To be launched on Aug 2015
Sponsored by Biophysical Society of China and Institute of Biophysics, CAS, P.R. China.
Online published by SpringerLink.

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An efficient two-step subcellular fractionation method for the enrichment of insulin granules from INS-1 cells
Yan Chen, Zhiping Xia, Lifen Wang, Yong Yu, Pingsheng Liu, Eli Song, Tao Xu
Biophysics Reports    2015, 1 (1): 34-40.   DOI: 10.1007/s41048-015-0008-x
Abstract   PDF (1234KB)
Insulin is one of the key regulators for blood glucose homeostasis. More than 99% of insulin is secreted from the pancreatic β-cells. Within each β-cell, insulin is packaged and processed in insulin secretary granules (ISGs) before its exocytosis. Insulin secretion is a complicated but well-organized dynamic process that includes the budding of immature ISGs (iISGs) from the trans-Golgi network, iISG maturation, and mature ISG (mISG) fusion with plasma membrane. However, the molecular mechanisms involved in this process are largely unknown. It is therefore crucial to separate and enrich iISGs and mISGs before determining their distinct characteristics and protein contents. Here, we developed an efficient two-step subcellular fractionation method for the enrichment of iISGs and mISGs from INS-1 cells: OptiPrep gradient purification followed by Percoll solution purification. We demonstrated that by using this method, iISGs and mISGs can be successfully distinguished and enriched. This method can be easily adapted to investigate SGs in other cells or tissues, thereby providing a useful tool for elucidating the mechanisms of granule maturation and secretion.
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Phosphorylation and function of DGAT1 in skeletal muscle cells
Jinhai Yu, Yiran Li, Fei Zou, Shimeng Xu, Pingsheng Liu
Biophysics Reports    2015, 1 (1): 41-50.   DOI: 10.1007/s41048-015-0004-1
Abstract   PDF (5854KB)
Aberrant intramuscular triacylglycerol (TAG) storage in human skeletal muscle is closely related to insulin insensitivity. Excessive lipid storage can induce insulin resistance of skeletal muscle, and under severe conditions, lead to type 2 diabetes. The balance of interconversion between diacylglycerol and TAG greatly influences lipid storage and utilization. Diacylglycerol O-acyltransferase 1 (DGAT1) plays a key role in this process, but its activation and phosphorylation requires further dissection. In this study, 12 putative conserved phosphorylation sites of DGAT1 were identified by examining amino acid conservation of DGAT1 in different species. Another 12 putative phosphorylation sites were also found based on bioinformatics predictions and previous reports. Meanwhile, several phosphorylation sites of DGAT1 were verified by phosphorylation mass spectrometry analysis of purified DGAT1 from mouse myoblast C2C12 cells. Using single point mutations, a regulatory role of 3 putative phosphorylation sites was dissected. Finally, using truncation mutations, a potential domain of DGAT1 that was involved in the regulation of enzymatic activity was revealed. This study provides useful information for further understanding DGAT1 activity regulation.
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Biophysics Reports    2016, 2 (5-6): 0-0.   DOI:
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Biophysics Reports    2018, 4 (2): 0-0.   DOI:
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Analysis of chromatin bersin Hela cells with electron tomography
Xiaomin Li, Hongli Feng, Jianguo Zhang, Lei Sun, Ping Zhu
Biophysics Reports    2015, 1 (1): 51-60.   DOI: 10.1007/x41048-015-0009-9
Abstract   PDF (2590KB)
The presence and folding pattern of chromatin in eukaryotic cells remain elusive and controversial. In this study, we prepared ultra-thin sections of Hela cells with three different fixation and sectioning methods, i.e., chemical fixation, high pressure freezing with freeze substitution, and cryo-ultramicro- tomy with SEM-FIB (focused ion beam), and analyzed in vivo architecture of chromatin fibers in Hela nuclei with electron tomography technology. The results suggest that the chromatin fibers in eukaryotic Hela cells are likely organized in an architecture with a diameter of about 30 nm.
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Biophysics Reports: focus on theoretical and technical advances
Tao Xu
Biophysics Reports    2015, 1 (1): 1-1.   DOI: 10.1007/s41048-015-0010-3
Abstract   PDF (301KB)
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Biophysics Reports    2018, 4 (3): 0-0.   DOI:
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Biophysics Reports    DOI:
Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry
Zhou Gong, Yue-He Ding, Xu Dong, Na Liu, E. Erquan Zhang, Meng-Qiu Dong, Chun Tang
Biophysics Reports    2015, 1 (3): 127-138.   DOI: 10.1007/s41048-015-0015-y
Abstract   PDF (1992KB)
Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-μmol/L binding affinity. In contrast,we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular crosslinks to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes.
