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The metallocarboxypeptidases (MCPs) belonging to the clan MC were studied by the Optimal Docking Area (ODA) method to evaluate protein-protein binding sites and to provide a basis for the identification of binding partners for this class of enzymes. The ODA method identifies surface patches with optimal desolvation energy based on the selection of low-energy docking regions, generated from a set of surface points around the protein. With few exceptions, the ODA method identified surface patches with a significant low-energy docking surface for all the MCPs with known three-dimensional structure. Overall, in 14 out of 24 cases, the detected ODA patches were correctly located (i.e. more than 50% of the predicted residues were in known protein-protein binding sites), yielding a global success rate of 58%. More specifically, the success rate increased up to 80% on the ODA patches detected for the catalytic domains of the M14A subfamily, independently on the partner. Interestingly, the ODA residues on the catalytic domain were correctly located in the interface with the N-terminal pro domain in all MCPs. The spatial distribution of the ODA patches for the different members of the family is in relation to the origin and function of the particular MCP, which allowed distinguishing between them. In good agreement with the experimentally characterized protein interfaces, the total average surface area of the theoretically derived ODA patches for the catalytic domain of MCPs is around 1700 A2 and their content in hydrophobic residues is about 40%. As a particular case, the average surface area of the ODA patches in MCPs of crop insect pests is about twice that of the MCPs of vertebrates, which might be related to their particular function. We recognized two binding regions for the catalytic domain of the MCPs, one of them accounting for nearly all the known intermolecular interactions made up by the enzymes. Protein inhibitors seem to have evolved to dock on this subset of ODA patches, evoking the binding mode of the N-terminal pro domains. The second binding region detected, for which no ligands have been identified so far, seems to be related to the acquisition/maintenance of the native structure of the peptidase. Overall, the ODA method has been successful in identifying low-energy docking areas in a set of structurally and functionally related proteins, suggesting that it can be easily extended to other families in the search for protein-protein binding sites and for their functional significance.
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http://dx.doi.org/10.1002/prot.21390 | DOI Listing |
J Am Chem Soc
May 2023
Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan.
Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds.
View Article and Find Full Text PDFBiol Open
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Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
In the cytoplasm, filamentous actin (F-actin) plays a critical role in cell regulation, including cell migration, stress fiber formation, and cytokinesis. Recent studies have shown that actin filaments that form in the nucleus are associated with diverse functions. Here, using live imaging of an F-actin-specific probe, superfolder GFP-tagged utrophin (UtrCH-sfGFP), we demonstrated the dynamics of nuclear actin in zebrafish (Danio rerio) embryos.
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View Article and Find Full Text PDFInt J Comput Assist Radiol Surg
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Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan.
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View Article and Find Full Text PDFSci Rep
September 2022
Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.
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