Article
Chemistry, Physical
Christian Sogaard, Krzysztof Kolman, Max Christensson, Ayse Birsen Otyakmaz, Zareen Abbas
Summary: Understanding the interaction of ions with charged silica nanoparticles is crucial for producing gels and determining long term stability. In mixtures, monovalent ions generally follow the Hofmeister series, but divalent ions do not. At pH < 9, mixtures of divalent and monovalent salts follow the normal Hofmeister series, while at pH > 9 a reversal is observed.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2021)
Article
Polymer Science
Shuang Wei, Zechuan Zhang, Weibin Dong, Ting Liang, Junyi Ji, Wen Tian, Shuai Tan, Qiang Zhao, Caihong Wang, Yong Wu
Summary: Ionic species play an important role in the phase separation behavior of PNIPAm in aqueous solutions, with different ions having varying effects on clouding temperatures. Particularly, the structure of azobenzene molecules under visible light irradiation affects the temperature response of PNIPAm.
MACROMOLECULAR RAPID COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Vladimir Vanik, Zuzana Bednarikova, Gabriela Fabriciova, Steven S. -S. Wang, Zuzana Gazova, Diana Fedunova
Summary: Amyloid fibrils can be modulated by ionic liquids, and the speed and morphology of fibrillization depend on the concentration and type of ions. The presence of different ions in ionic liquids can promote or hinder the formation of amyloid fibrils. The specific protein-ion interactions and long-range electrostatic shielding play important roles in the impact of ionic liquids.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Applied
Congde Qiao, Xujie Wang, Jianlong Zhang, Jinshui Yao
Summary: The study found that strongly hydrated anions facilitate gelation of gelatin solutions, while weakly hydrated anions hinder the formation of gel structures. The gelation temperature of proteins is directly correlated to the hydration entropy of anions, indicating different salts have distinct effects on gel structures.
FOOD HYDROCOLLOIDS
(2021)
Article
Biology
William N. Zagotta, Brandon S. Sim, Anthony K. Nhim, Marium M. Raza, Eric G. B. Evans, Yarra Venkatesh, Chloe M. Jones, Ryan A. Mehl, E. James Petersson, Sharona E. Gordon
Summary: With the recent explosion in high-resolution protein structures, there is a new frontier in biology to elucidate the mechanisms of conformational rearrangements in proteins to meet the changing needs of cells. By rigorously measuring protein energetics and dynamics through new methods like tmFRET, differences in conformational states and accurate quantification of distributions can be revealed. This new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
Article
Biotechnology & Applied Microbiology
Linghao Hu, Nianchao Wang, Joshua Bryant, Lin Liu, Linglin Xie, A. Phillip West, Alex Walsh
Summary: Autofluorescence lifetime imaging combined with machine learning models can detect metabolic perturbations between glycolysis and oxidative metabolism of living samples at a cellular level, providing a label-free technology to study cellular metabolism and metabolic heterogeneity.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Gleiston G. Dias, Marieli O. Rodrigues, Esther R. S. Paz, Mateus P. Nunes, Maria H. Araujo, Fabiano S. Rodembusch, Eufranio N. da Silva Junior
Summary: Fluorescent and colorimetric sensors are important tools for investigating chemical compositions of different matrices. These sensors have high sensitivity, low interference, and low detection limits, inspiring research in ion and molecule detection. This Review focuses on phenanthro[9,10-d]imidazoles, discussing different strategies for obtaining them and their optical properties when interacting with specific analytes.