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Using integrated correlative cryo-light and electron microscopy to directly observe syntaphilin-immobilized neuronal mitochondria in situ
Shengliu Wang, Shuoguo Li, Gang Ji, Xiaojun Huang, Fei Sun
Biophysics Reports    2017, 3 (1-3): 8-16.   DOI: 10.1007/s41048-017-0035-x
Abstract   PDF (3069KB)
Correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) system has been fast becoming a powerful technique with the advantage to allow the fluorescent labeling and direct visualization of the close-to-physiologic ultrastructure in cells at the same time, offering unique insights into the ultrastructure with specific cellular function. There have been various engineered ways to achieve cryo-CLEM including the commercial FEI iCorr system that integrates fluorescence microscope into the column of transmission electron microscope. In this study, we applied the approach of the cryo-CLEMbased iCorr to image the syntaphilin-immobilized neuronal mitochondria in situ to test the performance of the FEI iCorr system and determine its correlation accuracy. Our study revealed the various morphologies of syntaphilin-immobilized neuronal mitochondria that interact with microtubules and suggested that the cryo-CLEM procedure by the FEI iCorr system is suitable with a half micron-meter correlation accuracy to study the cellular organelles that have a discrete distribution and large size, e.g. mitochondrion, Golgi complex, lysosome, etc.
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Choosing proper fluorescent dyes, proteins, and imaging techniques to study mitochondrial dynamics in mammalian cells
Xingguo Liu, Liang Yang, Qi Long, David Weaver, György Hajnóczky
Biophysics Reports    2017, 3 (4-6): 64-72.   DOI: 10.1007/s41048-017-0037-8
Abstract   PDF (459KB)
Mitochondrial dynamics refers to the processes maintaining mitochondrial homeostasis, including mitochondrial fission, fusion, transport, biogenesis, and mitophagy. Mitochondrial dynamics is essential for maintaining the metabolic function of mitochondria as well as their regulatory roles in cell signaling. In this review, we summarize the recently developed imaging techniques for studying mitochondrial dynamics including:mitochondrial-targeted fluorescent proteins and dyes, live-cell imaging using photoactivation, photoswitching and cell fusion, mitochondrial transcription and replication imaging by in situ hybridization, and imaging mitochondrial dynamics by super-resolution microscopy. Moreover, we discuss examples of how to choose and combine proper fluorescent dyes and/or proteins.
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Dye-based mito-thermometry and its application in thermogenesis of brown adipocytes
Tao-Rong Xie, Chun-Feng Liu, Jian-Sheng Kang
Biophysics Reports    2017, 3 (4-6): 85-91.   DOI: 10.1007/s41048-017-0039-6
Abstract   PDF (5803KB)
Mitochondrion is the main intracellular site for thermogenesis and attractive energy expenditure targeting for obesity therapy. Here, we develop a method of mitochondrial thermometry based on Rhodamine B methyl ester, which equilibrates as a thermosensitive mixture of nonfluorescent and fluorescent resonance forms. Using this approach, we are able to demonstrate that the efficacy of norepinephrine-induced thermogenesis is low, and measure the maximum transient rate of temperature increase in brown adipocytes.
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Energy coupling mechanisms of AcrB-like RND transporters
Xuejun C. Zhang, Min Liu, Lei Han
Biophysics Reports    2017, 3 (4-6): 73-84.   DOI: 10.1007/s41048-017-0042-y
Abstract   PDF (1543KB)
Prokaryotic AcrB-like proteins belong to a family of transporters of the RND superfamily, and as main contributing factor to multidrug resistance pose a tremendous threat to future human health. A unique feature of AcrB transporters is the presence of two separate domains responsible for carrying substrate and generating energy. Significant progress has been made in elucidating the three-dimensional structures of the homo-trimer complexes of AcrB-like transporters, and a three-step functional rotation was identified for this class of transporters. However, the detailed mechanisms for the transduction of the substrate binding signal, as well as the energy coupling processes between the functionally distinct domains remain to be established. Here, we propose a model for the interdomain communication in AcrB that explains how the substrate binding signal from the substrate-carrier domain triggers protonation in the transmembrane domain. Our model further provides a plausible mechanism that explains how protonation induces conformational changes in the substrate-carrier domain. We summarize the thermodynamic principles that govern the functional cycle of the AcrB trimer complex.
