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Updated: Aug 25, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
The effect of protein internal cavities on ligand migration and binding in myoglobin
Karin Nienhaus1, Gerd U Nienhaus
1Department of Biophysics, University of Ulm, Ulm 89069, Germany. karin.nienhaus@physik.uni-ulm.de
Abstract:
Using Fourier Transform Infrared Spectroscopy at cryogenic temperatures, we have studied carbon monoxide (CO) migration in the interior of sperm whale myoglobin and binding to teh heme iron. The effect of protein internal cavities was examined by comparing the wild-type protein with mutants in which the cavities were blocked by bulky amino acid sidechains. After photodissociation at 3 K, CO ligands reside in the primary docking site (B) from where they can migrate to other sites (C, D) that were identified as the Xe4 and Xe1 cavities. These studies were complemented by flash photolysis experiments at room temperature, which revealed that the protein cavities enable efficient excape of ligands from the protein after dissociation from the heme iron.
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