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Biophysics Reports

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https://www.readbyqxmd.com/read/29756010/mitochondrial-protein-sulfenation-during-aging-in-the-rat-brain
#1
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://www.readbyqxmd.com/read/29756009/molecular-architecture-of-mouse-and-human-pancreatic-zymogen-granules-protein-components-and-their-copy-numbers
#2
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://www.readbyqxmd.com/read/29756008/fabrication-and-modification-of-implantable-optrode-arrays-for-in-vivo-optogenetic-applications
#3
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
https://www.readbyqxmd.com/read/29756007/mapping-disulfide-bonds-from-sub-micrograms-of-purified-proteins-or-micrograms-of-complex-protein-mixtures
#4
Shan Lu, Yong Cao, Sheng-Bo Fan, Zhen-Lin Chen, Run-Qian Fang, Si-Min He, Meng-Qiu Dong
Disulfide bonds are vital for protein functions, but locating the linkage sites has been a challenge in protein chemistry, especially when the quantity of a sample is small or the complexity is high. In 2015, our laboratory developed a sensitive and efficient method for mapping protein disulfide bonds from simple or complex samples (Lu et al . in Nat Methods 12:329, 2015). This method is based on liquid chromatography-mass spectrometry (LC-MS) and a powerful data analysis software tool named pLink. To facilitate application of this method, we present step-by-step disulfide mapping protocols for three types of samples-purified proteins in solution, proteins in SDS-PAGE gels, and complex protein mixtures in solution...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29756006/theoretical-model-and-characteristics-of-mitochondrial-thermogenesis
#5
Jian-Sheng Kang
Based on the first law of thermodynamics and the thermal diffusion equation, the deduced theoretical model of mitochondrial thermogenesis satisfies the Laplace equation and is a special case of the thermal diffusion equation. The model settles the long-standing question of the ability to increase cellular temperature by endogenous thermogenesis and explains the thermogenic characteristics of brown adipocytes. The model and calculations also suggest that the number of free available protons is the major limiting factor for endogenous thermogenesis and its speed...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29577069/identification-of-natural-products-as-novel-ligands-for-the-human-5-ht-2c-receptor
#6
Yao Peng, Simeng Zhao, Yiran Wu, Haijie Cao, Yueming Xu, Xiaoyan Liu, Wenqing Shui, Jianjun Cheng, Suwen Zhao, Ling Shen, Jun Ma, Ronald J Quinn, Raymond C Stevens, Guisheng Zhong, Zhi-Jie Liu
G protein-coupled receptors (GPCRs) constitute the largest human protein family with over 800 members, which are implicated in many important medical conditions. Serotonin receptors belong to the aminergic GPCR subfamily and play important roles in physiological and psychological activities. Structural biology studies have revealed the structures of many GPCRs in atomic details and provide the basis for the identification and investigation of the potential ligands, which interact with and modulate the receptors...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29577068/identification-of-small-orf-encoded-peptides-in-mouse-serum
#7
Yaqin Deng, Adekunle Toyin Bamigbade, Mirza Ahmed Hammad, Shimeng Xu, Pingsheng Liu
Identification of the coding elements in the genome is fundamental to interpret the development of living systems and species diversity. Small peptides (length < 100 amino acids) have played an important role in regulating the biological metabolism, but their identification has been limited by their size and abundance. Serum is the most important body fluid and is full of small peptides. In this study, we have established a small ORF-encoded peptides (SEPs) database from mouse GENCODE release. This database provides about half a million putative translated SEPs in mouse...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29577067/pi4kii%C3%AE-regulates-insulin-secretion-and-glucose-homeostasis-via-a-pkd-dependent-pathway
#8
Lunfeng Zhang, Jiangmei Li, Panpan Zhang, Zhen Gao, Yingying Zhao, Xinhua Qiao, Chang Chen
Insulin release by pancreatic β cells plays a key role in regulating blood glucose levels in humans, and to understand the mechanism for insulin secretion may reveal therapeutic strategies for diabetes. We found that PI4KIIα transgenic (TG) mice have abnormal glucose tolerance and higher serum glucose levels than wild-type mice. Glucose-stimulated insulin secretion was significantly reduced in both PI4KIIα TG mice and PI4KIIα-overexpressing pancreatic β cell lines. A proximity-based biotin labeling technique, BioID, was used to identify proteins that interact with PI4KIIα, and the results revealed that PI4KIIα interacts with PKD and negatively regulates its activity...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29577066/aim-interneurons-mediate-feeding-suppression-through-the-tyra-2-receptor-in-c-elegans
#9
Jiajun Fu, Haining Zhang, Wenming Huang, Xinyu Zhu, Yi Sheng, Eli Song, Tao Xu
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 Gαi/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...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29577065/docking-based-inverse-virtual-screening-methods-applications-and-challenges
#10
REVIEW
Xianjin Xu, Marshal Huang, Xiaoqin Zou
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...
