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
  • EPR Techniques to Probe Insertion and Conformation of Spin-Labeled Proteins in Lipid Bilayers
    Item type: Book Chapter
    Bordignon, Enrica; Kucher, Svetlana; Polyhach, Yevhen (2019)
    Methods in Molecular Biology ~ Lipid-Protein Interactions: Methods and Protocols
  • Structural Studies of Amyloids by Quenched Hydrogen–Deuterium Exchange by NMR
    Item type: Book Chapter
    Vilar, Marçal; Wang, Lei; Riek, Roland (2012)
    Methods in Molecular Biology ~ Amyloid Proteins
    The elucidation of the structure of amyloid fi brils and related aggregates is an important step towards understanding the pathogenesis of diseases such as Alzheimer’s and Parkinson’s, which feature protein misfolding and/or aggregation. However, the large size and poor solubility of amyloid-like fibrils make them resistant to high-resolution structure determination. Here, we describe the use of hydrogen–deuterium exchange coupled with NMR as an indirect strategy to determine the folding regions of amyloid-forming proteins at residue level resolution.
  • Adenovirus-mediated transduction of auto- and dual-regulated transgene expression in mammalian cells
    Item type: Book Chapter
    Gonzalez-Nicolini, Valeria; Fussenegger, Martin (2008)
    Methods in Molecular Biology ~ Gene therapy protocols. 2, Design and Characterization of Gene Transfer Vectors
  • Genome Engineering of Hybridomas to Generate Stable Cell Lines for Antibody Expression
    Item type: Book Chapter
    Parola, Cristina; Mason, DM; Zingg, Andreas; et al. (2018)
    Methods in Molecular Biology ~ Recombinant Protein Expression in Mammalian Cells
  • The Listeria Cell Wall and Associated Carbohydrate Polymers
    Item type: Book Chapter
    Loessner, Martin J.; Eugster, Marcel R.; Loessner, Martin (2014)
    Methods in Molecular Biology ~ Listeria Monocytogenes
    Understanding molecular interactions of bacteria with their environment requires the purification and characterization of cell wall components. Here, we describe detailed experimental methods for the extraction, purification, and analysis of wall teichoic acids (WTA), which assume important roles as major constituents of Gram-positive cell walls, such as mediating interaction with cell wall-associated proteins, eukaryotic host cells, and bacteriophages. Specifically, we present a procedure for compositional WTA characterization to study large diversity of carbohydrate substitution on Listeria monocytogenes WTA. This protocol may also be used and adapted to analyze WTA from other bacteria.
  • Quality considerations and selection of surface chemistry for glass-based DNA, peptide, antibody, carbohydrate, and small molecule microarrays
    Item type: Book Chapter
    Sobek, Jens; Aquino, Catharine; Schlapbach, Ralph (2007)
    Methods in Molecular Biology ~ Microarrays
  • Population Dynamics Analysis of Ciprofloxacin-Persistent S. Typhimurium Cells in a Mouse Model for Salmonella Diarrhea.
    Item type: Book Chapter
    Kaiser Patrick; Regoes, Roland R.; Hardt, Wolf-Dietrich (2016)
    Methods in Molecular Biology ~ Bacterial Persistence: Methods and Protocols
  • Molecular Scaffold Hopping via Holistic Molecular Representation
    Item type: Book Chapter
    Grisoni, Francesca; Schneider, Gisbert (2021)
    Methods in Molecular Biology ~ Protein-Ligand Interactions and Drug Design
    Molecular descriptors encode a variety of molecular representations for computer-assisted drug discovery. Here, we focus on the Weighted Holistic Atom Localization and Entity Shape (WHALES) descriptors, which were originally designed for scaffold hopping from natural products to synthetic molecules. WHALES descriptors capture molecular shape and partial charges simultaneously. We introduce the key aspects of the WHALES concept and provide a step-by-step guide on how to use these descriptors for virtual compound screening and scaffold hopping. The results presented can be reproduced by using the code freely available from URL: github.com/ETHmodlab/scaffold_hopping_whales.
  • Mobile and Three-Dimensional Presentation of Adhesion Proteins Within Microwells
    Item type: Book Chapter
    Andreasson-Ochsner, Mirjam; Reimhult, Erik (2013)
    Methods in Molecular Biology ~ Adhesion Protein Protocols
    On traditional cell culture substrates cells adhere to a planar 2D surface where ligands are presented immobile. A more realistic presentation of cell adhesion ligands which can account for lateral mobility and a more tissue-like 3D presentation would allow studies addressing fundamental questions of significant importance for applications such as tissue engineering and implant intregration. To study the effect of lateral mobility of cell membrane interaction cues in three dimensions, we have developed and characterized a platform which generically enables patterning of single cells into microwells presenting a cell membrane mimetic interface pre-patterned to its walls. Here, we describe its application in presenting a soluble cell adhesive ligand coupled through streptavidin-antibody linkage to lipids in a supported lipid bilayer (SLB) coated microwell. The lateral mobility of the presented ligands was controlled through a small change in temperature. The SLB phospholipid composition was choosen such that below its melting transition at 30 °C the ligands are immobile, while above 30 °C they are laterally mobile. The platform thus enables the investigation of cell adhesion to either laterally immobile or mobile E-cadherin ligand presented on the same cell membrane mimetic surface.
  • Purification of Human Monoclonal Antibodies and Their Fragments
    Item type: Book Chapter
    Müller-Späth, Thomas; Morbidelli, Massimo (2014)
    Methods in Molecular Biology ~ Human Monoclonal Antibodies
    This chapter summarizes the most common chromatographic mAb and mAb fragment purification methods, starting by elucidating the relevant properties of the compounds and introducing the various chromatography modes that are available and useful for this application. A focus is put on the capture step affinity and ion exchange chromatography. Aspects of scalability play an important role in judging the suitability of the methods. The chapter introduces also analytical chromatographic methods that can be utilized for quantification and purity control of the product. In the case of mAbs, for most purposes the purity obtained using an affinity capture step is sufficient. Polishing steps are required if material of particularly high purity needs to be generated. For mAb fragments, affinity chromatography is not yet fully established, and the capture step potentially may not provide material of high purity. Therefore, the available polishing techniques are touched upon briefly. In the case of mAb isoform and bispecific antibody purification, countercurrent chromatography techniques have been proven to be very useful and a part of this chapter has been dedicated to them, paying tribute to the rising interest in these antibody formats in research and industry.
Publications 1 - 10 of 126