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R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35.

Yokoyama T, Neya S, Tsuneshige A, Yonetani T, Park SY, Tame JR
J Mol Biol 356 790-801 (2006)
Related entries: 2d5x, 2d5z

Cited: 31 times
EuropePMC logo PMID: 16403522

Abstract

Although detailed crystal structures of haemoglobin (Hb) provide a clear understanding of the basic allosteric mechanism of the protein, and how this in turn controls oxygen affinity, recent experiments with artificial effector molecules have shown a far greater control of oxygen binding than with natural heterotropic effectors. Contrary to the established text-book view, these non-physiological compounds are able to reduce oxygen affinity very strongly without switching the protein to the T (tense) state. In an earlier paper we showed that bezafibrate (BZF) binds to a surface pocket on the alpha subunits of R state Hb, strongly reducing the oxygen affinity of this protein conformation. Here we report the crystallisation of Hb with L35, a related compound, and show that this binds to the central cavity of both R and T state Hb. The mechanism by which L35 reduces oxygen affinity is discussed, in relation to spectroscopic studies of effector binding.

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  1. New look at hemoglobin allostery. Yuan Y, Tam MF, Simplaceanu V, Ho C. Chem Rev 115 1702-1724 (2015)

Articles - 2d60 mentioned but not cited (7)

  1. Characterization of diadzein-hemoglobin binding using optical spectroscopy and molecular dynamics simulations. Sengupta B, Chakraborty S, Crawford M, Taylor JM, Blackmon LE, Biswas PK, Kramer WH. Int J Biol Macromol 51 250-258 (2012)
  2. A CRITICAL STUDY ON THE INTERACTIONS OF HESPERITIN WITH HUMAN HEMOGLOBIN: FLUORESCENCE SPECTROSCOPIC AND MOLECULAR MODELING APPROACH. Chakraborty S, Chaudhuri S, Pahari B, Taylor J, Sengupta PK, Sengupta B. J Lumin 132 1522-1528 (2012)
  3. Ameliorative effects of quercetin against bisphenol A-caused oxidative stress in human erythrocytes: an in vitro and in silico study. Sangai NP, Patel CN, Pandya HA. Toxicol Res (Camb) 7 1091-1099 (2018)
  4. Dynamics based clustering of globin family members. Tobi D. PLoS One 13 e0208465 (2018)
  5. In vitro α-amylase and hemoglobin glycation inhibitory potential of Nigella sativa essential oil, and molecular docking studies of its principal components. Dalli M, Daoudi NE, Abrigach F, Azizi SE, Bnouham M, Kim B, Gseyra N. Front Pharmacol 13 1036129 (2022)
  6. Two physics-based models for pH-dependent calculations of protein solubility. Spassov VZ, Kemmish H, Yan L. Protein Sci 31 e4299 (2022)
  7. Human Hemoglobin and Antipsychotics Clozapine, Ziprasidone and Sertindole: Friends or Foes? Platanić Arizanović L, Gligorijević N, Cvijetić I, Mijatović A, Ristivojević MK, Minić S, Kokić AN, Miljević Č, Nikolić M. Int J Mol Sci 24 8921 (2023)


Reviews citing this publication (3)

  1. Hemoglobin: Structure, Function and Allostery. Ahmed MH, Ghatge MS, Safo MK. Subcell Biochem 94 345-382 (2020)
  2. Protein dynamics explain the allosteric behaviors of hemoglobin. Yonetani T, Laberge M. Biochim Biophys Acta 1784 1146-1158 (2008)
  3. How does hemoglobin generate such diverse functionality of physiological relevance? Yonetani T, Kanaori K. Biochim Biophys Acta 1834 1873-1884 (2013)

Articles citing this publication (20)