Article
Biochemistry & Molecular Biology
Bengt Svensson, Florentin R. Nitu, Robyn T. Rebbeck, Lindsey M. Mcgurran, Tetsuro Oda, David D. Thomas, Donald M. Bers, Razvan L. Cornea
Summary: Current studies have shown that Ca2+ leakage from cardiomyocyte sarcoplasmic reticulum through hyperactive resting cardiac ryanodine receptor channels (RyR2) has a pro-arrhythmic effect. An exogenous peptide (DPc10) binding promotes leaky RyR2 in cardiomyocytes and reports on the endogenous state. Conversely, binding of calmodulin (CaM) inhibits RyR2 leak and low CaM affinity is indicative of leaky RyR2. These findings have led to the development of a FRET biosensor for drug discovery targeting RyR2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Daniel C. Morris, Adrian R. Morris, William S. Price, Stuart W. Prescott, Jason B. Harper
Summary: NMR diffusometry was used to determine the self-diffusion coefficients of pyridine and 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imides mixtures in acetonitrile. The nature of solvation changed significantly with the proportion of salt in the mixtures. Increased diffusion coefficients for the molecular components were observed with higher proportion of ionic liquid and longer alkyl chain length on the cation. Discontinuities in diffusion data were observed between hexyl and octyl derivatives, indicating changes in solution structuring.
Article
Chemistry, Physical
Olivera Drecun, Alberto Striolo, Cecilia Bernardini
Summary: Aqueous salt solutions are studied to understand their impact on system dynamics, with a focus on molecular interfacial area and the strength of interaction with hydration-shell water molecules. Simulation predictions are consistent with experimental observations, suggesting potential applications in formulating aqueous systems for advanced catalyst manufacturing.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Plant Sciences
Nina Gloeckner, Sven zur Oven-Krockhaus, Leander Rohr, Frank Wackenhut, Moritz Burmeister, Friederike Wanke, Eleonore Holzwart, Alfred J. Meixner, Sebastian Wolf, Klaus Harter
Summary: Protein-protein interaction studies are crucial for understanding cellular signaling. This study used three-fluorophore FRET and FRET-fluorescence lifetime imaging microscopy techniques to demonstrate the formation of a ternary complex involving Receptor-Like Protein 44, Brassinosteroid Insensitive 1, and Brassinosteroid Insensitive 1 Associated Kinase 1 in living plant cells. The researchers also found that this complex is localized in a distinct plasma membrane nanodomain.
Article
Chemistry, Analytical
Rajannya Sen, Liang Li, Alexander V. Zhdanov, Rafael D. L. Gaspar, Dmitri B. Papkovsky
Summary: This study evaluated four different detection platforms for phosphorescence lifetime (PLT) measurements. The results showed that the Victor 2 fluorescence reader produced stable but inaccurate readings at low PLT values, while the Cary Eclipse luminescence spectrometer was able to partly correct this issue. The Tpx3Cam camera-based macroscope and the confocal laser-scanning FLIM/PLIM microscope provided more accurate and informative PLT data.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Pharmacology & Pharmacy
Malgorzata Tarnowska, Yves Chevalier, Stephanie Briancon, Claire Bordes, Jacqueline Resende de Azevedo, Delphine Arquier, Thierry Pourcher, Marie-Alexandrine Bolzinger
Summary: Non-ideal behavior of mixed ions is observed in skin absorption experiments, with enhanced penetration of chaotropic ions from mixed solutions. Statistical analysis using a Scheffe'{3,2} simplex-lattice allows the investigation of the full ternary diagram of anion mixtures. Specific interactions between mixed bromide and iodide ions lead to absorption enhancement, indicating the formation of neutral complex species with endogenous magnesium or calcium inside the stratum corneum.
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Chemistry, Physical
F. Gamez, L. F. Sedano, S. Blazquez, J. Troncoso, C. Vega
Summary: The temperature of the maximum in density (TMD) of aqueous solutions of halides with various ions was experimentally evaluated. Adding salts diminished the TMD of the solutions compared to pure water, and the magnitude of the change depended on the nature of the electrolyte. The experimental values of the shift in the TMD can be split into individual ion contributions, allowing for the establishment of an ion ranking based on their efficiency in shifting down the TMD.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemical Research Methods
Agnes Batta, Timea Hajdu, Peter Nagy
Summary: Forster resonance energy transfer (FRET) is a radiationless interaction used to study protein oligomerization and structure with distance dependence. This study presents a method that improves FRET measurement precision by using microbeads with a calibrated number of antibody binding sites and a donor-acceptor mixture. The proposed method demonstrates superior reproducibility compared to the conventional approach and can be widely applied for the quantification of FRET experiments in biological research.
