Simple Rules Govern Protein Assembly and Evolution
BGU researchers uncover simple rules guiding protein assembly, revealing how complex structures remain stable and functional across evolution.
Researchers at Ben-Gurion University of the Negev have identified simple rules that explain how complex protein structures assemble correctly and remain functional over time, despite having many theoretically possible configurations.
The study, published in Proceedings of the National Academy of Sciences (PNAS), focuses on bacterioferritin, a bacterial protein complex responsible for safely storing iron. Unlike simpler protein assemblies made of identical parts, many bacterioferritins are built from two different types of subunits, each with a distinct role.
“Although there are thousands of ways these subunits could assemble, we found that only a small number of arrangements actually occur,” said Prof. Raz Zarivach, one of the study’s authors. “This indicates that assembly is guided by underlying rules, not randomness.”
Using high-resolution cryo–electron microscopy and computational analysis, the researchers identified two key principles. One rule prevents certain subunits from pairing at all, eliminating many nonfunctional structures. The second favors pairings that bring the protein’s two essential functions, iron oxidation and electron transfer, into close proximity.
“These rules sharply limit the number of viable configurations while still allowing flexibility,” said Daniel Stein, the lead author of the study.
Dr. Gabriel Frank, a senior author on the study, noted that the findings demonstrate how evolutionary constraints can be encoded as the rules of a 3D puzzle: although many arrangements are possible, only those that obey a small set of rules produce a stable, functional structure without requiring strict external control.
By analyzing bacterioferritin proteins from multiple species, the researchers showed that these rules are conserved across evolution, pointing to a broader biological principle: complex molecular systems can maintain stability through a small number of structural constraints rather than rigid control.
The study was conducted by researchers from Ben-Gurion University of the Negev’s Department of Life Sciences, Stein Faculty of Computer and Information Science, and the Ilse Katz Institute for Nanoscale Science and Technology, in collaboration with international partners.
The researchers acknowledged generous support from the Guzik Foundation to BGU’s cryo–electron microscopy unit. The study was supported by the European Research Council Horizon 2020 (grant 678765), the Israel Science Foundation (grants 1065/20, 2891/21, 163/22, and 364/20), the Federal Ministry of Education and Research (BMBF) through the MagBioFab grant, and a U.S. National Science Foundation–Binational Science Foundation (NSF–BSF) collaborative grant (2231900 / 2022614).
