Review Article - Journal of Systems Biology & Proteome Research (2022) Volume 3, Issue 4

Improved interpretation of ligand occupancy and protein conformational differences

Proteins and complexes that are present in natural or native-like environments can now be uniquely structurally characterised by chemical cross-linking in complex samples, cells, or even tissues. Based on sequence homology, the public database XLinkDB automatically maps crosslinks to accessible structures. Cross-linked residues must be separated by Euclidean distances within the maximal span of the applied cross-linker in order to generate the structures that are most likely to reflect protein conformations in the cross-linked sample. The solvent accessible surface distance (SASD), as opposed to the Euclidean distance, is a better predictor of consistency because it takes into account the accessibility of the cross-linked residues and the path connecting them. However, SASDs of structures are computationally expensive to calculate and not publicly available. In this section, we explain in XLinkDB version 4.0 the automatic calculation of SASDs using Jwalk for all cross-links mapped to structures, both with and without reference to ligands, and we estimate empirical maximum SASD spans for BDP-NHP and DSSO cross-linkers of, respectively, 51 and 63. We highlight cross-links sensitive to ADP binding in mitochondria isolated from HEK293 cells and show how SASDs can be utilised to help predict sample protein conformations and ligand occupancy. We also describe ligands close to cross-links in structures. A key task in medicinal chemistry and drug development comprehends the dynamics of ligands attached to proteins. However, X-ray crystallography, which is the most common method for figuring out protein-ligand structures, cannot adequately account for dynamics and cannot precisely characterise the motions of ligands in protein binding sites. In order to comprehend the conformational variability of ligands in protein crystal structures, ensemble refinement, a different technique, is employed in this work on six protein-ligand complexes.

Author(s): Gourab Ranjan Das

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