[
    {
        "id": "authors:j3t96-2zk72",
        "collection": "authors",
        "collection_id": "j3t96-2zk72",
        "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120227-084239400",
        "type": "book_section",
        "title": "Three decades of studies to understand the functions of the ubiquitin family",
        "book_title": "Ubiquitin family modifiers and the proteasome: reviews and protocols",
        "author": [
            {
                "family_name": "Varshavsky",
                "given_name": "Alexander",
                "orcid": "0000-0002-4011-258X",
                "clpid": "Varshavsky-A"
            }
        ],
        "contributor": [
            {
                "family_name": "Dohmen",
                "given_name": "R. J\u00fcrgen",
                "clpid": "Dohmen-R-J"
            },
            {
                "family_name": "Scheffner",
                "given_name": "Martin",
                "clpid": "Scheffner-M"
            }
        ],
        "abstract": "Many intracellular proteins are metabolically unstable or can\nbecome unstable during their lifetime in a cell. The in vivo half-lives\nof specific proteins range from less than a minute to many days.\nAmong the functions of intracellular proteolysis are the elimination\nof misfolded or otherwise abnormal proteins; maintenance of\namino acid pools in cells affected by stresses such as starvation; and\ngeneration of protein fragments that act as hormones, antigens, or\nother effectors. One major function of proteolytic pathways is the\nselective destruction of proteins whose concentrations must vary\nwith time and alterations in the state of a cell. Short in vivo half-lives\nof such proteins provide a way to generate their spatial gradients\nand to rapidly adjust their concentration or subunit\ncomposition through changes in the rate of their degradation.\nThe regulated (and processive) degradation of intracellular proteins\nis carried out largely by the ubiquitin\u2013proteasome system (Ub\nsystem), in conjunction with autophagy-lysosome pathways. Other\ncontributors to intracellular proteolysis include cytosolic and\nnuclear proteases, such as caspases, calpains, and separases. They\noften function as \"upstream\" components of the Ub system, which\ndestroys protein fragments that had been produced by these (nonprocessive)\nproteases. Ub, a 76-residue protein, mediates selective\nproteolysis through its enzymatic conjugation to proteins that contain\nprimary degradation signals (degrons (1)), thereby marking\nsuch proteins for degradation by the 26S proteasome, an ATPdependent\nmultisubunit protease. Ub conjugation involves the\nformation of a poly-Ub chain that is linked (in most cases) to the \u03b5-amino group of an internal Lys residue in a substrate protein.\nUb is a \"secondary\" degron, in that Ub is conjugated to proteins\nthat contain primary degradation signals. Ub has nonproteolytic\nfunctions as well. The design of the Ub system is summarized in\nFig. 1.",
        "doi": "10.1007/978-1-61779-474-2_1",
        "isbn": "9781617794742",
        "publisher": "Humana Press",
        "place_of_publication": "New York",
        "publication_date": "2012",
        "pages": "1-11"
    },
    {
        "id": "authors:m3ck0-6xj67",
        "collection": "authors",
        "collection_id": "m3ck0-6xj67",
        "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210122-162658053",
        "type": "book_section",
        "title": "Electrophoretic assay for DNA-binding proteins",
        "book_title": "Methods in Enzymology",
        "author": [
            {
                "family_name": "Varshavsky",
                "given_name": "Alexander",
                "orcid": "0000-0002-4011-258X",
                "clpid": "Varshavsky-A"
            }
        ],
        "abstract": "This chapter describes a generally applicable assay for specific DNA-binding proteins in crude extracts. The assay is based on gel electrophoretic separation of protein\u2013DNA complexes from each other and from free DNA. This assay employed in several laboratories to detect a variety of DNA-binding proteins. In spite of relatively brief experience with the electrophoretic assay as a detection tool, its exceptionally high sensitivity has already made this assay the method of choice in many experimental settings. The electrophoretic assay has been successfully applied to the detection of both highly sequence-specific, nonabundant DNA-binding proteins and abundant DNA-binding proteins of relatively low nucleotide sequence specificity. After briefly describing some of the alternative techniques suitable for the detection of DNA-binding proteins in crude extracts, it discusses the electrophoretic assay, its recent modifications, and consider other applications of the assay. Although nondenaturing electrophoretic systems have existed for almost as long as the method of gel electrophoresis itself, the arrival of powerful analytical applications of this technology is quite recent and other useful variations of the theme are still to come.",
        "doi": "10.1016/s0076-6879(87)51044-8",
        "isbn": "9780121820527",
        "publisher": "Academic Press",
        "publication_date": "1987",
        "pages": "551-565"
    }
]