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Studies of the Ubiquitin Proteasome System

Abstract Table of Contents Materials Figures Literature Cited Abstract A concept that has arisen over the last decade is that proteins can, in general, be covalently modified by poly

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Using Biacore to Measure the Binding Kinetics of an Antibody‐Antigen Interaction

Abstract Table of Contents Materials Figures Literature Cited Abstract The optical phenomenon of surface plasmon resonance (SPR) used by Biacore systems enables the detection and measurement of protein?pr

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Overview of Biacore Systems and Their Applications

Abstract Table of Contents Literature Cited Abstract Surface plasmon resonance (SPR) allows for the investigation of the functional nature of binding interactions and provides detailed kinetic information across a wide range of molecular weights, including small molecules,

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Fluorescence Quenching Methods to Study Lipid‐Protein Interactions

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes how fluorescence quenching methods can be used to determine binding constants for phospholipids binding to intrin

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Rational Design and Evaluation of FRET Experiments to Measure Protein Proximities in Cells

Abstract Table of Contents Figures Literature Cited Abstract Fluorescence resonance energy transfer (FRET) refers to the nonradiative transfer of energy from one fluorescent molecule (the donor) to another fluorescent molecule (the accepto

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Quantitative Determination of Protein Stability and Ligand Binding by Pulse Proteolysis

Abstract Table of Contents Materials Figures Literature Cited Abstract Pulse proteolysis exploits the difference in proteolytic susceptibility between folded and unfolded proteins for facile but quantitat

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Circular Dichroism to Study Protein Interactions

Abstract Table of Contents Figures Literature Cited Abstract Circular dichroism (CD) is a powerful technique for studying the structures of proteins in solution, as well as structural changes that may occur when proteins bind to ligands. C

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Identifying Small‐Molecule Modulators of Protein‐Protein Interactions

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit outlines methods for identifying cyclic peptides that inhibit protein?protein interactions. Proteins of interest are cloned

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Benzodiazepine Binding to GABAA Receptors

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes ligand binding assays for the characterization of the benzodiazepine (BZ) site of GABAA receptors in the central ne

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Preparation of 2′‐Deoxy‐2′‐Methylseleno‐Modified Phosphoramidites and RNA

Abstract Table of Contents Materials Figures Literature Cited Abstract The derivatization of nucleic acids with selenium is a useful approach to facilitate phase determination during three?dimensional str

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Identification and Analysis of Multiprotein Complexes Through Chemical Crosslinking

Abstract Table of Contents Materials Figures Literature Cited Abstract Chemical crosslinking provides information about protein?protein interactions in the context of intact protein complexes; therefore,

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Determination of Protein Contacts by Chemical Cross‐Linking With EDC and Mass Spectrometry

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes a method for analyzing protein complexes by chemically cross?linking closely positioned amino acids. The cross?li

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Characterization of Dopamine Receptors

Abstract Table of Contents Materials Figures Literature Cited Abstract Dopamine receptors are the principal targets of drugs used for the treatment of neuropsychiatric disorders such as schizophrenia and

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Characterization of Adrenoceptors

Abstract Table of Contents Materials Figures Literature Cited Abstract Norepinephrine and epinephrine are important neurotransmitters in both the peripheral and the central nervous systems. The actions of

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Characterization of Histaminergic Receptors

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes radioligand binding protocols for histamine H1, H2, H3, and H4 receptors. Because these rec

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Solid‐Phase Oligonucleotide Labeling with DOTA

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes a method to construct oligonucleotide conjugates labeled with 1,4,7,10?tetraazacyclododecane?1,4,7,10?tetraacetic

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Flexible Ligand Docking with Glide

Abstract Table of Contents Figures Literature Cited Abstract Glide is a ligand docking program for predicting protein?ligand binding modes and ranking ligands via high?throughput virtual screening. Glide utilizes two different scoring func

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ChIP‐chip for Genome‐Wide Analysis of Protein Binding in Mammalian Cells

Abstract Table of Contents Materials Figures Literature Cited Abstract ChIP?chip combines chromatin immunoprecipitation (ChIP) with microarrays (chip) to determine protein?DNA interactions occurring in li

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High‐Throughput Cytotoxicity Screening by Propidium Iodide Staining

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes a system for the automated high?throughput analysis of cell cytotoxicity in 96?well and 384?well microplates. Dis

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Chromosome Conformation Capture Carbon Copy Technology

Abstract Table of Contents Materials Figures Literature Cited Abstract Chromosome conformation capture (3C) is used to quantify physical DNA contacts in vivo at high resolution. 3C was first used in yeast

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