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  • Table of Content
      Dec. 2018, Volume 4 Issue 6 Previous Issue   
    Cover Story
    Insulin secretory granules (ISGs),a group of distinguishing organelles in pancreatic β cells,are responsible for the storage and secretion of insulin to maintain blood glucose homeostasis.The molecular mechanisms of ISG biogenesis,maturation,transportation,and exocytosis are still largely unknown because the proteins involved in these distinct steps have not been fully identified.Subcellular fractionation by density gradient centrifugation has been successfully employed to analyze the proteomes of numero [Detail] ...
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    Biophysics Reports. 2018, 4 (6): 0-0.  
    Abstract   HTML   PDF (3279KB) ( 4 )
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    A critique of the alternating access transporter model of uniport glucose transport
    Richard J. Naftalin
    Biophysics Reports. 2018, 4 (6): 287-299.   DOI: 10.1007/s41048-018-0076-9
    Abstract   HTML   PDF (3353KB) ( 18 )
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    Thermodynamics of voltage-gated ion channels
    Xuejun C. Zhang, Hanting Yang, Zhenfeng Liu, Fei Sun
    Biophysics Reports. 2018, 4 (6): 300-319.   DOI: 10.1007/s41048-018-0074-y
    Abstract   HTML   PDF (1440KB) ( 19 )
    Ion channels are essential for cellular signaling. Voltage-gated ion channels (VGICs) are the largest and most extensively studied superfamily of ion channels. They possess modular structural features such as voltage-sensing domains that encircle and form mechanical connections with the pore-forming domains. Such features are intimately related to their function in sensing and responding to changes in the membrane potential. In the present work, we discuss the thermodynamic mechanisms of the VGIC superfamily, including the two-state gating mechanism, sliding-rocking mechanism of the voltage sensor, subunit cooperation, lipid-infiltration mechanism of inactivation, and the relationship with their structural features.
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    Electron microscopy combined with spatial analysis: quantitative mapping of the nano-assemblies of plasma membrane-associating proteins and lipids
    Yong Zhou, John F. Hancock
    Biophysics Reports. 2018, 4 (6): 320-328.   DOI: 10.1007/s41048-018-0060-4
    Abstract   HTML   PDF (711KB) ( 48 )
    The plasma membrane (PM) is a complex environment consisting of > 700 species of lipids and many different types of membrane-associating proteins. These lipids and membrane proteins are distributed heterogeneously into nanometer-sized domains, called nanoclusters. The lateral spatial segregation in the PM gives rise to different curvature and lipid composition, which determines the efficiency of effector binding and signal transmission. Here, we describe an electron microscopy (EM)-spatial mapping technique to quantify the extent of nanoclusters formation in the PM. The nano-assemblies in the PM are quantified via expressing the GFP-tagged proteins or lipid-binding domains in the cells, which are then immunolabeled with the gold nanoparticles pre-coupled to the anti-GFP antibody. The gold nanoparticles are visualized via the transmission EM at high magnification. The statistical analysis of the Ripley's K-function calculates the spatial distribution of the gold nanoparticles. Important spatial parameters, such as the extent of nanoclustering, the clustered fraction, the number of proteins per cluster, the optimal size of a nanocluster, and the number of proteins localized to the PM, can be calculated. Further detailed aggregation pattern, such as the populations of monomers, dimers, trimers, and higher ordered oligomers, can also be extracted from the spatial analysis. The EM-bivariate analysis quantifies the extent of co-localization between two different components in the PM and provides key information on the protein-protein and the protein-lipid interactions over a long-distance scale from 8 to 240 nm.
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    Proteomic analysis of insulin secretory granules in INS-1 cells by protein correlation profiling
    Min Li, Wen Du, Maoge Zhou, Li Zheng, Eli Song, Junjie Hou
    Biophysics Reports. 2018, 4 (6): 329-338.   DOI: 10.1007/s41048-018-0061-3
    Abstract   HTML   PDF (1562KB) ( 44 )
    Insulin secretory granules (ISGs), a group of distinguishing organelles in pancreatic β cells, are responsible for the storage and secretion of insulin to maintain blood glucose homeostasis. The molecular mechanisms of ISG biogenesis, maturation, transportation, and exocytosis are still largely unknown because the proteins involved in these distinct steps have not been fully identified. Subcellular fractionation by density gradient centrifugation has been successfully employed to analyze the proteomes of numerous organelles. However, use of this method to elucidate the ISG proteome is limited by co-fractionated contaminants because ISGs are very dynamic and have abundant exchanges or contacts with other organelles, such as the Golgi apparatus, lysosomes, and endosomes. In this study, we developed a new strategy for identifying ISG proteins by protein correlation profiling (PCP)-based proteomics, which included ISG purification by OptiPrep density gradient centrifugation, label-free quantitative proteome, and identification of ISG proteins by correlating fractionation profiles between candidates and known ISG markers. Using this approach, we were able to identify 81 ISG proteins. Among them, TM9SF3, a nine-transmembrane protein, was considered a high confidence ISG candidate protein highlighted in the PCP network. Further biochemical and immunofluorescence assays indicated that TM9SF3 localized in ISGs, suggesting that it is a potential new ISG marker.
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    In situ protein micro-crystal fabrication by cryo-FIB for electron diffraction
    Xinmei Li, Shuangbo Zhang, Jianguo Zhang, Fei Sun
    Biophysics Reports. 2018, 4 (6): 339-347.   DOI: 10.1007/s41048-018-0075-x
    Abstract   HTML   PDF (1397KB) ( 10 )
    Micro-electron diffraction (MicroED) is an emerging technique to use cryo-electron microscope to study the crystal structures of macromolecule from its micro-/nano-crystals, which are not suitable for conventional X-ray crystallography. However, this technique has been prevented for its wide application by the limited availability of producing good micro-/nano-crystals and the inappropriate transfer of crystals. Here, we developed a completeworkflowto prepare suitable crystals efficiently for MicroED experiment.Thisworkflow includes in situ on-grid crystallization, single-side blotting, cryo-focus ion beam (cryo-FIB) fabrication, and cryo-electron diffraction of crystal cryo-lamella. This workflow enables us to apply MicroED to study many small macromolecular crystals with the size of 2-10 μm, which is too large for MicroED but quite small for conventional X-ray crystallography. We have applied this method to solve 2.5 Å crystal structure of lysozyme from its micro-crystal within the size of 10×10×10 μm3. Our work will greatly expand the availability space of crystals suitable for MicroED and fill up the gap between MicroED and X-ray crystallography.
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