Conservation of the conformation of the porphyrin macrocycle in hemoproteins

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Abstract

The out-of-plane distortions of porphyrins in hemoproteins are characterized by displacements along the lowest-frequency out-of-plane normal coordinates of the D(4h)-symmetric macrocycle. X-ray crystal structures are analyzed using a computational procedure developed for determining these orthogonal displacements. The x-ray crystal structures of the heme groups are described within experimental error, using the set composed of only the lowest frequency normal coordinate of each out-of-plane symmetry type. That is, the distortion is accurately simulated by a linear combination of these orthonormal deformations, which include saddling (B(2u)), ruffling (B(1u)), doming (A(2u)), waving(E(g)), and propellering (A(1u)). For example, orthonormal structural decomposition of the hemes in deoxymyoglobins reveals a predominantly dom heme deformation combined with a smaller wav(y) deformation. Generally, the heme conformation is remarkably similar for proteins from different species. For cytochromes c, the conformation is conserved as long as the amino acids between the cysteine linkages to the heme are homologous. Differences occur if this short segment varies in the number or type of residues, suggesting that this small segment causes the nonplanar distortion. Some noncovalently linked hemes like those in the peroxidases also have highly conserved characteristic distortions. Conservation occurs even for some proteins with a large natural variation in the amino acid sequence.

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Jentzen, W., Ma, J. G., & Shelnutt, J. A. (1998). Conservation of the conformation of the porphyrin macrocycle in hemoproteins. Biophysical Journal, 74(2 I), 753–763. https://doi.org/10.1016/S0006-3495(98)74000-7

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