Searching similar local 3D micro-environments in protein structure databases with MicroMiner

Abstract

The available protein structure data are rapidly increasing. Within these structures, numerous local structural sites depict the details characterizing structure and function. However, searching and analyzing these sites extensively and at scale poses a challenge. We present a new method to search local sites in protein structure databases using residue-defined local 3D micro-environments. We implemented the method in a new tool called MicroMiner and demonstrate the capabilities of residue micro-environment search on the example of structural mutation analysis. Usually, experimental structures for both the wild-type and the mutant are unavailable for comparison. With MicroMiner, we extracted $>255 \times 10^{6}$ amino acid pairs in protein structures from the PDB, exemplifying single mutations' local structural changes for single chains and $>45 \times 10^{6}$ pairs for protein-protein interfaces. We further annotate existing data sets of experimentally measured mutation effects, like $\Delta \Delta G$ measurements, with the extracted structure pairs to combine the mutation effect measurement with the structural change upon mutation. In addition, we show how MicroMiner can bridge the gap between mutation analysis and structure-based drug design tools. MicroMiner is available as a command line tool and interactively on the https://proteins.plus/ webserver.

Keywords: micro-environment; mutation effect prediction; mutation modeling; protein site; protein structure.