Biophysics

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    Protocols in Current Issue
    A Fast and Efficient Decellularization Method for Tissue Slices

    The study and use of decellularized extracellular matrix (dECM) in tissue engineering, regenerative medicine, and pathophysiology have become more prevalent in recent years. To obtain dECM, numerous decellularization procedures have been developed

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    A Fast and Efficient Decellularization Method for Tissue Slices
    [Abstract]

    The study and use of decellularized extracellular matrix (dECM) in tissue engineering, regenerative medicine, and pathophysiology have become more prevalent in recent years. To obtain dECM, numerous decellularization procedures have been developed for the entire organ or tissue blocks, employing either perfusion of decellularizing agents through

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    In situ cryo-FIB/SEM Specimen Preparation Using the Waffle Method
    [Abstract]

    Cryo-focused ion beam (FIB) milling of vitrified specimens is emerging as a powerful method for in situ specimen preparation. It allows for the preservation of native and near-native conditions in cells, and can reveal the molecular structure of protein complexes when combined with cryo-electron tomography (cryo-ET) and sub-tomogram averaging.

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    Binding Affinity Measurements Between DNA Aptamers and their Virus Targets Using ELONA and MST
    Authors:  Gregory T. Pawel, Yuan Ma, Yuting Wu, Yi Lu and Ana Sol Peinetti, date: 11/05/2022, view: 486, Q&A: 0
    [Abstract]

    Aptamers have been selected with strong affinity and high selectivity for a wide range of targets, as recently highlighted by the development of aptamer-based sensors that can differentiate infectious from non-infectious viruses, including human adenovirus and SARS-CoV-2. Accurate determination of the binding affinity between the DNA aptamers and

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    A Fluorescence-based Approach Utilizing Self-labeling Enzyme Tags to Determine Protein Orientation in Large Unilamellar Vesicles
    Authors:  Laura Charlotte Paweletz, Sarina Veit and Thomas Günther Pomorski, date: 11/05/2022, view: 461, Q&A: 0
    [Abstract]

    Reconstitution of membrane proteins into large unilamellar vesicles is an essential approach for their functional analysis under chemically defined conditions. The orientation of the protein in the liposomal membrane after reconstitution depends on many parameters, and its assessment is important prior to functional measurements. Common approaches

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    X-ray Crystallography: Seeding Technique with Cytochrome P450 Reductase
    Authors:  Bixia Zhang, Jacob A. Lewis, Rishi Hazra and ChulHee Kang, date: 11/05/2022, view: 452, Q&A: 0
    [Abstract]

    Cytochrome P450 reductase (CPR) is a multi-domain protein that acts as a redox partner of cytochrome P450s. The CPR contains a flavin adenine dinucleotide (FAD)–binding domain, a flavin mononucleotide (FMN)-binding domain, and a connecting domain. To achieve catalytic events, the FMN-binding domain needs to move relative to the FAD-binding

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    Single-molecule Force Spectroscopy on Biomembrane Force Probe to Characterize Force-dependent Bond Lifetimes of Receptor–ligand Interactions on Living Cells
    Authors:  Tongtong Zhang, Chenyi An, Wei Hu and Wei Chen, date: 10/20/2022, view: 881, Q&A: 0
    [Abstract]

    The transmembrane receptor–ligand interactions play a vital role in the physiological and pathological processes of living cells, such as immune cell activation, neural synapse formation, or viral invasion into host cells. Mounting evidence suggests that these processes involve mechanosensing and mechanotransduction, which are directly

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    Single Protein Detection and Imaging with Evanescent Scattering Microscopy
    Authors:  Pengfei Zhang, Lei Zhou, Rui Wang, Xinyu Zhou, Jiapei Jiang, Zijian Wan and Shaopeng Wang, date: 10/20/2022, view: 660, Q&A: 0
    [Abstract]

    Single-molecule measurements provide statistical distributions of molecular properties, in addition to the ensemble averages. Evanescent detection approaches have been widely used for single-molecule detection because the evanescent field can significantly enhance the light-analyte interaction and reduce the background noise. However, current

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    Negative Staining Transmission Electron Microscopy of HIV Viral Particles Permeabilized with PFO and Capsid Stabilized with IP6
    Authors:  Derrick Lau, Chantal L. Márquez, Michael W. Parker and Till Böcking, date: 10/20/2022, view: 622, Q&A: 0
    [Abstract]

    The human immunodeficiency virus 1 (HIV-1) consists of a viral membrane surrounding the conical capsid. The capsid is a protein container assembled from approximately 1,500 copies of the viral capsid protein (CA), functioning as a reaction and transport chamber for the viral genome after cell entry. Transmission electron microscopy (TEM) is a

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    Staphylococcus aureus 30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis
    Authors:  Margarita Belinite, Iskander Khusainov and Stefano Marzi, date: 10/20/2022, view: 851, Q&A: 0
    [Abstract]

    The ribosome is a complex cellular machinery whose solved structure allowed for an incredible leap in structural biology research. Different ions bind to the ribosome, stabilizing inter-subunit interfaces and structurally linking rRNAs, proteins, and ligands. Besides cations such as K+ and Mg2+, polyamines are known to stabilize the folding of RNA

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    Serial Room Temperature Crystal Loading, Data Collection, and Data Processing of Human Glutaminase C in Complex with Allosteric Inhibitors
    Authors:  Shawn K. Milano, D. Marian Szebenyi and Richard A. Cerione, date: 09/20/2022, view: 508, Q&A: 0
    [Abstract]

    Cancer cells often overexpress glutaminase enzymes, in particular glutaminase C (GAC). GAC resides in the mitochondria and catalyzes the hydrolysis of glutamine to glutamate. High levels of GAC have been observed in aggressive cancers and the inhibition of its enzymatic activity has been shown to reduce their growth and survival. Numerous GAC

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