Reagents & Protocols
Antibodies applied in organoid staining (Whole mount staining and IHC) protocols (P04)
Antibodies applied in organoid staining (Whole mount staining and IHC) protocols can be found here
Tools for proteome-wide structural predictions for all 9 human herpesviruses (P09)
Structure predictions have become invaluable tools for wet lab science by accelerating the generation of structure-based hypotheses. We provide proteome-wide monomer structure predictions for all nine human herpesviruses at www.bosse-lab.org/herpesfolds through an interactive, searchable, and open-access web interface to make these resources available to everyone.
HerpesFolds: A proteome-wide structural systems approach reveals insights into protein families and activities of all nine human herpesviruses.
Moreover, it is now possible to perform protein-protein interaction screens in silico using structural predictions. At www.bosse-lab.org/herpesppis, we also provide the complete predicted protein interactome for HSV-1, HCMV, and KSHV with stringent scoring. Its graphical user interface also allows easy access and provides information on conserved protein complexes.
Protocols
The native polyacrylamide gel electrophoresis (NAGE) can be used to investigate whether a protein forms multimeric structures (e.g . dimers). In this regard, for example, NAGE can be used to investigate the importance of certain amino acid positions for the formation of such multimeric structures by mutagenesis and comparison to the wildtype protein. The protocol can be found here.
Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites, and possibly define cistromes. The protocol can be found here.
The TriPPPro system facilitates live imaging of cellular and viral genomes through the use of a pronucleotide linked to a dienophile and a fluorogenic linked to a diene. The protocol can be found here.
Sterrenberg VT, Stalling D, Knaack JIH, Soh TK, Bosse JB, Meier C. A TriPPPro-Nucleotide Reporter with Optimized Cell-Permeable Dyes for Metabolic Labeling of Cellular and Viral DNA in Living Cells. Angewandte Chemie Jul 2023. (DOI: https://doi.org/10.1002/ange.202308271). PDF