Article
Biochemical Research Methods
Maja Leskovec, Andrej Raspor, Veronika Fujs, Andrej Mihevc, Ales Strancar
Summary: Preferential exclusion chromatography (PXC), also known as hydrophobic interaction chromatography, is a technique for purifying Adeno-associated viruses using high molarity of preferentially excluded cosolvent (salt). However, the high salt concentration can cause aggregation and precipitation of compounds from the sample. PXC can be used as the first chromatographic step to concentrate and purify AAV, especially when the impurity concentration is lower in the excreted viruses compared to cell lysates.
Article
Chemistry, Multidisciplinary
Yadong Wu, Haoyang Ling, Yongchao Qian, Yuhao Hu, Bo Niu, Xiangbin Lin, Xiang-Yu Kong, Lei Jiang, Liping Wen
Summary: Membrane separation is an effective method for addressing the global water crisis. The introduction of liquid-liquid interfaces in membrane systems can enhance wetting and reduce transport resistance, improving water flow without sacrificing rejection performance. This study provides insights for designing advanced membrane systems for water purification and energy conversion processes.
Article
Chemistry, Physical
Kui Xu, Xinhua Zheng, Ruihao Luo, Jifei Sun, Yirui Ma, Na Chen, Mingming Wang, Li Song, Qingbiao Zhao, Wei Chen
Summary: A three-dimensional nano-copper host modified by zincophilic antimony nanoparticles (ZA@3D-nanoCu) is designed for dendrite-free and anode-free zinc batteries. The ZA@3D-nanoCu structure provides sufficient zincophilic sites and uniform current density distribution, enabling reversible zinc plating/stripping with high stability and utilization.
MATERIALS TODAY ENERGY
(2023)
Article
Environmental Sciences
Martin A. Briggs, Kevin E. Jackson, Fiona Liu, Eric M. Moore, Alaina Bisson, Ashley M. Helton
Summary: Groundwater discharge to rivers takes many forms, including preferential groundwater discharge points (PDPs) along riverbanks. The physical controls on the spatial distribution of PDPs along riverbanks are not well-defined. This study investigates the local riverbank sediment controls on PDP occurrence and uses drone-based and handheld thermal infrared imaging to map PDP locations along two mainstem rivers.
Article
Biology
Joao Victor de Souza, Victor H. R. Nogueira, Alessandro S. Nascimento
Summary: The correct evaluation of ligand binding free energies by computational methods is still a challenging research area. Four main categories of methods, including molecular docking, thermodynamic ensembles, alchemical methods, and biased simulations, are commonly used for these calculations. In this study, the Monte Carlo Recursion (MCR) method is introduced as an intermediate approach for ligand binding evaluation, showing good correlation with experimental data and providing insights into the binding energy funnel.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Chemistry, Physical
Bing Zheng, Jing He, Zhe Wang, Ying Xie, Yin -yin Qian, Jiao Zhang, Yi-nan Tang, Li-ying Cui, Yin -mei Wu, Lin Yang, Hai-tao Yu
Summary: This study investigates the structural stability of seven typical borophene classes (alpha, alpha 1, alpha 5, chi 3, beta 12, delta 6, and delta 3) with 1-3 layers. The results show that alpha and alpha 5 borophene exhibit the highest level of stability in the 1-3 layer series. The study also examines the electronic structures and work functions of 1-5 layer alpha and alpha 5 borophene. The findings suggest that alpha type boron nanotubes formed by alpha-borophene enhance interlayer bonding strength and can be used as alternative materials to graphene.
APPLIED SURFACE SCIENCE
(2023)
Article
Engineering, Chemical
Junxia Liu, Zhiwei Tang, Haiyan Yang, Xianhui Li, Xuri Yu, Zhihong Wang, Tianyi Huang, Chuyang Y. Tang
Summary: This study systematically investigated the influence of membrane defects on fouling through simulations. The results show that membrane defects significantly affect fouling by influencing the interaction between foulants and the membrane. Under certain energy barrier conditions, membrane defects can accelerate foulant deposition and shorten or eliminate the metastable period of the membrane.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Biochemical Research Methods
Rongfan Tang, Pengcheng Chen, Zhe Wang, Lingling Wang, Haiping Hao, Tingjun Hou, Huiyong Sun
Summary: “Drug design targeting protein-protein interactions associated with disease development is crucial. Besides interrupting interactions, stabilizing protein-protein interactions can also be beneficial for therapy. However, characterizing the stabilization effect of stabilizers is challenging, which highlights the importance of developing reliable computational strategies.”
