Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 2002 Jun;82(6):3224–3245. doi: 10.1016/S0006-3495(02)75665-8

New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations.

Liliane Mouawad 1, David Perahia 1, Charles H Robert 1, Christophe Guilbert 1
PMCID: PMC1302112  PMID: 12023247

Abstract

It is still difficult to obtain a precise structural description of the transition between the deoxy T-state and oxy R-state conformations of human hemoglobin, despite a large number of experimental studies. We used molecular dynamics with the Path Exploration with Distance Constraints (PEDC) method to provide new insights into the allosteric mechanism at the atomic level, by simulating the T-to-R transition. The T-state molecule in the absence of ligands was seen to have a natural propensity for dimer rotation, which nevertheless would be hampered by steric hindrance in the "joint" region. The binding of a ligand to the alpha subunit would prevent such hindrance due to the coupling between this region and the alpha proximal histidine, and thus facilitate completion of the dimer rotation. Near the end of this quaternary transition, the "switch" region adopts the R conformation, resulting in a shift of the beta proximal histidine. This leads to a sliding of the beta-heme, the effect of which is to open the beta-heme's distal side, increasing the accessibility of the Fe atom and thereby the affinity of the protein. Our simulations are globally consistent with the Perutz strereochemical mechanism.

Full Text

The Full Text of this article is available as a PDF (1.7 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baldwin J., Chothia C. Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism. J Mol Biol. 1979 Apr 5;129(2):175–220. doi: 10.1016/0022-2836(79)90277-8. [DOI] [PubMed] [Google Scholar]
  2. Barrick D., Ho N. T., Simplaceanu V., Ho C. Distal ligand reactivity and quaternary structure studies of proximally detached hemoglobins. Biochemistry. 2001 Apr 3;40(13):3780–3795. doi: 10.1021/bi002165q. [DOI] [PubMed] [Google Scholar]
  3. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  4. Borgstahl G. E., Rogers P. H., Arnone A. The 1.9 A structure of deoxy beta 4 hemoglobin. Analysis of the partitioning of quaternary-associated and ligand-induced changes in tertiary structure. J Mol Biol. 1994 Feb 25;236(3):831–843. doi: 10.1006/jmbi.1994.1192. [DOI] [PubMed] [Google Scholar]
  5. Bruno S., Bettati S., Manfredini M., Mozzarelli A., Bolognesi M., Deriu D., Rosano C., Tsuneshige A., Yonetani T., Henry E. R. Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals. Protein Sci. 2000 Apr;9(4):683–692. doi: 10.1110/ps.9.4.683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Di Cera E., Robert C. H., Gill S. J. Allosteric interpretation of the oxygen-binding reaction of human hemoglobin tetramers. Biochemistry. 1987 Jun 30;26(13):4003–4008. doi: 10.1021/bi00387a039. [DOI] [PubMed] [Google Scholar]
  7. Duan Y., Wang L., Kollman P. A. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9897–9902. doi: 10.1073/pnas.95.17.9897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Eaton W. A., Henry E. R., Hofrichter J. Application of linear free energy relations to protein conformational changes: the quaternary structural change of hemoglobin. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4472–4475. doi: 10.1073/pnas.88.10.4472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ech-Cherif el-Kettani M. A., Durup J. Theoretical determination of conformational paths in citrate synthase. Biopolymers. 1992 May;32(5):561–574. doi: 10.1002/bip.360320512. [DOI] [PubMed] [Google Scholar]
  10. Fermi G., Perutz M. F., Shaanan B., Fourme R. The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. J Mol Biol. 1984 May 15;175(2):159–174. doi: 10.1016/0022-2836(84)90472-8. [DOI] [PubMed] [Google Scholar]
  11. Fujii M., Hori H., Miyazaki G., Morimoto H., Yonetani T. The porphyrin-iron hybrid hemoglobins. Absence of the Fe-His bonds in one type of subunits favors a deoxy-like structure with low oxygen affinity. J Biol Chem. 1993 Jul 25;268(21):15386–15393. [PubMed] [Google Scholar]
