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Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect.

Kovalevsky AY, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher Z, Langan P, Morimoto Y
J Mol Biol 398 276-91 (2010)
Cited: 20 times
EuropePMC logo PMID: 20230836

Abstract

We have investigated the protonation states of histidine residues (potential Bohr groups) in the deoxy form (T state) of human hemoglobin by direct determination of hydrogen (deuterium) positions with the neutron protein crystallography technique. The reversible binding of protons is key to the allosteric regulation of human hemoglobin. The protonation states of 35 of the 38 His residues were directly determined from neutron scattering omit maps, with 3 of the remaining residues being disordered. Protonation states of 5 equivalent His residues--alpha His20, alpha His50, alpha His89, beta His143, and beta His146--differ between the symmetry-related globin subunits. The distal His residues, alpha His58 and beta His63, are protonated in the alpha 1 beta 1 heterodimer and are neutral in alpha 2 beta 2. Buried residue alpha His103 is found to be protonated in both subunits. These distal and buried residues have the potential to act as Bohr groups. The observed protonation states of His residues are compared to changes in their pK(a) values during the transition from the T to the R state and the results provide some new insights into our understanding of the molecular mechanism of the Bohr effect.

Reviews - 3kmf mentioned but not cited (2)

  1. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography. Chen JC, Unkefer CJ. IUCrJ 4 72-86 (2017)
  2. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD. Acta Crystallogr D Struct Biol 74 800-813 (2018)

Articles - 3kmf mentioned but not cited (5)

  1. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics. Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR. PLoS One 10 e0123146 (2015)
  2. Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography. Kovalevsky A, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher SZ, Langan P, Morimoto Y. Acta Crystallogr D Biol Crystallogr 66 1144-1152 (2010)
  3. Macromolecular neutron crystallography at the Protein Crystallography Station (PCS). Kovalevsky A, Fisher Z, Johnson H, Mustyakimov M, Waltman MJ, Langan P. Acta Crystallogr D Biol Crystallogr 66 1206-1212 (2010)
  4. Visualizing the Bohr effect in hemoglobin: neutron structure of equine cyanomethemoglobin in the R state and comparison with human deoxyhemoglobin in the T state. Dajnowicz S, Seaver S, Hanson BL, Fisher SZ, Langan P, Kovalevsky AY, Mueser TC. Acta Crystallogr D Struct Biol 72 892-903 (2016)
  5. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Acta Crystallogr D Struct Biol 79 1056-1070 (2023)


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  1. Trapping of human hemoglobin by haptoglobin: molecular mechanisms and clinical applications. Ratanasopa K, Chakane S, Ilyas M, Nantasenamat C, Bulow L. Antioxid Redox Signal 18 2364-2374 (2013)
  2. Structural origin of cooperativity in human hemoglobin: a view from different roles of α and β subunits in the α2β2 tetramer. Nagatomo S, Nagai M, Kitagawa T. Biophys Rev 14 483-498 (2022)
  3. The use of neutron scattering to determine the functional structure of glycoside hydrolase. Nakamura A, Ishida T, Samejima M, Igarashi K. Curr Opin Struct Biol 40 54-61 (2016)

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  2. Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. Gapsys V, de Groot BL. Elife 8 e44718 (2019)
  3. Influence of inflammation-related changes on conformational characteristics of HLA-B27 subtypes as detected by IR spectroscopy. Fabian H, Loll B, Huser H, Naumann D, Uchanska-Ziegler B, Ziegler A. FEBS J 278 1713-1727 (2011)
  4. Room-temperature neutron and X-ray data collection of 3CL Mpro from SARS-CoV-2. Kneller DW, Phillips G, Kovalevsky A, Coates L. Acta Crystallogr F Struct Biol Commun 76 483-487 (2020)
  5. Collective dynamics underlying allosteric transitions in hemoglobin. Vesper MD, de Groot BL. PLoS Comput Biol 9 e1003232 (2013)
  6. Molecular modeling of the human hemoglobin-haptoglobin complex sheds light on the protective mechanisms of haptoglobin. Nantasenamat C, Prachayasittikul V, Bulow L. PLoS One 8 e62996 (2013)
  7. Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. El Hage K, Hédin F, Gupta PK, Meuwly M, Karplus M. Elife 8 e45318 (2019)
  8. Protein charge ladders reveal that the net charge of ALS-linked superoxide dismutase can be different in sign and magnitude from predicted values. Shi Y, Abdolvahabi A, Shaw BF. Protein Sci 23 1417-1433 (2014)
  9. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobin. Sakipov S, Rafikova O, Kurnikova MG, Rafikov R. Redox Biol 11 516-523 (2017)
  10. Determination of Histidine Protonation States in Proteins by Fast Magic Angle Spinning NMR. Zadorozhnyi R, Sarkar S, Quinn CM, Zadrozny KK, Ganser-Pornillos BK, Pornillos O, Gronenborn AM, Polenova T. Front Mol Biosci 8 767040 (2021)


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