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Optics
Isabela M. S. Diogenis, Emille M. Rodrigues, Italo O. Mazali, Fernando A. Sigoli
Summary: The study analyzed the excitation and emission spectra profiles of Eu-III sensitized by Gd-III ions in hierarchical structured beta-NaYF4 nanoparticles, indicating preferential sensitization of Eu-III ions at the core@shell interface by IET. This preferential sensitization may help explain the upconversion emission bands intensities observed in UCNPs and confirms that Gd-III-mediated emission occurs spatially in a narrow core@shell interfacial region.
JOURNAL OF LUMINESCENCE
(2021)
Article
Chemistry, Physical
Yujuan Niu, Jiufeng Dong, Yifei He, Xinwei Xu, Shuai Li, Kai Wu, Qing Wang, Hong Wang
Summary: In this study, a high-temperature dielectric based on polyimide and polyetherimides was developed, which effectively suppressed high-field electrical conduction at high temperatures by creating a molecular stacking structure at the interface and accumulating space charges. The material exhibited excellent capacitive performance even at high temperatures and was compatible with roll-to-roll processing.
Article
Materials Science, Multidisciplinary
Z. J. Bergstrom, L. Yang, B. D. Wirth
Summary: Density functional theory (DFT) calculations have been used to study the trapping and segregation strength of hydrogen at noble gas interfaces in tungsten, revealing variations in binding energy and migration energy with noble gas density and surface orientation. The de-trapping energy of hydrogen at these interfaces was found to be less sensitive to noble gas density.
JOURNAL OF NUCLEAR MATERIALS
(2021)
Article
Plant Sciences
Huifang Song, Yibo Cao, Xinyan Zhao, Lingyun Zhang
Summary: This study identified a candidate gene VcHKT1;1 involved in leaf Na+ exclusion and salt tolerance in blueberry. It was found that VcHKT1;1 promotes leaf Na+ exclusion by retrieving Na+ from xylem sap. The study also discovered a naturally occurring mutation in the promoter of VcHKT1;1 that increases its transcription level and promotes leaf Na+ exclusion and salt tolerance in blueberry.
Article
Chemistry, Physical
Xinqiang Ding, Bin Zhang
Summary: The fast and accurate calculation of standard binding free energy is crucial for drug design. The new method DeepBAR combines deep generative models with the Bennett acceptance ratio method to achieve an order-of-magnitude improvement in efficiency compared to traditional methods. DeepBAR is exact and does not suffer from approximations for entropic contributions, making it a valuable tool for computing standard binding free energy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Nur Syahirah Suhalim, Norherdawati Kasim, Ebrahim Mahmoudi, Intan Juliana Shamsudin, Abdul Wahab Mohammad, Fathiah Mohamed Zuki, Nor Laili-Azua Jamari
Summary: Nanofiltration technology is an effective solution for heavy metal-induced water pollution, with advantages of small footprint and low energy consumption. However, the rejection mechanisms of NF membranes are complex, posing challenges for novice researchers.
Article
Chemistry, Multidisciplinary
Xinda You, Li Cao, Yawei Liu, Hong Wu, Runlai Li, Qianxiang Xiao, Jinqiu Yuan, Runnan Zhang, Chunyang Fan, Xiaoyao Wang, Pengfei Yang, Xiaoyu Yang, Yu Ma, Zhongyi Jiang
Summary: Ionic covalent organic framework membranes (iCOFMs) with charged framework nanochannels and high charge density have been developed to control ion transport. These membranes enable ion exclusion while maintaining high water permeability, and hold great potential for water purification, ionic separation, sensing, and energy conversion.
Article
Biochemistry & Molecular Biology
Tine Maja Frimann, Suk Kyu Ko, Pernille Harris, Jens Thostrup Bukrinski, Gunther H. J. Peters
Summary: In this study, we used molecular dynamics simulations to investigate the binding of glucagon-like peptide-1 (GLP-1) and acylated GLP-1 analogues with the endogenous receptor (GLP-1R). The results showed that the fatty acid (FA) chain structure, acylation position on the peptide, and presence of a linker all played important roles in the binding. Analysis of the simulations revealed that the major differences between the systems were due to the FA interactions and positioning of acylation on the peptide. Hydrophobic interactions between the FA chain and a hydrophobic patch on the extracellular domain significantly contributed to the binding affinity. Furthermore, the presence of a charged linker between the peptide and FA chain could stabilize the complex by forming hydrogen bonds. These findings provide important insights into designing acylated agonists for GLP-1R.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Nicolai Tidemand Johansen, Frederik Gronbaek Tidemand, Martin Cramer Pedersen, Lise Arleth
Summary: We have witnessed significant progress in the design, optimization, and utilization of carrier particle systems for studying membrane proteins in near-native environments over the past decade. New and improved systems continue to emerge, pushing the boundaries of existing carrier systems, while specific carrier systems establish themselves as the preferred choice for certain types of target membrane proteins. This review covers the most commonly used carrier systems, highlighting their similarities and differences, as well as current trends and future directions in the field. Special attention is given to the biophysical properties and membrane mimicking ability of each system, and how they may impact the study of embedded membrane proteins and their structure or function.