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Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL
Zhou Gong, Zhu Liu, Xu Dong, Yue-He Ding, Meng-Qiu Dong, Chun Tang
Biophysics Reports    2017, 3 (4-6): 100-108.   DOI: 10.1007/s41048-017-0044-9
Abstract   PDF (788KB)
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigidbody refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein-protein complexes, and is freely available at
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Biophysics Reports    2017, 3 (1-3): 0-0.   DOI:
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Docking-based inverse virtual screening: methods, applications, and challenges
Xianjin Xu, Marshal Huang, Xiaoqin Zou
Biophysics Reports    2018, 4 (1): 1-16.   DOI: 10.1007/s41048-017-0045-8
Abstract   PDF (610KB)
Identifying potential protein targets for a small-compound ligand query is crucial to the process of drug development. However, there are tens of thousands of proteins in human alone, and it is almost impossible to scan all the existing proteins for a query ligand using current experimental methods. Recently, a computational technology called docking-based inverse virtual screening (IVS) has attracted much attention. In docking-based IVS, a panel of proteins is screened by a molecular docking program to identify potential targets for a query ligand. Ever since the first paper describing a docking-based IVS program was published about a decade ago, the approach has been gradually improved and utilized for a variety of purposes in the field of drug discovery. In this article, the methods employed in dockingbased IVS are reviewed in detail, including target databases, docking engines, and scoring function methodologies. Several web servers developed for non-expert users are also reviewed. Then, a number of applications are presented according to different research purposes, such as target identification, side effects/toxicity, drug repositioning, drug-target network development, and receptor design. The review concludes by discussing the challenges that docking-based IVS needs to overcome to become a robust tool for pharmaceutical engineering.
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AIM interneurons mediate feeding suppression through the TYRA-2 receptor in C. elegans
Jiajun Fu, Haining Zhang, Wenming Huang, Xinyu Zhu, Yi Sheng, Eli Song, Tao Xu
Biophysics Reports    2018, 4 (1): 17-24.   DOI: 10.1007/s41048-018-0046-2
Abstract   PDF (1528KB)
Feeding behavior is the most fundamental behavior in C. elegans. Our previous results have dissected the central integration circuit for the regulation of feeding, which integrates opposing sensory inputs and regulates feeding behavior in a nonlinear manner. However, the peripheral integration that acts downstream of the central integration circuit to modulate feeding remains largely unknown. Here, we find that a Gai/o-coupled tyramine receptor, TYRA-2, is involved in peripheral feeding suppression. TYRA-2 suppresses feeding behavior via the AIM interneurons, which receive tyramine/octopamine signals from RIM/RIC neurons in the central integration circuit. Our results reveal previously unidentified roles for the receptor TYRA-2 and the AIM interneurons in feeding regulation, providing a further understanding of how biogenic amines tyramine and octopamine regulate feeding behavior.
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The application of CorrSightTM in correlative light and electron microscopy of vitrified biological specimens
Xiaomin Li, Jianlin Lei, Hong-Wei Wang
Biophysics Reports    2018, 4 (3): 143-152.   DOI: 10.1007/s41048-018-0059-x
Abstract   PDF (3677KB)
Correlative light and electron microscopy is a powerful technique for identification and determination of the structures of interested macromolecules in situ. Combined with sample vitrification, it would be much easier to preserve the native state of macromolecule complexes and distinguish them from the crowded structure environment. In this article, we present a detailed process for the application of the CorrSight system, a light microscope equipped with a cryo module, in combination with a cryo-electron microscope. A relatively long course of up to 7-8 h for cryo module preparation and multichannel light microscopy imaging of vitrified specimen can be sustained. Correlation of light and electron microscopy images at both grid levels to locate squares and square level to locate target particles, and verification of target particles can be performed with the help of AutoEMation software. Cryo-electron tomography is used for obtaining the three-dimensional structure information.
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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   PDF (711KB)
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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Biophysics Reports    2018, 4 (5): 0-0.   DOI:
Abstract   PDF (1022KB)
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Biophysics Reports    2018, 4 (6): 0-0.   DOI:
Abstract   PDF (3279KB)
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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   PDF (3353KB)
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Energy coupling mechanism of FO in a rotary ATP synthase: a model update
Xuejun C. Zhang, Min Liu
Biophysics Reports    2019, 5 (2): 61-64.   DOI: 10.1007/s41048-018-0077-8
Abstract   PDF (676KB)
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A genetically encoded ratiometric calcium sensor enables quantitative measurement of the local calcium microdomain in the endoplasmic reticulum
Chen Luo, Huiyu Wang, Qi Liu, Wenting He, Lin Yuan, Pingyong Xu
Biophysics Reports    2019, 5 (1): 31-42.   DOI: 10.1007/s41048-019-0082-6
Abstract   PDF (3170KB)
The local Ca2+ release from the heterogeneously distributed endoplasmic reticulum (ER) calcium store has a critical role in calcium homeostasis and cellular function. However, single fluorescent proteinbased ER calcium probes experience challenges in quantifying the ER calcium store in differing live cells, and intensity-based measurements make it difficult to detect local calcium microdomains in the ER. Here, we developed a genetically encoded ratiometric ER calcium indicator (GCEPIA1-SNAPER) that can detect the real-time ER calcium store and local calcium microdomains in live cells. GCEPIA1-SNAPER was located in the lumen of the ER and showed a linear, reversible and rapid response to changes in the ER calcium store. The GCEPIA1-SNAPER probe effectively monitored the depletion of the ER calcium store by TG or starvation treatment, and through its use we identified heterogeneously distributed calcium microdomains in the ER which were correlated with the distribution of STIM1 clusters upon ER calcium store depletion. Lastly, GCEPIA1-SNAPER can be used to detect the ER calcium store by highthroughput flow cytometry and confers the ability to study the function of calcium microdomains of the ER.
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Protocol for analyzing protein liquid–liquid phase separation
Zheng Wang, Gangming Zhang, Hong Zhang
Biophysics Reports    2019, 5 (1): 1-9.   DOI: 10.1007/s41048-018-0078-7
Abstract   PDF (2122KB)
Numerous cellular functions occur in spatially and temporally confined regions. Recent studies have shown that membrane-less organelles and compartments in the cell are assembled via liquid–liquid phase separation (LLPS). In vitro LLPS assays using recombinant expressed and purified proteins are necessary for us to further understand how the assembly of phase-separated compartments is regulated in cells. However, uniform standards and protocols are lacking for these In vitro studies. Here, we describe a step-by-step protocol commonly used to investigate In vitro LLPS using purified proteins. This protocol includes expression and purification of the studied proteins, induction of LLPS of the purified proteins, and studies of the biophysical properties of the liquid droplets formed by LLPS. These protocols can be easily followed by researchers to investigate the LLPS behaviors of proteins of interest.
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Detection of cancer cells based on glycolytic-regulated surface electrical charges
Wenjun Le, Bingdi Chen, Zheng Cui, Zhongmin Liu, Donglu Shi
Biophysics Reports    2019, 5 (1): 10-18.   DOI: 10.1007/s41048-018-0080-0
Abstract   PDF (1389KB)
Over the past decades, cell surface charge, although experimentally observed, has not been well understood particularly from the viewpoint of biophysics. Our recent studies have shown that all cancer cells exhibit negative surface charges that are directly proportional to the secreted lactic acid, a unique cancer metabolic characteristic: high rate of glycolysis. We have therefore designed and developed a set of electrically-charged, fluorescent, and super-paramagnetic nanoprobes, capable of sensitive detection of cancer cells based on the surface charges. These probes are utilized to bind onto cells via electrostatic reaction for capture and magnetic separation. In this fashion, we are able to characterize cell surface charges that are regulated by different metabolic patterns, therefore effectively distinguishing the cancer cells from the normal cells. All 22 cancer cells of different organs are found to be negativelycharged therefore bound strongly by the positively-charged nanoprobes, whereas the normal cells show insignificant binding to the nanoprobes of either charge signs (positive or negative). This finding suggests that all tested cancer cells are negatively-charged and normal cells are either charge-neutral or slightly positive. For diagnosis, cancer cells can be detected, electrostatically bound, and magnetically separated in blood by charged and super-paramagnetic nanoprobes. In therapeutics, circulating cancer cells (CTCs) can be filtered and removed in a continuous fashion to reduce the risk of cancer metastasis. If successful, this new nanotechnology will revolutionize early cancer diagnosis and potentially enable new therapeutics in clinical settings.
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Biophysics Reports    2019, 5 (2): 0-0.   DOI:
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Determining the target protein localization in 3D using the combination of FIB-SEM and APEX2
Yang Shi, Li Wang, Jianguo Zhang, Yujia Zhai, Fei Sun
Biophysics Reports    2017, 3 (4-6): 92-99.   DOI: 10.1007/s41048-017-0043-x
Abstract   PDF (1163KB)
Determining the cellular localization of proteins of interest at nanometer resolution is necessary for elucidating their functions. Besides super-resolution fluorescence microscopy, conventional electron microscopy (EM) combined with immunolabeling or clonable EM tags provides a unique approach to correlate protein localization information and cellular ultrastructural information. However, there are still rare cases of such correlation in three-dimensional (3D) spaces. Here, we developed an approach by combining the focus ion beam scanning electron microscopy (FIB-SEM) and a promising clonable EM tag APEX2 (an enhanced ascorbate peroxidase 2) to determine the target protein localization within 3D cellular ultrastructural context. We further utilized this approach to study the 3D localization of mitochondrial dynamics-related proteins (MiD49/51, Mff, Fis1, and Mfn2) in the cells where the target proteins were overexpressed. We found that all the target proteins were located at the surface of the mitochondrial outer membrane accompanying with mitochondrial clusters. Mid49/51, Mff, and hFis1 spread widely around the mitochondrial surface while Mfn2 only exists at the contact sites.
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Biophysics Reports    2019, 5 (4): 0-0.   DOI:
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