Functional Proteomics Driven by Chemical and Computational Approaches

• Published in: Chinese journal of chemistry Vol. 40; no. 5; pp. 628 - 634
• Main Authors: Chen, Ying, Qin, Wei, Wang, Chu
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY‐VCH Verlag GmbH & Co. KGaA 01.03.2022; Wiley Subscription Services, Inc
• Subjects: Activity‐based protein profiling; Biological activity; Biology; Careers; Computer applications; Functionals; Knee; Metabolites; Natural products; Personality; Probes; Protein design; Protein modifications; Proteins; Proteomics; Selenoproteins; Soccer; Students; Target deconvolution; Target recognition; Television programs
• ISSN: 1001-604X; 1614-7065
• DOI: 10.1002/cjoc.202100785

Comprehensive Summary Functional proteomics is a powerful approach to globally investigate protein functions and their biological significance. Activity‐based protein profiling (ABPP) has been widely applied to explore the activity and ligandability of proteins in complex biological systems. Herein, we summarized our efforts in developing chemical probes and chemical proteomic pipelines to identify protein targets of certain post‐translational modifications (PTMs), covalent drugs, natural products and cellular metabolites. Furthermore, computer‐aided proteomic strategies were developed to globally identify functional residues including hyper‐reactive cysteines, active sites of selenoproteins and proximal anchors for protein activation. How do you get into this specific field? Could you please share some experiences with our readers? When I finished my Ph.D. in computational structure biology, I was attracted to chemical biology as it is a highly interdisciplinary field. I was fascinated by how chemical probes can capture and reveal important functions of proteins, particularly in complexed biological settings. How do you supervise your students? I tend to let my students explore freely on research subjects they are interested in as long as the topics fit in the scope of functional proteomics. I enjoy the experience of working with them instead of supervising them. What is the most important personality for scientific research? In my opinion, the most important personality for scientific research is perseverance, passion and logical thinking. How do you keep balance between research and family? Research and family should not conflict with each other and they are both inseparable parts of my life. Practically, I just leave enough family time on my schedule so that they are not interfered by my research works. What are your hobbies? My hobbies are watching soccer games and sitcoms. I used to play soccer quite a lot but sadly my knees do not allow it any more. My favorite soccer club is AC Milan and my favorite sitcom is Friends. Could you please give us some advices on improving Chinese Journal of Chemistry? Stay diversified, in terms of both research subjects published as well as career stages of contributing authors. Functional proteomics, which focuses on the elucidation of protein activities, multiprotein complexes and signaling pathways, is a powerful approach to globally investigate protein functions and their biological significance. In this review, we summarized recent progress of our lab in functional proteomics including development of pipelines to identify protein targets of post‐translational modifications (PTMs), covalent drugs, natural products and cellular metabolites. Furthermore, computer‐aided proteomic strategies were also developed to globally identify functional residues including hyper‐reactive cysteines, active sites of selenoproteins and proximal anchors for protein activation.