Article
Chemistry, Multidisciplinary
Durgesh K. Rai, Richard E. Gillilan, Qingqiu Huang, Robert Miller, Edmund Ting, Alexander Lazarev, Mark W. Tate, Sol M. Gruner
Summary: Pressure plays a crucial role in determining the behavior of biological macromolecules, affecting protein denaturation, enzyme kinetics, and molecular shape. The development of a high-pressure SAXS sample cell provides researchers with a valuable tool for studying biological materials under extreme conditions.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Biophysics
Cody P. Aplin, Robert C. Miller, Taryn M. Kay, Ahmed A. Heikal, Arnold J. Boersma, Erin D. Sheets
Summary: This study investigated the fluorescence depolarization dynamics of ionic strength biosensors in different salt solutions, revealing a decrease in FRET efficiency and an increase in donor-acceptor distance with higher ionic strength. Chemical equilibrium analyses showed that the equilibrium constant and free energy changes of conformational state transition were dependent on ionic strength. The results suggest that the depolarization dynamics of genetically encoded donor-acceptor pairs can serve as a quantitative means for FRET analysis in future in vivo studies.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Pengkun Zhao, Shuaidong Huo, Jilin Fan, Junlin Chen, Fabian Kiessling, Arnold J. Boersma, Robert Goestl, Andreas Herrmann
Summary: This study reports two systems enabling the ultrasound-induced activation of thrombin to control biological function. One is the design of polyaptamers that can inhibit thrombin's catalytic activity, while the other is the use of split aptamers conjugated to the surface of gold nanoparticles.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Taryn M. Kay, Cody P. Aplin, Rowan Simonet, Julie Beenken, Robert C. Miller, Christin Libal, Arnold J. Boersma, Erin D. Sheets, Ahmed A. Heikal
Summary: The study developed a simple approach using FCS to investigate FRET of genetically encoded crTC2.1, finding that the molecular brightness of the cleaved form is higher than the intact form at 405nm, but similar at 488nm. FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of time constants associated with autocorrelation curves, allowing for potential use in living cells with low expression levels of genetically encoded constructs to limit interference with cell machinery.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Physical
Margaret L. Clapham, Ryan E. Leighton, Christopher J. Douglas, Renee R. Frontiera
Summary: Polymorphism is a challenge across scientific fields, particularly in the realm of organic photovoltaic materials where it can significantly alter electronic properties. By combining lattice phonon Raman spectroscopy and microscopy, polymorphs can be efficiently characterized nondestructively, providing information on size and morphology. This technique allows for large-scale batch characterization of crystals grown from solution and physical vapor transport, as demonstrated in a case study optimizing a crystal growth method for rubrene electronic device applications.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Review
Biotechnology & Applied Microbiology
William P. Katt, Cody Aplin, Richard A. Cerione
Summary: Tissue transglutaminase (tTG) is a unique enzyme that plays important roles in cellular processes and cancer progression, especially in glioblastoma. This review provides an overview of the transglutaminase family, discusses the biochemical activities of tTG, and considers current approaches to target tTG.
ONCOTARGETS AND THERAPY
(2022)
Article
Chemistry, Multidisciplinary
Luis P. B. Guerzoni, Andre V. C. de Goes, Milara Kalacheva, Jakub Hadula, Matthias Mork, Laura De Laporte, Arnold J. Boersma
Summary: This article presents a method for generating monodisperse liposomes with minimal oil content and tunable macromolecular crowding using PDMS-based microfluidics. The method can stably produce liposomes with high concentrations of macromolecular crowders, and the oil phase can be removed after production to obtain highly crowded liposomes.
