Webinar Report: Unpuzzling proteins

Ivan Dikic, eLife Senior Editor, and his guests discussed the most exciting discoveries and challenges at the forefront of protein biochemistry.
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In the first webinar of the Biochemistry and Chemical Biology series, our panelists talked about the latest research in proteins and new techniques that make these possible. Ivan Dikic (eLife Senior Editor, Goethe University Frankfurt, Germany), Manu Hegde (eLife Reviewing Editor, MRC Laboratory of Molecular Biology, UK), Anne-Claude Gingras (Lunenfeld-Tanenbaum Research Institute, Canada) and Wade Harper (Harvard Medical School, USA) also reflected on the most important challenges currently under investigation.

Making proteins – translation and folding

Manu Hegde talked about some of the most active areas in the field of protein translation and maturation. While the chemistry of translation is relatively well understood, it continues to be an active field because translation is extensively regulated during development, environmental changes and disease. Since translation is coupled to protein localisation, assembly, and quality control – it is of particularly great interest in understanding diseases of protein misfolding. Next, Dr. Hegde discussed advances in technology that have driven some of the most recent discoveries in this area. Genome-wide views of translation under a variety of conditions have emerged with the development of ribosome profiling coupled with selective tagging or isolation methods that provide spatial information. In parallel, Dr. Hegde highlighted how electron cryomicroscopy (Cryo-EM) is complementing such global analyses with molecular and mechanistic insights into specific events occurring at the ribosome. According to Hegde, the ability to monitor protein translation and its related processes in vivo with high spatial and temporal resolution remains an important challenge in this discipline.

Connecting proteins – interaction networks

Anne-Claude Gingras first discussed the different types of interactions proteins undergo: from relatively stable molecular machines such as a ribosome, to signalling pathways, which can involve multistage processes, mediated by a number of factors. She then talked about the different approaches and techniques to monitor such interactions. She pointed out that this area, especially within biochemical methods is growing, with almost weekly advancements of available techniques. Among the binary approaches, she mentioned the yeast two-hybrid, which in recent years became more popular when combining both positive and negative references for assays. Among forward screening approaches, where proteins are identified with the use of mass spectrometry, she noted the more classic affinity purification, as well as the newer methods of protein correlation profiling, proximity-dependant biotinylation and chemical cross-linking. Dr. Gingras covered in detail the advantages and disadvantages of the main approaches. Following the review of leading methods, she proceeded to list the greatest challenges she sees to protein interactions research at this point in time.

Monitoring proteins – quantitative proteomics

Wade Harper discussed the proteome complexity and what it means for the abundance of different proteins, highlighting the stark differences – of up to seven orders of magnitude – in the amounts of different protein molecules present in the cell. He then covered investigating how these are organised into the different cell organelles. He discussed quantitative proteomics as a framework for studying cell organisation and signalling. The framework involves coupling enrichment and labelling strategies to disentangle complex arrays of proteins, and how to use the power of mass spectrometry to measure concentrations of different proteins. He then proceeded to talk about the use of quantitative proteomics in analysing complexes, pathways and modifications in response to stimuli. To conclude, Prof. Harper discussed the drivers for formation, stoichiometry and turnover of proteins, understanding modification states, and quantitative changes in cellular organisation, as key current challenges in the area of monitoring proteins.

It boggles the mind how all of these proteins get made, how they get assembled.

– Wade Harper, Harvard Medical School, USA

Removing proteins – degradation via UPS and autophagy

Ivan Dikic’s closing presentation covered the depth of insight gained only recently into the domain of protein degradation. He mentioned Cell Biology by Numbers website which allows one to calculate the time of ribosome polymerisation as well as proteasome degradation of proteins, and noted these are always similar to preserve balance in active cells. Prof. Dikic mentioned different techniques currently used for studying these problems, in particular he highlighted the importance of CryoEM tomography for investigating localisation and conformation of protein substrates. He also mentioned novel clinical applications for resulting methods that allow targeted degradation of proteins. He then discussed the process of autophagy and it’s leading role in eliminating proteasome, and pointed out that selectivity of this process is a very active field of research at the moment. In his presentation, Prof. Dikic listed the main challenges in the area of protein degradation, highlighting clinical relevance as the key opportunity in this domain.

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