2018: Biophysics Reports
https://www.readbyqxmd.com/read/29238747/protocol-for-analyzing-protein-ensemble-structures-from-chemical-cross-links-using-dynaxl
#11
Zhou Gong, Zhu Liu, Xu Dong, Yue-He Ding, Meng-Qiu Dong, Chun Tang
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...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/29238746/determining-the-target-protein-localization-in-3d-using-the-combination-of-fib-sem-and-apex2
#12
Yang Shi, Li Wang, Jianguo Zhang, Yujia Zhai, Fei Sun
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...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/29238745/dye-based-mito-thermometry-and-its-application-in-thermogenesis-of-brown-adipocytes
#13
Tao-Rong Xie, Chun-Feng Liu, Jian-Sheng Kang
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...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/29238744/energy-coupling-mechanisms-of-acrb-like-rnd-transporters
#14
Xuejun C Zhang, Min Liu, Lei Han
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...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/29238743/choosing-proper-fluorescent-dyes-proteins-and-imaging-techniques-to-study-mitochondrial-dynamics-in-mammalian-cells
#15
Xingguo Liu, Liang Yang, Qi Long, David Weaver, György Hajnóczky
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...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/29238742/class-c-g-protein-coupled-receptors-reviving-old-couples-with-new-partners
#16
Thor C Møller, David Moreno-Delgado, Jean-Philippe Pin, Julie Kniazeff
G protein-coupled receptors (GPCRs) are key players in cell communication and are encoded by the largest family in our genome. As such, GPCRs represent the main targets in drug development programs. Sequence analysis revealed several classes of GPCRs: the class A rhodopsin-like receptors represent the majority, the class B includes the secretin-like and adhesion GPCRs, the class F includes the frizzled receptors, and the class C includes receptors for the main neurotransmitters, glutamate and GABA, and those for sweet and umami taste and calcium receptors...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28782000/particle-segmentation-algorithm-for-flexible-single-particle-reconstruction
#17
Qiang Zhou, Niyun Zhou, Hong-Wei Wang
As single particle cryo-electron microscopy has evolved to a new era of atomic resolution, sample heterogeneity still imposes a major limit to the resolution of many macromolecular complexes, especially those with continuous conformational flexibility. Here, we describe a particle segmentation algorithm towards solving structures of molecules composed of several parts that are relatively flexible with each other. In this algorithm, the different parts of a target molecule are segmented from raw images according to their alignment information obtained from a preliminary 3D reconstruction and are subjected to single particle processing in an iterative manner...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28781999/accelerating-electron-tomography-reconstruction-algorithm-icon-with-gpu
#18
Yu Chen, Zihao Wang, Jingrong Zhang, Lun Li, Xiaohua Wan, Fei Sun, Fa Zhang
Electron tomography (ET) plays an important role in studying in situ cell ultrastructure in three-dimensional space. Due to limited tilt angles, ET reconstruction always suffers from the "missing wedge" problem. With a validation procedure, iterative compressed-sensing optimized NUFFT reconstruction (ICON) demonstrates its power in the restoration of validated missing information for low SNR biological ET dataset. However, the huge computational demand has become a major problem for the application of ICON...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28781998/the-advent-of-structural-biology-in-situ-by-single-particle-cryo-electron-tomography
#19
Jesús G Galaz-Montoya, Steven J Ludtke
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28781997/using-integrated-correlative-cryo-light-and-electron-microscopy-to-directly-observe-syntaphilin-immobilized-neuronal-mitochondria-in-situ
#20
Shengliu Wang, Shuoguo Li, Gang Ji, Xiaojun Huang, Fei Sun
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...
2017: Biophysics Reports
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