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Biophysics Reports

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https://read.qxmd.com/read/30596142/-in-situ-protein-micro-crystal-fabrication-by-cryo-fib-for-electron-diffraction
#1
Xinmei Li, Shuangbo Zhang, Jianguo Zhang, Fei Sun
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 complete workflow to prepare suitable crystals efficiently for MicroED experiment...
2018: Biophysics Reports
https://read.qxmd.com/read/30596141/proteomic-analysis-of-insulin-secretory-granules-in-ins-1-cells-by-protein-correlation-profiling
#2
Min Li, Wen Du, Maoge Zhou, Li Zheng, Eli Song, Junjie Hou
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...
2018: Biophysics Reports
https://read.qxmd.com/read/30596140/electron-microscopy-combined-with-spatial-analysis-quantitative-mapping-of-the-nano-assemblies-of-plasma-membrane-associating-proteins-and-lipids
#3
Yong Zhou, John F Hancock
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...
2018: Biophysics Reports
https://read.qxmd.com/read/30596139/thermodynamics-of-voltage-gated-ion-channels
#4
Xuejun C Zhang, Hanting Yang, Zhenfeng Liu, Fei Sun
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...
2018: Biophysics Reports
https://read.qxmd.com/read/30596138/a-critique-of-the-alternating-access-transporter-model-of-uniport-glucose-transport
#5
Richard J Naftalin
No abstract text is available yet for this article.
2018: Biophysics Reports
https://read.qxmd.com/read/30533492/significant-expansion-and-red-shifting-of-fluorescent-protein-chromophore-determined-through-computational-design-and-genetic-code-expansion
#6
Li Wang, Xian Chen, Xuzhen Guo, Jiasong Li, Qi Liu, Fuying Kang, Xudong Wang, Cheng Hu, Haiping Liu, Weimin Gong, Wei Zhuang, Xiaohong Liu, Jiangyun Wang
Fluorescent proteins (FPs) with emission wavelengths in the far-red and infrared regions of the spectrum provide powerful tools for deep-tissue and super-resolution imaging. The development of red-shifted FPs has evoked widespread interest and continuous engineering efforts. In this article, based on a computational design and genetic code expansion, we report a rational approach to significantly expand and red-shift the chromophore of green fluorescent protein (GFP). We applied computational calculations to predict the excitation and emission wavelengths of a FP chromophore harboring unnatural amino acids (UAA) and identify in silico an appropriate UAA, 2-amino-3-(6-hydroxynaphthalen-2-yl)propanoic acid (naphthol-Ala)...
2018: Biophysics Reports
https://read.qxmd.com/read/30533491/raman-spectra-of-the-gfp-like-fluorescent-proteins
#7
Ye Yuan, Dianbing Wang, Jibin Zhang, Ji Liu, Jian Chen, Xian-En Zhang
The objective of the study was to elucidate optical characteristics of the chromophore structures of fluorescent proteins. Raman spectra of commonly used GFP-like fluorescent proteins (FPs) with diverse emission wavelengths (green, yellow, cyan and red), including the enhanced homogenous FPs EGFP, EYFP, and ECFP (from jellyfish) as well as mNeptune (from sea anemone) were measured. High-quality Raman spectra were obtained and many marker bands for the chromophore of the FPs were identified via assignment of Raman spectra bands...
2018: Biophysics Reports
https://read.qxmd.com/read/30533490/small-animal-spect-ct-imaging-of-cancer-xenografts-and-pulmonary-fibrosis-using-a-99m-tc-labeled-integrin-%C3%AE-v%C3%AE-6-targeting-cyclic-peptide-with-improved-in-vivo-stability
#8
Hao Liu, Liquan Gao, Xinhe Yu, Lijun Zhong, Jiyun Shi, Bing Jia, Nan Li, Zhaofei Liu, Fan Wang
Integrin αvβ6 is expressed at an undetectable level in normal tissues, but is remarkably upregulated during many pathological processes, especially in cancer and fibrosis. Noninvasive imaging of integrin αvβ6 expression using a radiotracer with favorable in vivo pharmacokinetics would facilitate disease diagnosis and therapy monitoring. Through disulfide-cyclized method, we synthesized in this study, a new integrin αvβ6-targeted cyclic peptide (denoted as cHK), and radiolabeled it with 99m Tc. The ability of the resulting radiotracer 99m Tc-HYNIC-cHK to detect integrin αvβ6 expression in pancreatic cancer xenografts and idiopathic pulmonary fibrosis was evaluated using small-animal single-photon emission computed tomography (SPECT)/computed tomography (CT)...
