Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation

Shigenori Nagatomo; Mitsuo Shoji; Takuto Terada; Kiyoharu Nakatani; Yasuteru Shigeta; Shun Hirota; Sachiko Yanagisawa; Minoru Kubo; Teizo Kitagawa; Masako Nagai; Mio Ohki; Sam-Yong Park; Naoya Shibayama

doi:10.1016/j.bpj.2022.06.012

Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation

Biophys J. 2022 Jul 19;121(14):2767-2780. doi: 10.1016/j.bpj.2022.06.012. Epub 2022 Jun 9.

Authors

Affiliations

¹ Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan. Electronic address: nagatomo@chem.tsukuba.ac.jp.
² Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan; JST-PRESTO, Kawaguchi, Saitama, Japan.
³ Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
⁴ Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
⁵ Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.
⁶ Graduate School of Science, University of Hyogo, Ako-gun, Hyogo, Japan.
⁷ Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan.
⁸ Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan; School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
⁹ Protein Design Laboratory, Yokohama City University, Tsurumi, Yokohama, Japan.
¹⁰ Department of Physiology, Division of Biophysics, Jichi Medical University, Shimotsuke, Tochigi, Japan.

Abstract

Hemoglobins M (Hbs M) are human hemoglobin variants in which either the α or β subunit contains a ferric heme in the α₂β₂ tetramer. Though the ferric subunit cannot bind O₂, it regulates O₂ affinity of its counterpart ferrous subunit. We have investigated resonance Raman spectra of two Hbs, M Iwate (α87His → tyrosine [Tyr]) and M Boston (α58His → Tyr), having tyrosine as a heme axial ligand at proximal and distal positions, respectively, that exhibit unassigned resonance Raman bands arising from ferric (not ferrous) hemes at 899 and 876 cm^-1. Our quantum chemical calculations using density functional theory on Fe-porphyrin models with p-cresol and/or 4-methylimidazole showed that the unassigned bands correspond to the breathing-like modes of Fe³⁺-bound Tyr and are sensitive to the Fe-O-C(Tyr) angle. Based on the frequencies of the Raman bands, the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston were predicted to be 153.5° and 129.2°, respectively. Consistent with this prediction, x-ray crystallographic analysis showed that the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston in the T quaternary structure were 153.6° and 134.6°, respectively. It also showed a similar Fe-O bond length (1.96 and 1.97 Å) and different tilting angles.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Crystallography
Density Functional Theory
Heme / chemistry
Hemoglobin M* / chemistry
Hemoglobin M* / metabolism
Humans
Spectrum Analysis, Raman
Tyrosine / chemistry
Vibration

Substances

Tyrosine
Heme
Hemoglobin M