Protein Science Best Paper awards annoucement


Credit: Brian Matthews, Editor of Protein Science

Warmest congratulations to Charlotte Miton1 and Zach Schaefer2 (Figure 1), the recipients of the Protein Society's Year 2016 "Best Paper" awards. At the beginning of each year, two "best papers" are selected from articles published in Protein Science during the preceding 12 months. A junior author (typically the first author) is designated as the award winner and invited to give a talk at the following Annual Protein Society Symposium.

Charlotte Miton has already been something of a world traveler. Following completion of her Master's degree in France, she participated in research projects in Mexico and Italy before undertaking her Ph.D. in Cambridge with Drs. F. Hollfelder and M. Hyvonen.

As Charlotte then narrates "Following my PhD work, I joined Dr. Nobuhiko Tokuriki at UBC in Vancouver, with whom I share a passion for tracking and elucidating the mechanisms behind functional transitions, mutational interactions and conformational changes that result from evolutionary selection. We had worked together during my time at Cambridge and felt that there were many potential pathways we could explore. This led to the core motivation behind the paper in Protein Science: based on the data being generated in the field on single evolutionary trajectories, how prevalent were the trends we were observing in the laboratory and to what degree could we use that information to make inferences from their protein structures? We felt that a general consensus on the role of mutational epistasis, i.e. non-additive interactions between mutations, based on a quantitative survey of its type and prevalence, remained to be established. By 2016 we were able to gather, analyse and compare complete mutational data from nine evolutionary trajectories curated from the literature. This analysis revealed that epistasis plays a major, albeit hidden, role constraining evolutionary trajectories: about half of the mutations fixed during these nine trajectories were neutral or detrimental in the original WT background and only became positive at later rounds of evolution, following the prior fixation of permissive mutations." 2

Dr. Tokuriki describes Charlotte as a "bona fide" scientist. She is, he says, an "old-school scientist", but meant in the best way. "She is really meticulous and dives into every detail of the project…which often led to exciting findings". Nobu explains that for some time he and Charlotte have had the idea to characterize and compare various examples of mutational epistasis during adaptive evolution, building on the milestone 2004 paper of Weireich and Harl. He says that Charlotte led their paper and brought it to a level that he did not anticipate at the beginning.

The second Best Paper awardee, Zach Schaefer, worked with Tony Kossiakoff, who describes Zach "in a nutshell" as follows: "Zach was an undergrad at Reed. After graduation, he decided to take a year or two off to 'find the meaning of life'. That sounds very Reed-like, you get the picture. He applied to my lab as a technician to see whether science was his thing. I usually don't like to be part of this type of experiment, but his mentor at Reed thought he was a good bet. So did I, and it was a good bet. He spent a couple of years with me and I put him on a number of hard projects. Interestingly, the work that is described in the Protein Science paper was completely initiated by Zach and a postdoc, Luke Bailey. They worked together on this, mainly in the background of other things. They had been working on projects that required Fabs to be coupled in a bivalent format and found that some of the best Fabs for an application actually became highly aggregated when put in this form. So, developing the polar ring was an important step leading to the ability to make bivalent Fab constructs.

As a good boss, I was happy to take a victory lap with them. But, as I said, I was really only a spectator during the process."

Zach, himself, adds the following: "I have held a long-term interest in how the extraordinary diversity of life and its capabilities could have emerged from the limited palette of biological molecules. After graduating from Reed College as chemistry major, I was eager to explore how structural features constrain and direct the roles of proteins within the cell. More specifically, I wanted to understand how molecular features of proteins allow them to coordinate with and contribute to biological processes.

Joining the laboratory of Dr. Anthony A. Kossiakoff at the University of Chicago was a wonderful opportunity to learn more about the chemical basis of molecular recognition–a protein's ability to selectively interact with a target partner in the complex milieu of the body's interior. Dr. Kossiakoff's research contributed extensively to our understanding of the molecular determinates for specific and high affinity protein-protein interactions. With this knowledge, the lab has developed a powerful minimalist synthetic antibody discovery platform, which provided new models to explore the basis for protein interaction specificity. Our findings shed light on the mechanisms governing an important constraint for all cellular proteins, which is the requirement to maintain interaction specificity. This research has important implications for the design of affinity reagents, and demonstrates that protein interaction specificity can be directly targeted without compromising affinity.

Currently, I am a graduate student of microbiology in the laboratory of Dr. Steven S. Blanke at the University of Illinois Urbana-Champaign. My research focuses on the mechanisms by which bacterial toxins subvert host cellular physiology. Like antibodies, bacterial toxins are hard-wired to target specific biological features, and the proteins that I study possess the ability to traverse the interior of the host cell and target specific sub-cellular compartments. My current research is to identify and understand molecular determinates that allow the genotoxin, cytolethal distending toxin, to efficiently pass through at least five cellular compartments to target the host nucleus. Understanding the process underlying this behavior will hopefully provide insight into the features of other toxins that allow for targeted delivery of proteins to different areas of cellular physiology. In the future I hope to continue to study protein structure-function relationships that relate to important human health outcomes. As knowledge in this field develops, there is increasing opportunity to address 3 critical deficiencies in our toolkit to treat and cure illness and disease. As a researcher, I hope to contribute to our understanding of protein interactions and their role in the basic functions of life."

Also looking toward the future, Charlotte feels that "The extreme complexity of biological systems will always require detailed studies if we are to identify the key molecular factors that drive functional transitions. In an era of big data reliant on high-throughput systems, I believe that "more" will not systematically provide "all" the answers we seek, by which I mean that exploring molecular evolution and epistasis through the systematic comparison of small but diverse sets of alternative trajectories will be the key to uncovering the molecular mechanisms of evolutionary change. These trajectories can be derived from both natural evolution and parallel experimental evolution that is repeatedly started from a unique genotype, or from various orthologous genes, toward distinct targets or under slightly different conditions (alternative cofactors, environments, etc.).

The real challenge now resides in combining the approaches and insights from studies that 'zoom out' and broadly characterize many genotypes with studies that 'zoom in' and uncover, in great detail, the molecular functions of a small subset of highly interesting genotypes. In the future, I would like to further collaborate with labs investigating higher order interactions (such as cases of long-term organismal evolution or natural evolution, including human lineages). Only this way will we unveil the complex historical and ongoing mechanisms that cause evolutionary changes to occur. It's all about exploring the small picture embedded within the big one!"


Background Information

All articles published in Protein Science are candidates for the "Best Paper" awards. No nomination statement is required. At the same time, if authors submitting a manuscript feel that it will be a strong candidate for a "best paper" award, they are very welcome to include a brief note in the submission letter explaining why the contribution is especially worthy of consideration.

Brian W. Matthews Editor


1. Miton CM, Tokuriki N (2016) How mutational epistasis impairs predictability in protein evolution and design. Protein Sci 25:1260-1272.
2. Schaefer ZP, Bailey LJ, Kossiakoff AA (2016) A polar ring endows improved specificity to an antibody fragment. Protein Sci 25:1290-1298.

Figure Caption

Figure 1. Award winners. (A) Charlotte Miton. (B) Zach Schaefer

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