Article
Biochemistry & Molecular Biology
Sune Schubert, Kay Schaller, Jenny Arnling Baath, Cameron Hunt, Kim Borch, Kenneth Jensen, Jesper Brask, Peter Westh
Summary: Bioprocessing of polyester waste is a promising approach for achieving a cyclic plastic economy. This study focuses on the enzymatic breakdown of poly(ethylene terephthalate) (PET) and reveals the crucial role of endo-lytic activity in overall enzyme performance. The release of soluble PET fragments with two or three aromatic rings through endo-lytic activity leads to efficient breakdown of the polymer in aqueous bulk, contributing to the formation of monoaromatic products.
Article
Chemistry, Physical
Helena D. D. Tjornelund, Jesper Brask, John M. M. Woodley, Gunther H. J. Peters
Summary: In this study, an optimized protocol for controlling the initial water activity in organic reaction mixtures with soluble lipase was proposed. The protocol ensures reproducible and consistent enzyme activity measurements. The importance of consistent stirring and volume correction to compensate for solvent evaporation was highlighted. The study also tested the protocol on soluble and immobilized lipase and found similar water activity profiles and the highest enzyme activity in hexane. This optimized protocol expands the possibilities for studying enzyme kinetics.
Article
Chemistry, Physical
Coralie Pasquier, Soren Roi Midtgaard, Marco Polimeni, Christian Isak Jorgensen, Lise Arleth, Thomas H. Callisen, Mikael Lund
Summary: In this study, protein-protein interactions in protein solutions were investigated using small angle X-ray scattering and molecular simulations. The results showed that as protein concentration increases, the balance between spatial and orientational correlations changes, and patchy interactions may occur. By analyzing experimental data and simulations, it was found that patchy interactions between proteins lead to dimer formation, and these dimers exist in an open conformation, maximizing hydrophobic attractions for inter-protein alignment.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Morten Sorlie, Malene Billeskov Keller, Peter Westh
Summary: In nature, the enzymatic degradation of recalcitrant polysaccharides involves the collaborative action of glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs) through different mechanisms. GHs use a hydrolytic approach, while LPMOs are oxidative. The interplay between LPMOs and GHs can provide rate enhancements and improved degradation of polysaccharides, although the exact magnitude of the enhancements depends on the nature of the specific GH and LPMO. The understanding of this interplay is important for enhancing enzymatic polysaccharide degradation.
ESSAYS IN BIOCHEMISTRY
(2023)
Article
Chemistry, Physical
Abigail Barclay, Birthe B. Kragelund, Lise Arleth, Martin Cramer Pedersen
Summary: Recent advances in protein expression protocols have allowed for the investigation of structurally complex and disordered biomolecules using small-angle scattering experiments. A modeling scheme has been developed that combines classical form factor based modeling with spherical harmonics-based formulation to accurately calculate scattering profiles from these complex samples. The scheme can account for flexible domains and other structurally elaborate components, and we demonstrate its utility through a case study on a growth hormone receptor membrane protein. We also explore how the scattering profiles vary under different contrasts and discuss the implications for data modeling.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Andreas Erichsen, Gunther H. J. Peters, Sophie R. Beeren
Summary: Delta-CD, a minor component of a complex mixture of linear and cyclic glucans, can be synthesized in unprecedented yields by employing a unique template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that delta-CD can form pseudorotaxanes with up to three bolaamphiphiles. This research provides a new method for the preparative-scale synthesis of delta-CD.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Medicine, Research & Experimental
Alina Kulakova, Dillen Augustijn, Inas El Bialy, Lorenzo Gentiluomo, Maria Laura Greco, Stefan Hervo-Hansen, Sowmya Indrakumar, Sujata Mahapatra, Marcello Martinez Morales, Christin Pohl, Marco Polimeni, Aisling Roche, Hristo L. Svilenov, Andreas Tosstorff, Matja Zalar, Robin Curtis, Jeremy P. Derrick, Wolfgang Friess, Alexander P. Golovanov, Mikael Lund, Allan Norgaard, Tarik A. Khan, Gunther H. J. Peters, Alain Pluen, Dierk Roessner, Werner W. Streicher, Christopher F. van der Walle, Jim Warwicker, Shahid Uddin, Gerhard Winter, Jens Thostrup Bukrinski, Asmund Rinnan, Pernille Harris
Summary: Therapeutic proteins are difficult to develop due to their complexity and the need for an acceptable formulation. A universal formulation strategy is currently lacking. This study used high-throughput characterization to analyze 14 different proteins formulated under various conditions. pH and ionic strength were identified as the most important factors affecting protein stability. Prediction methods were also developed for real-time and accelerated stress stability.
