5 articles published in JoVE

• Biochemistry

  
  2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes Marcin Luzarowski*¹, Izabela Wojciechowska*¹, Aleksandra Skirycz^{1 1}Max Planck Institute of Molecular Plant Physiology Protein-protein and protein-metabolite interactions are crucial for all cellular functions. Herein, we describe a protocol that allows parallel analysis of these interactions with a protein of choice. Our protocol was optimized for plant cell cultures and combines affinity purification with mass spectrometry-based protein and metabolite detection.

• Biochemistry

  
  A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample Mohamed Salem^1,2, Michal Bernach¹, Krzysztof Bajdzienko¹, Patrick Giavalisco^{1 1}Max Planck Institute of Molecular Plant Physiology, Golm, Germany, ²Department of Pharmacognosy, Faculty of Pharmacy, Cairo University A protocol for comprehensive extraction of lipids, metabolites and proteins from biological tissues using one sample is presented.

• Biochemistry

  
  High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE Toshio Moriya¹, Michael Saur¹, Markus Stabrin¹, Felipe Merino¹, Horatiu Voicu², Zhong Huang², Pawel A. Penczek², Stefan Raunser¹, Christos Gatsogiannis^{1 1}Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, ²Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston This paper presents a protocol for processing cryo-EM images using the software suite SPHIRE. The present protocol can be applied for nearly all single particle EM projects that target near-atomic resolution.

• Environment

  
  Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry Colin Ruprecht¹, Takayuki Tohge¹, Alisdair Fernie¹, Cara L. Mortimer², Amanda Kozlo², Paul D. Fraser², Norma Funke¹, Igor Cesarino^3,4, Ruben Vanholme^3,4, Wout Boerjan^3,4, Kris Morreel^3,4, Ingo Burgert^5,6, Notburga Gierlinger^5,6, Vincent Bulone⁷, Vera Schneider⁸, Andrea Stockero⁸, Juan Navarro-Aviñó⁹, Frank Pudel¹⁰, Bart Tambuyser¹¹, James Hygate¹², Jon Bumstead¹³, Louis Notley¹³, Staffan Persson^{1,14 1}Max Planck Institute for Molecular Plant Physiology, ²School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, ³Department of Plant Systems Biology, VIB, ⁴Department of Plant Biotechnology and Bioinformatics, UGhent, ⁵Institute for Building Materials, ETH Zurich, ⁶Applied Wood Materials, EMPA, ⁷Division of Glycoscience, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), ⁸European Research and Project Office GmbH, ⁹ABBA Gaia S.L., ¹⁰Pflanzenöltechnologie, ¹¹Capax Environmental Services, ¹²Green Fuels, ¹³Neutral Consulting Ltd, ¹⁴Plant Cell Biology Research Centre, School of Botany, University of Melbourne Plant biomass offers a renewable resource for multiple products, including fuel, feed, food, and a variety of materials. In this paper we investigate the properties of tobacco tree (Nicotiana glauca) and poplar as suitable sources for a biorefinery pipeline.

• Biology

  
  A Protocol for the Identification of Protein-protein Interactions Based on ¹⁵N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation Stefan Schmollinger^1,2, Daniela Strenkert^1,2, Vittoria Offeddu^1,2, André Nordhues^1,2, Frederik Sommer^1,2, Michael Schroda^{1,2 1}Max Planck Institute of Molecular Plant Physiology, ²University of Kaiserslautern We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on ^15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.