Journal: Methods in Molecular Biology

Abbreviation

Methods Mol Biol

Publisher

Humana Press

Journal Volumes

ISSN

1064-3745
1940-6029

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Publications 1 - 10 of 126
  • Analysis of the Degradome with the CLIP-CHIP™ Microarray
    Item type: Book Chapter
    Kappelhoff, Reinhild; auf dem Keller, Ulrich; Overall, Christopher M. (2010)
    Methods in Molecular Biology ~ Matrix metalloproteinase protocols
  • Identification of Distinct Amino Acids as ADP-Ribose Acceptor Sites by Mass Spectrometry
    Item type: Book Chapter
    Rosenthal, Florian; Messner, Simon; Roschitzki, Bernd; et al. (2011)
    Methods in Molecular Biology ~ Poly(ADP-ribose) Polymerase
    ADP-ribosylation is a well-known post-translational protein modification, which regulates a variety of cellular processes. The proteins able to catalyze mono- or poly ADP-ribosylation of proteins belong to the family of ADP-ribosyltransferases. A variety of nuclear proteins has been described to be ADP-ribosylated, including ARTD1 itself and histone proteins. Despite intensive research during the last 40 years, the acceptor amino acids in ARTD1 or histone proteins could be identified and confirmed only recently by MS/MS and by site-directed mutagenesis. The establishment of a standardized protocol including the specific enrichment of ADP-ribosylated proteins and peptides and subsequent mass spectrometric analysis allows the identification of ADP-ribose acceptor sites of modified proteins and to address the functional contribution of ADP-ribosylation in vitro as well as in vivo.
  • Transplantation of autologous dermo-epidermal skin substitutes in a pig model
    Item type: Book Chapter
    Fleischmann, Thea; Nicholls, Flora; Lipiski, Miriam; et al. (2019)
    Methods in Molecular Biology ~ Skin Tissue Engineering
  • In Silico Target Prediction for Small Molecules
    Item type: Book Chapter
    Byrne, Ryan; Schneider, Gisbert (2019)
    Methods in Molecular Biology ~ Systems Chemical Biology
    Drugs modulate disease states through their actions on targets in the body. Determining these targets aids the focused development of new treatments, and helps to better characterize those already employed. One means of accomplishing this is through the deployment of in silico methodologies, harnessing computational analytical and predictive power to produce educated hypotheses for experimental verification. Here, we provide an overview of the current state of the art, describe some of the well-established methods in detail, and reflect on how they, and emerging technologies promoting the incorporation of complex and heterogeneous data-sets, can be employed to improve our understanding of (poly)pharmacology.
  • Getting Started
    Item type: Book Chapter
    Stocker, Hugo; Gallant, Peter (2008)
    Methods in Molecular Biology ~ Drosophila : methods and protocols
  • Enzyme encapsulation in an engineered lumazine synthase protein cage
    Item type: Book Chapter
    Azuma, Yusuke; Hilvert, Donald (2018)
    Methods in Molecular Biology ~ Protein Scaffolds
  • Correlative 3D Imaging: CLSM and FIB-SEM Tomography Using High-Pressure Frozen, Freeze-Substituted Biological Samples
    Item type: Book Chapter
    Lucas, Miriam S.; Guenthert, Maja; Gasser, Philippe; et al. (2014)
    Methods in Molecular Biology ~ Electron Microscopy: Methods and Protocols
  • Plant Chromatin Immunoprecipitation
    Item type: Book Chapter
    Villar, Corina B.R.; Köhler, Claudia (2010)
    Methods in Molecular Biology ~ Plant developmental biology : methods and protocols
  • Design and construction of synthetic gene networks in mammalian cells
    Item type: Book Chapter
    Karlsson, Maria; Weber, Wilfried; Fussenegger, Martin (2012)
    Methods in Molecular Biology ~ Synthetic Gene Networks
    Advances in the development of molecular tools for the inducible control of transcription, translation, and protein degradation are the basis for the rapidly emerging design and construction of synthetic gene net works in mammalian cells. In this chapter, we describe such tools and how they can be integrated into a synthetic gene network with desired functionality. The network design and construction process is illustrated in the form of a detailed protocol for the implementation of a logic NOR gate based on an inducible promoter combined with an inducible protein degradation system.
  • Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics
    Item type: Book Chapter
    Niittylä, Totte; Chaudhuri, Bhavna; Sauer, Uwe; et al. (2009)
    Methods in Molecular Biology ~ Plant Systems Biology
    The recent development of analytic technologies allows fast analysis of metabolism in real time. Fluxomics aims to define the genes involved in regulation of flux through a metabolic or signaling pathway. Flux through a metabolic or signaling pathway is determined by the activity of its individual components; regulation can occur at many levels, including transcriptional, posttranslational, and allosteric levels. Currently two technologies are used to monitor fluxes. The first is pulse labeling of the organism with a tracer such as C13, followed by mass spectrometric analysis of the partitioning of label into different compounds. The second approach is based on the use of flux sensors, proteins that respond with a conformational change to ligand binding. Fluorescence resonance energy transfer (FRET) detects the conformational change and serves as a proxy for ligand concentration. Both methods provide high time resolution. In contrast to mass spectrometry assays, FRET nanosensors monitor only a single compound, but the advantage of FRET nanosensors is that they yield data with cellular and subcellular resolution.
Publications 1 - 10 of 126