  1. 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JR. J Mol Biol 360 690-701 (2006)
  2. Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics. Laberge M, Yonetani T. Biophys J 94 2737-2751 (2008)
  3. Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease. Sun K, D'Alessandro A, Ahmed MH, Zhang Y, Song A, Ko TP, Nemkov T, Reisz JA, Wu H, Adebiyi M, Peng Z, Gong J, Liu H, Huang A, Wen YE, Wen AQ, Berka V, Bogdanov MV, Abdulmalik O, Han L, Tsai AL, Idowu M, Juneja HS, Kellems RE, Dowhan W, Hansen KC, Safo MK, Xia Y. Sci Rep 7 15281 (2017)
  4. Molecular mechanism of photoactivation of a light-regulated adenylate cyclase. Ohki M, Sato-Tomita A, Matsunaga S, Iseki M, Tame JRH, Shibayama N, Park SY. Proc Natl Acad Sci U S A 114 8562-8567 (2017)
  5. Dynamic allostery in the ring protein TRAP. Heddle JG, Okajima T, Scott DJ, Akashi S, Park SY, Tame JR. J Mol Biol 371 154-167 (2007)
  6. Circular dichroism spectroscopy of tertiary and quaternary conformations of human hemoglobin entrapped in wet silica gels. Ronda L, Bruno S, Viappiani C, Abbruzzetti S, Mozzarelli A, Lowe KC, Bettati S. Protein Sci 15 1961-1967 (2006)
  7. Solution structure and dynamics of human hemoglobin in the carbonmonoxy form. Fan JS, Zheng Y, Choy WY, Simplaceanu V, Ho NT, Ho C, Yang D. Biochemistry 52 5809-5820 (2013)
  8. Identification of a novel class of covalent modifiers of hemoglobin as potential antisickling agents. Omar AM, Mahran MA, Ghatge MS, Chowdhury N, Bamane FH, El-Araby ME, Abdulmalik O, Safo MK. Org Biomol Chem 13 6353-6370 (2015)
  9. NO reactions with sol-gel and solution phase samples of the ferric nitrite derivative of HbA. Roche CJ, Friedman JM. Nitric Oxide 22 180-190 (2010)
  10. Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H4B's role in nitric oxide synthase. Liu H, Walker LA, Nanayakkara NP, Doerksen RJ. J Am Chem Soc 133 1172-1175 (2011)
  11. Structures of haemoglobin from woolly mammoth in liganded and unliganded states. Noguchi H, Campbell KL, Ho C, Unzai S, Park SY, Tame JR. Acta Crystallogr D Biol Crystallogr 68 1441-1449 (2012)
  12. Reverse engineering the cooperative machinery of human hemoglobin. Ren Z. PLoS One 8 e77363 (2013)
  13. Structure of the altitude adapted hemoglobin of guinea pig in the R2-state. Pairet B, Jaenicke E. PLoS One 5 e12389 (2010)
  14. Letter Stability and crystal structures of His88 mutant human transthyretins. Yokoyama T, Hanawa Y, Obita T, Mizuguchi M. FEBS Lett 591 1862-1871 (2017)
  15. Monodora myristica (African nutmeg) modulates redox homeostasis and alters functional chemistry in sickled erythrocytes. Erukainure OL, Ajiboye JA, Abbah UA, Asieba GO, Mamuru S, Zaruwa MZ, Manhas N, Singh P, Islam MS. Hum Exp Toxicol 37 458-467 (2018)
  16. Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice. Inoguchi N, Mizuno N, Baba S, Kumasaka T, Natarajan C, Storz JF, Moriyama H. PLoS One 12 e0174921 (2017)
  17. Binding modes of L35 to alpha- and beta-semihemoglobins: structural insights into the inequivalence of alpha- and beta-subunits of hemoglobin. De Rosa MC, Carelli Alinovi C, Russo A, Giardina B. Biochem Biophys Res Commun 354 720-726 (2007)
  18. Molecular Interaction of Functionalized Nanoplastics with Human Hemoglobin. Rajendran D, Chandrasekaran N. J Fluoresc 33 2257-2272 (2023)
  19. Bohr effect of human hemoglobin: Separation of tertiary and quaternary contributions based on the Wyman equation. Okonjo KO. Biophys Chem 228 87-97 (2017)
  20. Tertiary conformational transition in sheep hemoglobins induced by reaction with 5,5 -dithiobis(2-nitrobenzoate) and by binding of inositol hexakisphosphate. Okonjo KO, Adeogun IA, Babalola JO. Biophys Chem 146 65-75 (2010)


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