https://doi.org/10.1140/epjd/s10053-022-00452-0
Regular Article – Molecular Physics and Chemical Physics
The same, but different, but still the same: structural and dynamical differences of neutrophil elastase and cathepsin G
1
Department of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
2
Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
3
Research Centre for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
4
Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg Institut für Physik, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
Received:
25
April
2022
Accepted:
2
July
2022
Published online:
20
July
2022
Although the general mechanism for serine protease catalysis is well established, some questions still remain. For instance, the two enzymes, neutrophil elastase and cathepsin G, have a lot of structural resemblances. However, elastase degrades virulence factors, while cathepsin G does not. This paper studies both enzymes computationally to probe for their conformational differences. In the process, a methodology is established to not only quantify similarities between the protein trajectories describing proteins’ temporal evolution but also account for a varying number of amino acid residues comprising each structure. Our results indicate slight differences in the behavior of the active sites of neutrophil elastase and cathepsin G in the solvent. These subtle changes could indicate differences in the general behavior responsible for the different specificity of the two enzymes.
© The Author(s) 2022
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