MOLECULAR PHARMACEUTICS
(2023)
Review
Biochemistry & Molecular Biology
Yu Tian, Yu Wang, Yuyue Zhong, Marie Sofie Moller, Peter Westh, Birte Svensson, Andreas Blennow
Summary: Enzymatic hydrolysis of starch granules is fundamental for understanding starch degradation in plant cells, utilizing starch as an energy resource in foods, and developing efficient saccharification processes. However, the kinetics of hydrolysis for solid substrates like starch granules are slower and more complex. The multifaceted nature of the substrate surface and its changing properties during hydrolysis pose challenges for analysis.
Article
Biochemistry & Molecular Biology
Ida M. Vedel, Andreas Prestel, Zhenwei Zhang, Natalia T. Skawinska, Holger Stark, Pernille Harris, Birthe B. Kragelund, Gunther H. J. Peters
Summary: The structure and dynamics of Tryptophan hydroxylase 2 (TPH2) and its regulatory mechanism were investigated using NMR spectroscopy and cryo-EM techniques. The results revealed the complexity of TPH2 regulation and the presence of a monomer-dimer equilibrium. These findings provide important insights for understanding the regulatory mechanism of TPH2.
Article
Biology
Raul Araya-Secchi, Katrine Bugge, Pernille Seiffert, Amalie Petry, Gitte W. Haxholm, Kresten Lindorff-Larsen, Stine Falsig Pedersen, Lise Arleth, Birthe B. Kragelund
Summary: This study investigates the role of lipids in PRLR signaling and finds that co-structure formation locks the disordered domain of PRLR in an extended structure, enabling signal relay.
Article
Multidisciplinary Sciences
Rie Jonsson, Alexander Bjorling, Soren Roi Midtgaard, Grethe Vestergaard Jensen, Nicholas Skar-Gislinge, Lise Arleth, Steve Matthews, Karen Angeliki Krogfelt, Havard Jenssen
Summary: This study used small-angle X-ray scattering to reveal the structural morphology of the aggregative adherence fimbriae. The results showed that the fimbriae were arranged in a compact manner with Agg5A + Agg3B subunit proteins assembled pairwise on a flexible string. The study also suggests that the minor subunit plays a significant role in the assembled fimbriae by affecting the overall structure.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Bartlomiej M. Kolaczkowski, Olga V. Moroz, Elena Blagova, Gideon J. Davies, Marie Sofie Moller, Anne S. Meyer, Peter Westh, Kenneth Jensen, Keith S. Wilson, Kristian B. R. M. Krogh
Summary: Many eukaryotic proteins are N-glycosylated with high-mannose N-glycans and alpha-1,6-mannan backbones. GH92 alpha-mannosidases release mannose residues from these N-glycans, allowing alpha-endomannanases to degrade the alpha-mannan backbone. The structure and function of a multidomain GH92 alpha-mannosidase CBM have not been characterized. This study provides insights into the structure and function of a full-length five-domain GH92 alpha-mannosidase from Neobacillus novalis, demonstrating the importance of CBMs for the overall structural integrity of the enzyme.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Helena D. Tjornelund, Jesper Vind, Jesper Brask, John M. Woodley, Gunther H. J. Peters
Summary: This study investigates the molecular mechanism of the specific activity of Candida antarctica lipase B (CALB) in low-water environments using molecular dynamics simulations. Based on experiments and simulations, four criteria influencing the performance of the enzyme in organic media were proposed and it was shown that specific mutants can resist changes in water activity.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
