Papers › Topological characterization of the continuum of allosteric response
Topological characterization of the continuum of allosteric response
Jason W. Rocks, Eleni Katifori, Andrea J. Liu
The archive published only this paper's code-link row. Authors, date and abstract are from arXiv's metadata (CC0), read from the Kaggle arXiv metadata snapshot of 2026-09-12 where its title matched the archive's; the title is the archive's.
Allosteric regulation in proteins is often accompanied by conformational changes that facilitate transmission of mechanical signals between distant ligand binding sites. Typically, these deformations are classified in terms of specific archetypes, including various types of hinge mechanisms or allosteric pathways localized to sequences of amino acids.However, many allosteric deformations resist such strict categorization. Here, we introduce a quantitative topological description of allosteric deformation, unifying all archetypal mechanisms into a single framework. The topological description aligns with two key structural features often associated with allosteric deformations, namely hinge domains and allosteric pathways, enabling us to quantify the significance of each of these features. To develop the analysis, we tune computer-generated mechanical networks to perform allostery-like functions, obtaining an ensemble of networks that establish a range of possible allosteric deformations. The analysis shows that these networks' allosteric mechanisms cannot be described in terms of discrete archetypes - they fall on a continuum. We then apply the same analysis to a collection of allosteric proteins with similar results, showing that our framework encompasses these proteins as well as designed allosteric networks. Our results provide a new picture for allostery, demonstrating not only how it can be described quantitatively, but also giving insight into how it emerges as a collective property.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections