-Y Zeolite at Elevated Temperatures Has Two Distinct Stages: Chemisorption Followed by Surface Reactions 

      da Silva, Priscilla Dias; Wong, Michael S.; Zygourakis, Kyriacos (2021)
      This study evaluates the performance of continuous-flow adsorbers for adsorptive desulfurization. JP-8 fuel with 2230 ppmw of sulfur was treated in a flow-through adsorber packed with CuNa-Y zeolite pellets and operating at 180 °C and 200 psig with liquid hourly space velocities (LHSV) from 0.13 to 3.24 h–1. Our results showed that a flow-through ...
    • Molecular Mechanisms of Active Transport in Antiporters: Kinetic Constraints and Efficiency 

      Berlaga, Alex; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics (2021)
      A vital role in supporting successful functioning of biological cells is played by membrane channels called antiporters. These channel proteins utilize the concentration gradient of one type of species to move another type of species in the opposite direction and against their concentration gradient. It is believed that antiporters operate via ...
    • Understanding the molecular mechanisms of transcriptional bursting 

      Klindziuk, Alena; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics (2021)
      In recent years, it has been experimentally established that transcription, a fundamental biological process that involves the synthesis of messenger RNA molecules from DNA templates, does not proceed continuously as was expected. Rather, it exhibits a distinct dynamic behavior of alternating between productive phases when RNA molecules are actively ...
    • Synergistic inhibition of SARS-CoV-2 cell entry by otamixaban and covalent protease inhibitors: pre-clinical assessment of pharmacological and molecular properties 

      Hempel, Tim; Elez, Katarina; Krüger, Nadine; Raich, Lluís; Shrimp, Jonathan H. ; (2021)
      SARS-CoV-2, the cause of the COVID-19 pandemic, exploits host cell proteins for viral entry into human lung cells. One of them, the protease TMPRSS2, is required to activate the viral spike protein (S). Even though two inhibitors, camostat and nafamostat, are known to inhibit TMPRSS2 and block cell entry of SARS-CoV-2, finding further potent therapeutic ...
    • Single-cell stochastic modelling of the action of antimicrobial peptides on bacteria 

      Teimouri,Hamid; Nguyen, Thao N.; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics (2021)
      Antimicrobial peptides (AMPs) produced by multi-cellular organisms as their immune system's defence against microbes are actively considered as natural alternatives to conventional antibiotics. Although substantial progress has been achieved in studying the AMPs, the microscopic mechanisms of their functioning remain not well understood. Here, we ...
    • Urban mining by flash Joule heating 

      Deng, Bing; Luong, Duy Xuan; Wang, Zhe; Kittrell, Carter; McHugh, Emily A.; (2021)
      Precious metal recovery from electronic waste, termed urban mining, is important for a circular economy. Present methods for urban mining, mainly smelting and leaching, suffer from lengthy purification processes and negative environmental impacts. Here, a solvent-free and sustainable process by flash Joule heating is disclosed to recover precious ...
    • Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis 

      Alvarado, S. K.; Miller, M. D.; Bhardwaj, M.; Thorson, J. S.; Van Lanen, S. G.; (2021)
      The 1.5 Å resolution crystal structure of DynU16, a protein identified in the dynemicin-biosynthetic gene cluster, is reported. The structure adopts a di-domain helix-grip fold with a uniquely positioned open cavity connecting the domains. The elongated dimensions of the cavity appear to be compatible with the geometry of a linear polyene, suggesting ...
    • Oleuropein derivatives from olive fruit extracts reduce α-synuclein fibrillation and oligomer toxicity 

      Mohammad-Beigi, Hossein; Aliakbari, Farhang; Sahin, Cagla; Lomax, Charlotte; Tawfike, Ahmed; (2019)
      Aggregation of α-synuclein (αSN) is implicated in neuronal degeneration in Parkinson's disease and has prompted searches for natural compounds inhibiting αSN aggregation and reducing its tendency to form toxic oligomers. Oil from the olive tree (Olea europaea L.) represents the main source of fat in the Mediterranean diet and contains variable levels ...
    • The application of amine-based materials for carbon capture and utilisation: an overarching view 

