Sokurenko, E. | bioRxiv Science

bioRxiv2026

Programming N-linked glycan composition through de novo protein design

N-linked glycans are ubiquitous post-translational modifications that mediate diverse biological processes, including cell signaling and adhesion, molecular recognition, and host-pathogen interactions. Despite their importance, N-linked glycans have largely remained beyond the reach of biomolecular design due to a lack of methods capable of jointly modeling glycans and protein structure. Here, we develop a general all-atom computational pipeline for creating de novo glycoproteins in which the amino acid sequence encodes both the location and composition of N-linked glycans. The method uses three-dimensional protein structure to tune glycan accessibility to processing enzymes in the eukaryotic secretory pathway. Systematic increases in steric restriction progressively reduced processing, shifting glycans from heterogeneous complex-type structures toward increasingly underprocessed oligomannose-type species resembling those found on many viral glycoproteins. Despite this programmed restriction, the resulting oligomannose glycans remained accessible for biological recognition, inhibiting uropathogenic Escherichia coli adhesion to human bladder cells and binding mannose-binding lectin. These results establish steric control of N-glycan processing as a genetically encodable design principle and extend computational protein design to functional glycoproteins with programmed composition.

biochemistry↗

bioRxiv2025

Ultra-slow conformational dynamics and catch bond formation of a Bacterial Adhesin revealed by a single-domain variant of FimH.

Bacterial adhesins such as FimH are critical for host colonization and persistence under the mechanical forces encountered at sites of infection such as the urinary tract. Despite decades of research, the molecular mechanisms by which FimH--a key virulence factor of Escherichia coli--regulates its binding through conformational switching remain incompletely understood. FimH operates across a range of conformations that includes low- (LAS), intermediate-, high-affinity (HAS) states-- and forms catch bonds which paradoxically strengthen under force. The allosteric pathways governing these transitions remain poorly defined due to experimental limitations that restrict understanding of key dynamic phenomena that underlie ligand-triggered conformational shifts and force-induced long-lived interactions. Such understanding is central to drug discovery efforts to target bacterial adhesion. Here we present a model system that fully recapitulates the conformational repertoire of FimH in the absence of its pilin domain. Our findings demonstrate that a single mutation in the lectin domain induces the LAS while allowing for ligand-binding induced conformational change to the HAS and catch bond formation, mirroring the behavior of the native FimH adhesin. We propose a dynamic allosteric mechanism that involves ultra-slow, low-frequency dynamics for the ability of FimH and the bacteria that express it, to sustain long-lived interactions with mannose under both static and force conditions. SignificanceUrinary tract infections (UTIs) are among the most common bacterial infections, and their initiation depends on the ability of uropathogenic Escherichia coli (UPEC) to adhere to bladder cells. The adhesion is mediated by FimH, a protein on the outside of UPEC that binds mannose-containing glycoprotein receptors and strengthens its grip under shear stress via a catch-bond mechanism. To investigate FimH function, we engineered a variant that can adopt both low- and high-affinity states of FimH and can form catch bonds. We discovered that FimH is governed by ultra-slow conformational dynamics that vary even among structurally similar states. These findings provide a mechanistic framework for developing anti-adhesive therapies that target FimH dynamics, offering a novel strategy to prevent and treat UTIs.

biochemistry↗