Recently, a couple of OPIG members had the opportunity to attend and present at the 39th Annual Symposium of the Protein Society—a not-for-profit scholarly society founded in 1985 that focuses on protein structure, function, and design—held in San Francisco.
The PS39 schedule was well designed, offering a balance between plenary talks, themed parallel sessions, and networking opportunities. A wide range of topics was covered, including transient protein states, supramolecular assemblies, proteostasis, and circadian clocks. This allowed us to follow areas of personal interest, both related and unrelated to our research, while exploring unfamiliar fields. Although many talks were biology-heavy, they were generally pitched at an accessible level for those from other disciplines (ie. the small molecules side of OPIG). Presentations almost always included results from both in silico and experimental approaches, with relatively few focusing exclusively on one or the other; a very nifty thing to see as people who mostly just dream of experimental validation! In contrast to our generalisable-model-focus, many of the researchers presenting had dedicated years to studying a single protein or system, uncovering its nuances in a way that made for some neat storytelling.
Several talks stood out: Jeff Kelly’s Stein and Moore Award lecture addressed the origins of drugs that slow neurodegeneration; Sarah Alamdari discussed generative protein language models; and Andy LiWang’s Dorothy Crowfoot Hodgkin Award lecture explored circadian clock mechanisms. The 2024 Protein Science Young Investigator Award lecture by Dr Gabriela Schlau-Cohen (MIT) was a particular highlight: rather than butchering an explanation of it, we’ll just link to a recorded version here. The talk, which focuses on photosynthetic systems, felt especially relevant now, being close to climate change research and the resilience of food chains.
Talks on experimental approaches to measuring protein dynamics also drew considerable attention. Mass spectrometry (MS), in combination with other techniques, was a recurring theme for enhancing the study of both folded and flexible proteins. Elizabeth Komives (UCSD) presented work building on previous studies (DOI: 10.1021/acs.biochem.1c00277) using hydrogen–deuterium exchange (HDX) MS and NMR to investigate allostery in folded proteins upon binding. Darren N. Kahan, from Susan Marqusee’s group (Berkeley), described unpublished work demonstrating how MS can be combined with X-ray footprinting (XFMS) to study flexible linkers in proteins. In this technique, hydroxyl radicals generated by a high-intensity X-ray pulse covalently modify solvent-exposed side chains; the modified residues are then identified by MS, providing detailed insights into protein flexibility.
Another notable session, 20 Amino Acids and Beyond, addressed proteins constructed with fewer or more than the canonical 20 amino acids. Klara Hlouchova (Charles University, Prague) presented findings that extend previous research (DOI: 10.1098/rsob.220040) into how ancient proteins may have functioned without the full complement of amino acids. The work also examined the evolutionary acquisition of additional amino acids and their roles in ribosome emergence and subsequent functional diversification.
We both found feedback at PS39 differed from that received at other conferences, with a stronger emphasis on how our computational methods could be useful for experimentalists; a nice change of pace from speaking with purely ML people who are more interested in implementations than the actual applicability.
Overall, we both enjoyed it and would definitely recommend it to others who want to gain some more perspective on the biology side of the field. The next symposium — the 40th Anniversary Symposium — will take place on 19–22 July 2026 in Boston, Massachusetts, at the Westin Seaport Boston.
Lucy and Matteo
