Biophysics

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    Protocols in Current Issue
    NMR waterLOGSY as An Assay in Drug Development Programmes for Detecting Protein-Ligand Interactions–NMR waterLOGSY
    Authors:  Carole J. R. Bataille, Terence H. Rabbitts and Timothy D. W. Claridge, date: 07/05/2020, view: 228, Q&A: 0
    In drug development programmes, multiple assays are needed for the determination of protein-compound interactions and evaluation of potential use in assays with protein-protein interactions. In this protocol we describe the waterLOGSY NMR method for ...
    NMR waterLOGSY as An Assay in Drug Development Programmes for Detecting Protein-Ligand Interactions–NMR waterLOGSY
    Authors:  Carole J. R. Bataille, Terence H. Rabbitts and Timothy D. W. Claridge, date: 07/05/2020, view: 228, Q&A: 0
    [Abstract] In drug development programmes, multiple assays are needed for the determination of protein-compound interactions and evaluation of potential use in assays with protein-protein interactions. In this protocol we describe the waterLOGSY NMR method for confirming protein-ligand binding events.
    Preparation of Yeast tRNA Sample for NMR Spectroscopy
    Authors:  Marjorie Catala, Alexandre Gato, Carine Tisné and Pierre Barraud, date: 06/20/2020, view: 475, Q&A: 0
    [Abstract] Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional modifications during their biosynthesis. To fulfil their functions within cells, tRNAs undergo a tightly controlled biogenesis process leading to the formation of mature tRNAs. In addition, functions of tRNAs are often modulated by their modifications. Although the biological ...
    Purification of Rice Stripe Virus
    Authors:  Gang Lu, Min Yao, Yijun Zhou and Xiaorong Tao, date: 03/20/2020, view: 603, Q&A: 0
    [Abstract] Although many spherical and rod-shaped plant virus purification protocols are now available, only a few protocols on filamentous plant virus purification have been published. Here, we report a protocol for large-scale purification of Rice stripe virus (RSV) from RSV-infected rice tissues. RSV virions with high infectivity were first precipitated ...
    Surface Plasmon Resonance Analysis of the Protein-protein Binding Specificity Using Autolab ESPIRIT
    Authors:  Pragyan Parimita Rath, Gaurav Anand and Shalini Agarwal, date: 02/20/2020, view: 1123, Q&A: 0
    [Abstract] Direct protein-protein interactions are known to regulate a wide range of cellular activities. To understand these contacts one can employ various experimental methods like Dynamic Light Scattering (DLS), Fluorescence Resonance Energy Transfer (FRET), Isothermal titration calorimetry (ITC), Chemical crosslinking, Co-immunoprecipitation (Co-IP), ...
    Evaluating Whole Blood Clotting in vitro on Biomaterial Surfaces
    Authors:  Roberta M Sabino and Ketul C Popat, date: 02/05/2020, view: 1108, Q&A: 0
    [Abstract] Biomaterial-associated thrombosis is still a major concern for blood-contacting implants. After the medical device is implanted and comes in contact with blood, several complex reactions occur, which may lead to thrombus formation and failure of the device. Therefore, it is essential to evaluate the biomaterial interaction with the whole blood. ...
    Protocols for Processing and Interpreting cryoEM Data Using Bsoft: A Case Study of the Retinal Adhesion Protein, Retinoschisin
    Author:  J. Bernard Heymann, date: 01/20/2020, view: 784, Q&A: 0
    [Abstract] The goal of cryoEM is to determine the structures of biomolecules from electron micrographs. In many cases the processing is straightforward and can be handled with routine protocols. In other cases, the properties and behavior of the specimen require adaptions to properly interpret the data. Here I describe the protocols for examining the higher ...
    Studying Protein Aggregation in the Context of Liquid-liquid Phase Separation Using Fluorescence and Atomic Force Microscopy, Fluorescence and Turbidity Assays, and FRAP
    Authors:  W. Michael Babinchak and Witold K. Surewicz, date: 01/20/2020, view: 1236, Q&A: 0
    [Abstract] Liquid-liquid phase separation (LLPS) underlies the physiological assembly of many membrane-less organelles throughout the cell. However, dysregulation of LLPS may mediate the formation of pathological aggregates associated with neurodegenerative diseases. Here, we present complementary experimental approaches to study protein aggregation within ...
    Characterizing the Two-photon Absorption Properties of Fluorescent Molecules in the 680-1300 nm Spectral Range
    Authors:  Mikhail Drobizhev, Rosana S Molina and Thomas E Hughes, date: 01/20/2020, view: 736, Q&A: 0
    [Abstract] Two-photon laser scanning microscopy (2PLSM) is a state-of-the-art technique used for non-invasive imaging deep inside the tissue, with high 3D resolution, minimal out-of-focus photodamage, and minimal autofluorescence background. For optimal application of fluorescent probes in 2PLSM, their two-photon absorption (2PA) spectra, expressed in ...
    Whole-cell and Perforated Patch-clamp Recordings from Acutely-isolated Murine Sino-atrial Node Cells
    Authors:  Qadeer Aziz, Muriel Nobles and Andrew Tinker, date: 01/05/2020, view: 1262, Q&A: 0
    [Abstract] Cardiac pacemaker cells of the sino-atrial node are responsible for the initiation of the heart beat and express an array of ion channels. The patch-clamp technique is the gold standard method for investigating the function of ion channels expressed in electrically active cells. Conventional whole-cell and perforated patch-clamp techniques can be ...
    Evoked Potential Recordings of Auditory Brainstem Activity in the Mouse: An Optimized Method for the Assessment of Hearing Function of Mice
    Author:  Neil J. Ingham, date: 12/05/2019, view: 1256, Q&A: 0
    [Abstract] Hearing loss is a common sensory deficiency suffered by millions worldwide. It is a heterogeneous condition and genetics plays a critical role in its etiology. Gene variants can fundamentally alter hearing function, or predispose the auditory system towards loss of function resulting from other factors. In mouse studies of hearing loss and gene ...



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