生物化学

分类

    现刊
    Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom
    用NAMD和PTools/Heligeom模拟蛋白质丝的微尺度和中尺度扰动
    作者:Benjamin Boyer, Benoist Laurent, Charles H. Robert and Chantal Prévost日期:07/20/2021,浏览量:1317,Q&A: 0
    [Abstract]

    Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are difficult to model due to the helical character of the system. Here, we describe how distortions in RecA

    ...
    Resolving Structural Changes of Photoreceptors in Living Escherichia coli via In-cell Infrared Difference Spectroscopy
    利用细胞内红外差谱技术分析活大肠杆菌光感受器的结构变化
    作者:Lukas Goett-Zink, Jessica L. Klocke and Tilman Kottke日期:02/05/2021,浏览量:1941,Q&A: 0
    [Abstract]

    Several in-cell spectroscopic techniques have been developed recently to investigate the structure and mechanism of proteins in their native environment. Conditions in vivo differ dramatically from those selected for in vitro experiments. Accordingly, the cellular environment can affect the protein mechanism for example by molecular crowding or

    ...
    Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations
    使用HADDOCK了解高分子对接复合物:实验数据与计算之间的协同作用
    作者:Andrea Saponaro, Vincenzo Maione, Alexandre M. J. J. Bonvin and Francesca Cantini日期:10/20/2020,浏览量:1542,Q&A: 0
    [Abstract] This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of in silico analysis and experimental results. To this end, we use the integrative modelling software HADDOCK, which possesses the powerful ability to incorporate experimental data, such as NMR Chemical Shift Perturbations and biochemical ...
    Sequence Alignment Using Machine Learning for Accurate Template-based Protein Structure Prediction
    基于模板的蛋白质结构精确预测的机器学习序列比对
    作者:Shuichiro Makigaki and Takashi Ishida日期:05/05/2020,浏览量:3345,Q&A: 0
    [Abstract] Template-based modeling, the process of predicting the tertiary structure of a protein by using homologous protein structures, is useful when good templates can be available. Indeed, modern homology detection methods can find remote homologs with high sensitivity. However, the accuracy of template-based models generated from the ...
    F-actin Bundle Sedimentation Assay
    F-肌动蛋白束沉淀法
    作者:Shan-Shan Lin, Mei-Chun Chuang and Ya-Wen Liu日期:11/05/2019,浏览量:3115,Q&A: 0
    [Abstract] Understanding the molecular mechanism governing the higher-order regulation of actin dynamics requires chemically-defined and quantitative assays. Recently, the membrane remodeling large GTPase, dynamin, has been identified as a new actin cross-linking molecule. Dynamin regulates actin cytoskeleton through binding to, self-assembling around, and ...
    Probing Conformational States of a Target Protein in Escherichia coli Cells by in vivo Cysteine Cross-linking Coupled with Proteolytic Gel Analysis
    利用体内半胱氨酸交联结合蛋白水解凝胶分析检测大肠杆菌细胞中目的蛋白的构象状态
    作者:Sujeet Kumar and Natividad Ruiz 日期:06/20/2019,浏览量:2658,Q&A: 0
    [Abstract] Transporters are dynamic membrane proteins that are essential to the physiology of cells. To function, transporters must cycle between various conformational states, so to understand their mechanistic details, it is critical to characterize how their structure changes during the transport cycle. One approach to studying the dynamics of ...
    Detection of Internal Matrix Targeting Signal-like Sequences (iMTS-Ls) in Mitochondrial Precursor Proteins Using the TargetP Prediction Tool
    用TargetP预测工具在线粒体前体蛋白中检测内部类基质导向信号序列
    作者:Felix Boos, Timo Mühlhaus and Johannes M. Herrmann日期:09/05/2018,浏览量:5115,Q&A: 0
    [Abstract] Mitochondria contain hundreds of proteins which are encoded by the nuclear genome and synthesized in the cytosol from where they are imported into the organelle. Sorting signals encoded in the primary and secondary sequence of these proteins mediate the recognition of newly synthesized precursor proteins and their subsequent translocation through ...
    Structural Analysis of Target Protein by Substituted Cysteine Accessibility Method
    采用半胱氨酸取代法分析靶蛋白的结构
    作者:Tetsuo Cai and Taisuke Tomita日期:09/05/2018,浏览量:4229,Q&A: 0
    [Abstract] Substituted Cysteine Accessibility Method (SCAM) is a biochemical approach to investigate the water accessibility or the spatial distance of particular cysteine residues substituted in the target protein. Protein topology and structure can be annotated by labeling with methanethiosulfonate reagents that specifically react with the cysteine ...
    Host-regulated Hepatitis B Virus Capsid Assembly in a Mammalian Cell-free System
    宿主调控的乙型肝炎病毒衣壳在无哺乳动物细胞系统中的组装
    作者:Kuancheng Liu and Jianming Hu日期:04/20/2018,浏览量:4612,Q&A: 0
    [Abstract] The hepatitis B virus (HBV) is an important global human pathogen and represents a major cause of hepatitis, liver cirrhosis and liver cancer. The HBV capsid is composed of multiple copies of a single viral protein, the capsid or core protein (HBc), plays multiple roles in the viral life cycle, and has emerged recently as a major target for ...
    Hydrogen Deuterium Exchange Mass Spectrometry of Oxygen Sensitive Proteins
    氧敏感蛋白的氢氘交换质谱法
    作者:Luke Berry, Angela Patterson, Natasha Pence, John W. Peters and Brian Bothner日期:03/20/2018,浏览量:6876,Q&A: 0
    [Abstract] The protocol detailed here describes a way to perform hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) on oxygen sensitive proteins. HDX-MS is a powerful tool for studying the protein structure-function relationship. Applying this technique to anaerobic proteins provides insight into the mechanism of proteins that perform oxygen ...