Article
Chemistry, Physical
Cody Aplin, Shawn K. Milano, Kara A. Zielinski, Lois Pollack, Richard A. Cerione
Summary: This perspective article highlights recent advances in structural techniques for probing dynamic information about protein targets in drug design, including serial room-temperature crystallography, cryogenic electron microscopy, and small-angle X-ray scattering.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Robert C. Miller, Cody Cummings, Qingqiu Huang, Nozomi Ando, Richard E. Gillilan
Summary: This study investigates the use of continuously flowing SEC-SAXS under extreme high-pressure conditions for studying biological structure and function. The results demonstrate that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa, and pressure-induced changes in folding and oligomeric state can be observed.
Article
Chemistry, Physical
Ryan E. Leighton, Ariel M. Alperstein, David Punihaole, W. Ruchira Silva, Renee R. Frontiera
Summary: Super-resolution fluorescence microscopy plays a crucial role in understanding the nanoscale structure of biological systems, but the use of fluorescent labels brings challenges. Therefore, label-free super-resolution techniques like stimulated Raman scattering (SRS) and stimulated Raman depletion microscopy (SRDM) have attracted great interest. This study demonstrates suppression mechanisms in SRDM and explores super-resolution Raman microscopy on different sides of the spectrum. The findings lead to the development of inverse raman depletion microscopy (IRDM) and offer label-free super-resolution imaging over a wide spectral range.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Kara A. Zielinski, Andrea M. Katz, George D. Calvey, Suzette A. Pabit, Shawn K. Milano, Cody Aplin, Josue San Emeterio, Richard A. Cerione, Lois Pollack
Summary: Advances in time-resolved structural techniques have allowed for a detailed view of the dynamics of biological macromolecules and reactions between binding partners. Mix-and-inject techniques, particularly those utilizing a new chaotic advection mixer, enable faster diffusion and broader application in studying biological reactions. The combination of this versatile mixer and low sample consumption opens up new possibilities for mix-and-inject studies.
Article
Multidisciplinary Sciences
Theodoros Pittas, Weiyan Zuo, Arnold J. Boersma
Summary: The crowded environment inside cells affects the behavior of biomacromolecules. While biomacromolecule concentration is believed to be the main factor contributing to intracellular crowding effects, spatial organization also plays a significant role. Cell wall damage in Escherichia coli leads to increased crowding effects, surpassing the effects caused by hyperosmotic stress. This increase is not due to changes in crowder concentration, but rather to cytoplasmic mixing and nucleoid expansion.
Article
Chemistry, Physical
Ryan E. Leighton, Renee R. Frontiera
Summary: This article introduces a Raman-based method to monitor the activity of bacteriorhodopsin. The researchers used this method to monitor the activity of bacteriorhodopsin both in vitro and in vivo, and found that the native membrane environment affects its function.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemical Research Methods
Qi Wan, Sara N. Mouton, Liesbeth M. Veenhoff, Arnold J. Boersma
Summary: This study presents a fluorescence resonance energy transfer (FRET)-based method for monitoring protein self-assembly with continuous and high-throughput capabilities, allowing for the observation of transient intermediate states. The approach utilizes intermolecular FRET between donor and acceptor proteins on the same target protein, providing high sensitivity and straightforward ratiometric imaging. The method was successfully applied to monitor the self-assembly of three different proteins, revealing the regulatory role of the chaperone protein DNAJB6b.
CELL REPORTS METHODS
(2022)
Article
Chemistry, Multidisciplinary
Yu Zhou, Shuaidong Huo, Mark Loznik, Robert Goestl, Arnold J. Boersma, Andreas Herrmann
Summary: This study introduces a new method to control protein activity using ultrasound, by engineering protein structures to be sensitive to ultrasound and selectively activating or deactivating them. This concept could potentially serve as a blueprint for remotely controlling other bioactive molecules.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)