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Throughout their almost 40-year history, the Methods in Protein Structure Analysis (MPSA) meetings have advanced novel techniques for the study of proteins. Like proteins themselves, each conference has been different, with a shifting focus that reflects technological advances in protein chemistry. Each conference brings together scientists from various backgrounds to discuss the development and implementation of ways to understand proteins. This minireview series represents a sample of presentations from the 2012 conference held in Ottawa, Canada.

In the first minireview, Friedmann and Marmorstein compare the structures and catalytic mechanisms of non-histone acetyltransferases. Like phosphorylation, acetylation may critically modulate the localization, interactions, stability and activity of target proteins.

Protein stability in vitro has proven to be a critical roadblock with regard to engineering of proteins with novel function. In their minireview, Socha and Tokuriki describe an approach to modulating stability by combining ‘permanent’ compensatory mutations with ‘transient’ chaperone-containing solutions, favoring efforts to develop new biomedical tools.

Among desirable protein functions, enzyme catalysis is highly amenable to biomedical application but requires detailed understanding of the catalytic cycle. Two minireviews, one by Gagné and Doucet and the second by Veglia and Cembran, address the role of protein dynamics in enzymatic activity. Using separate enzymes, they present methods to examine conformational changes on different time scales. Hydrogen–deuterium exchange mass spectrometry is one approach to study protein dynamics. Resetca and Wilson describe a microfluidic set-up for automated implementation of these experiments, which provide real-time information about conformational changes in proteins.

Mass spectrometry is used not only to study isolated proteins, but also within a complex cellular environment. Drissi et al. present proteomics methods to enrich organelles for the investigation of subcellular localization. MacLeod and Varmuza report the proteomic characterization of spermatogenic cells, which provides new insight into male infertility.

Cellular signaling is regulated both by proteins and by the bioactive low-molecular-mass second messengers that interact with them. Xu et al. describe techniques for the study of lipid second messengers and how these studies have provided insight into their roles in disease.

Protein de-regulation in disease is being exploited to diagnose disease progression. The final three minireviews address proteomic methods for biomarker identification. First, Ma et al. review recent applications of proteomics approaches to the study of diabetic microangiopathy. Next, Zheng et al. describe an approach to develop biomarkers for diabetes using changing networks as opposed to individual proteins. Finally, Liu et al. examine the use of phosphorylation signatures to classify disease states.

This series offers a glimpse into the diversity of dynamics in living things. From the conformational movement of proteins to the orchestration of signaling pathways, flexibility is a key aspect of the ability to evolve. Similarly, methods to study proteins must be flexible and ever-changing to meet new biological challenges and answer fundamental questions.

Biographies

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  2. Biographies
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    Lisa M. Miller Jenkins is the Mass Spectrometry Facility Manager for the Collaborative Protein Technology Resource at the National Cancer Institute. Lisa obtained a BS with a double major in Biology and Chemistry from Winthrop University, South Carolina, and PhD in Biochemistry and Molecular Biology from the University of Georgia, Athens.

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    Daniel Figeys is the interim chair and professor in the Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, at the University of Ottawa. He is a Tier 1 Canada Research Chair in Proteomics and Systems Biology. Daniel obtained a BSc and an MSc in chemistry from the University of Montreal. He obtained a PhD in chemistry from the University of Alberta, Edmonton, and undertook postdoctoral studies at the University of Washington, Seattle. His laboratory focuses on the development and application of proteomics and lipidomics technologies. He has published over 120 papers and has been cited over 6000 times.