Protein ensemble modeling and analysis with MMMx.

Protein Sci

Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.

Published: March 2024

Proteins, especially of eukaryotes, often have disordered domains and may contain multiple folded domains whose relative spatial arrangement is distributed. The MMMx ensemble modeling and analysis toolbox (https://github.com/gjeschke/MMMx) can support the design of experiments to characterize the distributed structure of such proteins, starting from AlphaFold2 predictions or folded domain structures. Weak order can be analyzed with reference to a random coil model or to peptide chains that match the residue-specific Ramachandran angle distribution of the loop regions and are otherwise unrestrained. The deviation of the mean square end-to-end distance of chain sections from their average over sections of the same sequence length reveals localized compaction or expansion of the chain. The shape sampled by disordered chains is visualized by superposition in the principal axes frame of their inertia tensor. Ensembles of different sizes and with weighted conformers can be compared based on a similarity parameter that abstracts from the ensemble width.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10868441PMC
http://dx.doi.org/10.1002/pro.4906DOI Listing

Publication Analysis

Top Keywords

ensemble modeling
8
modeling analysis
8
protein ensemble
4
analysis mmmx
4
mmmx proteins
4
proteins eukaryotes
4
eukaryotes disordered
4
disordered domains
4
domains multiple
4
multiple folded
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!