17 Result(s)
within
Protocol
**u Tao
English
Protein Science
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Protocol
Antibody Aggregate Removal Using a Mixed-Mode Chromatography Resin
In monoclonal antibody (mAb) production, aggregates represent a major class of product-related impurities that needs to be removed by the downstream process. Protein A chromatography is generally less effectiv...
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Knocking in Multifunctional Gene Tags into SMC Complex Subunits Using Gene Editing
Condensin, a highly conserved pentameric chromosome complex, is required for the correct organization and folding of the genome. Here, we highlight how to knock protein tags into endogenous loci to faithfully ...
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Programmable Fabrication of Multilayer Collagen Nanosheets of Defined Composition
Two-dimensional nanostructures offer significant promise as components for the construction of functional biomaterials. However, the controllable fabrication of these structures remains a challenge. Ideally, o...
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Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles
Pseudouridylation is the most abundant and widespread RNA modification, and it plays an important role in modulating the structure and function of RNA. In eukaryotes and archaea, RNA pseudouridylation is catal...
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Identification of Direct Kinase Substrates via Kinase Assay-Linked Phosphoproteomics
Protein phosphorylation plays an essential role in the regulation of various cellular functions. Dysregulation of phosphorylation is implicated in the pathogenesis of certain cancers, diabetes, cardiovascular ...
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Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as...
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Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC–MS/MS
Comprehensive, quantitative information on abundances of proteins and their posttranslational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic i...
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Quantitation of the Phosphoproteome Using the Library-Assisted eXtracted Ion Chromatogram (LAXIC) Strategy
Phosphorylation is a key posttranslational modification that regulates many signaling pathways, but quantifying changes in phosphorylation between samples can be challenging due to its low stoichiometry within...
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Towards Comprehensive Analysis of Protein Family Quantitative Stability–Flexibility Relationships Using Homology Models
The Distance Constraint Model (DCM) is a computational modeling scheme that uniquely integrates thermodynamic and mechanical descriptions of protein structure. As such, quantitative stability–flexibility relat...
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Counterion Dye Staining of Proteins in One- and Two-Dimensional Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Tryptic Gel Digestion of Stained Protein for Mass Spectrometry
A fast and matrix-assisted laser desorption/ionization mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. I...
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NMR Studies of Large Protein Systems
Over the recent years, there has been increased interest in applying NMR spectroscopy for the characterization of proteins and protein complexes of large molecular weight. The combination of multidimensional N...
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Functionalized Soluble Nanopolymers for Phosphoproteome Analysis
Protein phosphorylation plays a critical role in the regulation of many cellular functions. Phosphoproteomic analyses facilitate an in-depth understanding of such phosphorylation-dependent signaling networks. ...
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Quantitative Phospho-proteomics Based on Soluble Nanopolymers
Phospho-proteomics, the global analysis of protein phosphorylation, holds great promise for the discovery of cell signaling events that link changes in dynamics of protein phosphorylation to the progression of...
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Protein Staining with Calconcarboxylic Acid in Polyacrylamide Gels
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) has become a highly reliable separation technique for protein characterization. Broad application of electrophoresis techniques has required...
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Detection of Proteins on Blots Using Direct Blue 71
The visualization of proteins blotted onto transfer membranes has important applications for the localization of bands prior to further steps and for the comparison of individual proteins detected by immunosta...
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Shotgun Protein Identification and Quantification by Mass Spectrometry
Shotgun proteomics is based on identification and quantification of peptides from digested proteins using tandem mass spectrometry. In this chapter, we discuss computational methods to analyze tandem mass spec...
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A Historical Perspective of Template-Based Protein Structure Prediction
This chapter presents a broad and a historical overview of the problem of protein structure prediction. Different structure prediction methods, including homology modeling, fold recognition (FR)/protein thread...
