Year: 2025
Type: conference-abstract
Abstract: Pairwise distance root mean square deviation defines a hyperspace where conformers with similar shape reside close to each other. The radius of gyration of protein ensembles in this abstract conformer space (ACS) converges at ensemble sizes between 50 and 500, depending on the extent of disorder. Upon further increase of ensemble size, the root mean square distance of conformers to their nearest neighbors decreases only slowly. Clustering in ACS can reveal distinct subensembles. For proteins that exist in two states, clustering in a common ACS reveals differences between the ensembles in the two states. The dimension of ACS can be reduced to 2D or 3D by multi‐dimensional scaling or principal component analysis. Visualization in these lower‐dimensional spaces also reveals differences between protein states or the existence of subensembles. The ratio between the gyration radius in ACS and its counterpart in real space is a global disorder parameter.
Source: Helvetica Chimica Acta
Author: Gunnar Jeschke
Institution: ETH Zurich
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,030
OpenAlex ID: W4410020170