2018: Biophysics Reports
https://read.qxmd.com/read/30533489/targeting-tumor-cells-with-antibodies-enhances-anti-tumor-immunity
#9
Zhichen Sun, Yang-Xin Fu, Hua Peng
Tumor-targeting antibodies were initially defined as a group of therapeutic monoclonal antibodies (mAb) that recognize tumor-specific membrane proteins, block cell signaling, and induce tumor-killing through Fc-driven innate immune responses. However, in the past decade, ample evidence has shown that tumor-targeting mAb (TTmAb) eradicates tumor cells via activation of cytotoxic T cells (CTLs). In this review, we specifically focus on how TTmAbs induce adaptive anti-tumor immunity and its potential in combination therapy with immune cytokines, checkpoint blockade, radiation, and enzyme-targeted small molecule drugs...
2018: Biophysics Reports
https://read.qxmd.com/read/30533488/animal-protein-toxins-origins-and-therapeutic-applications
#10
Na Chen, Siqi Xu, Yuhan Zhang, Feng Wang
Venomous animals on the earth have been found to be valuable resources for the development of therapeutics. Enzymatic and non-enzymatic proteins and peptides are the major components of animal venoms, many of which can target various ion channels, receptors, and membrane transporters. Compared to traditional small molecule drugs, natural proteins and peptides exhibit higher specificity and potency to their targets. In this review, we summarize the varieties and characteristics of toxins from a few representative venomous animals, and describe the components and applications of animal toxins as potential drug candidates in the treatment of human diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, neuropathic pain, as well as autoimmune diseases...
2018: Biophysics Reports
https://read.qxmd.com/read/30310859/dissection-of-structural-dynamics-of-chromatin-fibers-by-single-molecule-magnetic-tweezers
#11
Xue Xiao, Liping Dong, Yi-Zhou Wang, Peng-Ye Wang, Ming Li, Guohong Li, Ping Chen, Wei Li
The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level...
2018: Biophysics Reports
https://read.qxmd.com/read/30310858/hessian-single-molecule-localization-microscopy-using-scmos-camera
#12
Fudong Xue, Wenting He, Fan Xu, Mingshu Zhang, Liangyi Chen, Pingyong Xu
Single-molecule localization microscopy (SMLM) has the highest spatial resolution among the existing super-resolution imaging techniques, but its temporal resolution needs further improvement. An sCMOS camera can effectively increase the imaging rate due to its large field of view and fast imaging speed. Using an sCMOS camera for SMLM imaging can significantly improve the imaging time resolution, but the unique single-pixel-dependent readout noise of sCMOS cameras severely limits their application in SMLM imaging...
2018: Biophysics Reports
https://read.qxmd.com/read/30310857/ptb-nptb-master-regulators-of-neuronal-fate-in-mammals
#13
Jing Hu, Hao Qian, Yuanchao Xue, Xiang-Dong Fu
PTB was initially discovered as a polypyrimidine tract-binding protein (hence the name), which corresponds to a specific RNA-binding protein associated with heterogeneous ribonucleoprotein particle (hnRNP I). The PTB family consists of three members in mammalian genomes, with PTBP1 (PTB) expressed in most cell types, PTBP2 (also known as nPTB or brPTB) exclusively found in the nervous system, and PTBP3 (also known as ROD1) predominately detected in immune cells. During neural development, PTB is down-regulated, which induces nPTB, and the expression of both PTB and nPTB becomes diminished when neurons mature...
2018: Biophysics Reports
https://read.qxmd.com/read/30310856/structural-roles-of-lipid-molecules-in-the-assembly-of-plant-psii-lhcii-supercomplex
#14
Xin Sheng, Xiuying Liu, Peng Cao, Mei Li, Zhenfeng Liu
In plants, photosystem II (PSII) associates with light-harvesting complexes II (LHCII) to form PSII-LHCII supercomplexes. They are multi-subunit supramolecular systems embedded in the thylakoid membrane of chloroplast, functioning as energy-converting and water-splitting machinery powered by light energy. The high-resolution structure of a PSII-LHCII supercomplex, previously solved through cryo-electron microscopy, revealed 34 well-defined lipid molecules per monomer of the homodimeric system. Here we characterize the distribution of lipid-binding sites in plant PSII-LHCII supercomplex and summarize their arrangement pattern within and across the membrane...