      Hamdy, Louise B.; Goel, Chitrakshi; Rudd, Jennifer A.; Barron, Andrew R.; Andreoli, Enrico (2021)
      In the ongoing research campaign to reduce the global atmospheric CO2 concentration, technologies are being developed to enable the capture of CO2 from dilute sources and conversion into higher-value products. Amine and polyamine-based materials feature widely in the literature as solid CO2 sorbents and as catalyst modifiers for CO2 electrochemical ...
    • Synthesis of precision antibody conjugates using proximity-induced chemistry 

      Cao, Yu J.; Yu, Chenfei; Wu, Kuan-Lin; Wang, Xuechun; Liu, Dong; (2021)
      Rationale: Therapeutic antibody conjugates allow for the specific delivery of cytotoxic agents or immune cells to tumors, thus enhancing the antitumor activity of these agents and minimizing adverse systemic effects. Most current antibody conjugates are prepared by nonspecific modification of antibody cysteine or lysine residues, inevitably resulting ...
    • Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images 

      Zhang, Jiangguo; Comstock, Jessica A.; Cotter, Christopher R.; Murphy, Patrick A.; Nie, Weili; (2021)
      Myxococcus xanthus bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to ...
    • Macroscopic weavable fibers of carbon nanotubes with giant thermoelectric power factor 

      Komatsu, Natsumi; Ichinose, Yota; Dewey, Oliver S.; Taylor, Lauren W.; Trafford, Mitchell A.; (2021)
      Low-dimensional materials have recently attracted much interest as thermoelectric materials because of their charge carrier confinement leading to thermoelectric performance enhancement. Carbon nanotubes are promising candidates because of their one-dimensionality in addition to their unique advantages such as flexibility and light weight. However, ...
    • Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion 

      Dodero-Rojas, Esteban; Onuchic, Jose N; Whitford, Paul Charles; Center for Theoretical Biological Physics (2021)
      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to ...
    • Light emission from plasmonic nanostructures 

      Cai, Yi-Yu; Tauzin, Lawrence J.; Ostovar, Behnaz; Lee, Stephen; Link, Stephan (2021)
      The mechanism of light emission from metallic nanoparticles has been a subject of debate in recent years. Photoluminescence and electronic Raman scattering mechanisms have both been proposed to explain the observed emission from plasmonic nanostructures. Recent results from Stokes and anti-Stokes emission spectroscopy of single gold nanorods using ...
    • Local Anti–PD-1 Delivery Prevents Progression of Premalignant Lesions in a 4NQO-Oral Carcinogenesis Mouse Model 

      Shi, Yewen; Xie, Tong-xin; Leach, David G.; Wang, Bingbing; Young, Simon; (2021)
      Although the principle of systemic treatment to prevent the progression of oral premalignant lesions (OPL) has been demonstrated, there remains a lack of consensus about an optimal approach that balances clinical efficacy with toxicity concerns. Recent advances in cancer therapy using approaches targeting the tumor immune microenvironment (TIME) ...
    • Temporal order of mutations influences cancer initiation dynamics 

      Teimouri, Hamid; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics (2021)
      Cancer is a set of genetic diseases that are driven by mutations. It was recently discovered that the temporal order of genetic mutations affects the cancer evolution and even the nature of the decease itself. The mechanistic origin of these observations, however, remain not well understood. Here we present a theoretical model for cancer initiation ...
    • A synthetic circuit for buffering gene dosage variation between individual mammalian cells 

      Yang, Jin; Lee, Jihwan; Land, Michelle A.; Lai, Shujuan; Igoshin, Oleg A.; (2021)
      Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits – Equalizers – that buffer copy-number variation ...