Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin

Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physic...

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Bibliographic Details
Published in:	Life (Basel, Switzerland) Switzerland), 2022-01, Vol.12 (2), p.210
Main Authors:	Kondo, Hiroko X, Takano, Yu
Format:	Article
Language:	eng
Subjects:	Affinity Amino acids Distortion Electron transfer Heme heme distortion Hemoglobin MD simulation Molecular dynamics myoglobin Myoglobins Oxygen Physical properties pocket rigidity Porphyrins protein environment Proteins Quantum mechanics Redox potential Simulation Statistical analysis Statistics
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Summary:	Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physical properties of heme, such as oxygen affinity and redox potential. Therefore, clarification of the relationship between heme distortion and the protein environment is crucial in protein science. Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations as well as statistical analysis of the protein structures of hemoglobin and myoglobin stored in Protein Data Bank. Our computation and statistical analysis showed that the protein environment for hemoglobin and myoglobin prominently affects the doming distortion of heme porphyrin, which correlates with its oxygen affinity, and that the magnitude of distortion is different between hemoglobin and myoglobin. These results suggest that heme distortion is affected by its protein environment and fluctuates around its fitted conformation, leading to physical properties that are appropriate for protein functions.
ISSN:	2075-1729 2075-1729