Modeling with Alternate Locations in X-ray Protein Structures

Abstract

In many molecular modeling applications, the standard procedure is still to handle proteins as single, rigid structures. While the importance of conformational flexibility is widely known, handling it remains challenging. Even the crystal structure of a protein usually contains variability exemplified in alternate side chain orientations or backbone segments. This conformational variability is encoded in PDB structure files by so-called alternate locations (AltLocs). Most modeling approaches either ignore AltLocs or resolve them with simple heuristics early on during structure import. We analyzed the occurrence and usage of AltLocs in the PDB and developed an algorithm to automatically handle AltLocs in PDB files enabling all structure-based methods using rigid structures to take the alternative protein conformations described by AltLocs into consideration. A respective software tool named AltLocEnumerator can be used as a structure preprocessor to easily exploit AltLocs. While the amount of data makes it difficult to show impact on a statistical level, handling AltLocs has a substantial impact on a case-by-case basis. We believe that the inspection and consideration of AltLocs is a very valuable approach in many modeling scenarios.

Redocking the PDB

“…In this context, the inclusion of protein flexibility by a combined ensemble docking and restricted side chain flexibility approach is currently under development. The construction of protein structure ensembles could also be integrated into the JAMDA preprocessing pipeline, e.g., by a PDB-wide search for similar binding sites using the SIENA tool or our recently presented approach to translate alternate locations into protein structure ensembles …”

“…Here, the first encountered alternate location identifier is used for all atoms with alternate location identifiers in the structure. A recent discussion of alternate locations in PDB structures and different strategies to take them into account can be found in Gutermuth et al (2023). 104 Furthermore, during PDB file interpretation, only the atom coordinates in the PDB file are considered, i.e., the asymmetric unit for structures obtained from the PDB.…”

“…A recent discussion of alternate locations in PDB structures and different strategies to take them into account can be found in Gutermuth et al (2023). 104 Furthermore, during PDB file interpretation, only the atom coordinates in the PDB file are considered, i.e., the asymmetric unit for structures obtained from the PDB. 63 Disulfide bridges are detected using a distancebased criterion; i.e., two cysteines are assumed to be connected by a disulfide bridge if both sulfur atoms have a distance of at most 2.5 Å.…”

“…The construction of protein structure ensembles could also be integrated into the JAMDA preprocessing pipeline, e.g., by a PDB-wide search for similar binding sites using the SIENA tool 150 or our recently presented approach to translate alternate locations into protein structure ensembles. 104 ■ ASSOCIATED CONTENT…”

A dataset of alternately located segments in protein crystal structures

“…Gutermuth et al . recently argued this resource may have remained unnoticed since to date most modelling approaches either ignore altlocs altogether or resolve them with simple heuristics 4 . Indeed, whilst common structural visualization programs such Chimerax or Pymol display alternate side chain locations, only a single, default backbone conformation is shown unless the user specifically calls up the hidden alternate conformation.…”