2018: Biophysics Reports
https://read.qxmd.com/read/30310855/cancer-stem-cells-and-tumorigenesis
#15
REVIEW
Pingping Zhu, Zusen Fan
Cancer is one of the most serious diseases all over the world, and the cancer stem cell (CSC) model accounts for tumor initiation, metastasis, drug resistance, and relapse. The CSCs within tumor bulk have the capacity to self-renew, differentiate, and give rise to a new tumor. The self-renewal of CSCs is precisely regulated by various modulators, including Wnt/β-catenin signaling, Notch signaling, Hedgehog signaling, transcription factors, chromatin remodeling complexes, and non-coding RNAs. CSCs reside in their niches that are also involved in the self-renewal maintenance of CSCs and protection of CSCs from chemotherapy, radiotherapy, and even endogenous damages...
2018: Biophysics Reports
https://read.qxmd.com/read/30310854/roles-of-h3k36-specific-histone-methyltransferases-in-transcription-antagonizing-silencing-and-safeguarding-transcription-fidelity
#16
REVIEW
Chang Huang, Bing Zhu
Histone H3K36 methylation is well-known for its role in active transcription. In Saccharomyces cerevisiae , H3K36 methylation is mediated solely by SET2 during transcription elongation. In metazoans, multiple H3K36-specific methyltransferases exist and contribute to distinct biochemical activities and subsequent functions. In this review, we focus on the H3K36-specific histone methyltransferases in metazoans, and discuss their enzymatic activity regulation and their roles in antagonizing Polycomb silencing and safeguarding transcription fidelity...
2018: Biophysics Reports
https://read.qxmd.com/read/30310853/the-road-to-a-first-class-research-institute-creating-an-exceptional-environment-recruiting-outstanding-scientists-producing-high-impact-work-and-nurturing-a-culture-of-innovation-preface-to-the-60th-anniversary-special-issue
#17
https://read.qxmd.com/read/29756010/mitochondrial-protein-sulfenation-during-aging-in-the-rat-brain
#18
Xiaorong Yang, Jinzi Wu, Siqun Jing, Michael J Forster, Liang-Jun Yan
There is accumulating evidence that cysteine sulfenation (cys-SOH) in proteins plays an important role in cellular response to oxidative stress. The purpose of the present study was to identify mitochondrial proteins that undergo changes in cys-SOH during aging. Studies were conducted in rats when they were 5 or 30 months of age. Following blocking of free protein thiols with N -ethylmaleimide, protein sulfenic acids were reduced by arsenite to free thiol groups that were subsequently labeled with biotin-maleimide...
2018: Biophysics Reports
https://read.qxmd.com/read/29756009/molecular-architecture-of-mouse-and-human-pancreatic-zymogen-granules-protein-components-and-their-copy-numbers
#19
Jin-Sook Lee, Joseph A Caruso, Garrett Hubbs, Patricia Schnepp, James Woods, Jingye Fang, Chunying Li, Kezhong Zhang, Paul M Stemmer, Bhanu P Jena, Xuequn Chen
A molecular model of pancreatic zymogen granule (ZG) is critical for understanding its functions. We have extensively characterized the composition and membrane topology of rat ZG proteins. In this study, we report the development of targeted proteomics approaches to quantify representative mouse and human ZG proteins using LC-SRM and heavy isotope-labeled synthetic peptides. The absolute quantities of mouse Rab3D and VAMP8 were determined as 1242 ± 218 and 2039 ± 151 (mean ± SEM) copies per ZG...
2018: Biophysics Reports
https://read.qxmd.com/read/29756008/fabrication-and-modification-of-implantable-optrode-arrays-for-in-vivo-optogenetic-applications
#20
Lulu Wang, Kang Huang, Cheng Zhong, Liping Wang, Yi Lu
<AbstractText Label="Abstract" NlmCategory="UNASSIGNED">Recent advances in optogenetics have established a precisely timed and cell-specific methodology for understanding the functions of brain circuits and the mechanisms underlying neuropsychiatric disorders. However, the fabrication of optrodes, a key functional element in optogenetics, remains a great challenge. Here, we report reliable and efficient fabrication strategies for chronically implantable optrode arrays. To improve the performance of the fabricated optrode arrays, surfaces of the recording sites were modified using optimized electrochemical processes...
2018: Biophysics Reports
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