  12. Gao J., Kuczera K., Tidor B., Karplus M. Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science. 1989 Jun 2;244(4908):1069–1072. doi: 10.1126/science.2727695. [DOI] [PubMed] [Google Scholar]
  13. Gelin B. R., Lee A. W., Karplus M. Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative mechanism. J Mol Biol. 1983 Dec 25;171(4):489–559. doi: 10.1016/0022-2836(83)90042-6. [DOI] [PubMed] [Google Scholar]
  14. Harvey S. C., Gabb H. A. Conformational transitions using molecular dynamics with minimum biasing. Biopolymers. 1993 Aug;33(8):1167–1172. doi: 10.1002/bip.360330803. [DOI] [PubMed] [Google Scholar]
  15. Henry E. R., Jones C. M., Hofrichter J., Eaton W. A. Can a two-state MWC allosteric model explain hemoglobin kinetics? Biochemistry. 1997 May 27;36(21):6511–6528. doi: 10.1021/bi9619177. [DOI] [PubMed] [Google Scholar]
  16. Hofrichter J., Henry E. R., Szabo A., Murray L. P., Ansari A., Jones C. M., Coletta M., Falcioni G., Brunori M., Eaton W. A. Dynamics of the quaternary conformational change in trout hemoglobin. Biochemistry. 1991 Jul 2;30(26):6583–6598. doi: 10.1021/bi00240a031. [DOI] [PubMed] [Google Scholar]
  17. Janin J., Wodak S. J. Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers. 1985 Mar;24(3):509–526. doi: 10.1002/bip.360240307. [DOI] [PubMed] [Google Scholar]
  18. Janin J., Wodak S. J. The quaternary structure of carbonmonoxy hemoglobin ypsilanti. Proteins. 1993 Jan;15(1):1–4. doi: 10.1002/prot.340150102. [DOI] [PubMed] [Google Scholar]
  19. Kavanaugh J. S., Weydert J. A., Rogers P. H., Arnone A. High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,. Biochemistry. 1998 Mar 31;37(13):4358–4373. doi: 10.1021/bi9708702. [DOI] [PubMed] [Google Scholar]
  20. Kiger L., Poyart C., Marden M. C. Oxygen and CO binding to triply NO and asymmetric NO/CO hemoglobin hybrids. Biophys J. 1993 Sep;65(3):1050–1058. doi: 10.1016/S0006-3495(93)81164-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Levy A., Sharma V. S., Zhang L., Rifkind J. M. A new mode for heme-heme interactions in hemoglobin associated with distal perturbations. Biophys J. 1992 Mar;61(3):750–755. doi: 10.1016/S0006-3495(92)81879-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Liddington R., Derewenda Z., Dodson E., Hubbard R., Dodson G. High resolution crystal structures and comparisons of T-state deoxyhaemoglobin and two liganded T-state haemoglobins: T(alpha-oxy)haemoglobin and T(met)haemoglobin. J Mol Biol. 1992 Nov 20;228(2):551–579. doi: 10.1016/0022-2836(92)90842-8. [DOI] [PubMed] [Google Scholar]
  23. Luisi B., Liddington B., Fermi G., Shibayama N. Structure of deoxy-quaternary haemoglobin with liganded beta subunits. J Mol Biol. 1990 Jul 5;214(1):7–14. doi: 10.1016/0022-2836(90)90139-d. [DOI] [PubMed] [Google Scholar]
  24. Luisi B., Shibayama N. Structure of haemoglobin in the deoxy quaternary state with ligand bound at the alpha haems. J Mol Biol. 1989 Apr 20;206(4):723–736. doi: 10.1016/0022-2836(89)90579-2. [DOI] [PubMed] [Google Scholar]
  25. Mihailescu M. R., Fronticelli C., Russu I. M. Allosteric free energy changes at the alpha 1 beta 2 interface of human hemoglobin probed by proton exchange of Trp beta 37. Proteins. 2001 Aug 1;44(2):73–78. doi: 10.1002/prot.1074. [DOI] [PubMed] [Google Scholar]
  26. Mihailescu M. R., Russu I. M. A signature of the T ---> R transition in human hemoglobin. Proc Natl Acad Sci U S A. 2001 Mar 20;98(7):3773–3777. doi: 10.1073/pnas.071493598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Mouawad L., Perahia D. Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. J Mol Biol. 1996 May 3;258(2):393–410. doi: 10.1006/jmbi.1996.0257. [DOI] [PubMed] [Google Scholar]
  28. Mueser T. C., Rogers P. H., Arnone A. Interface sliding as illustrated by the multiple quaternary structures of liganded hemoglobin. Biochemistry. 2000 Dec 19;39(50):15353–15364. doi: 10.1021/bi0012944. [DOI] [PubMed] [Google Scholar]
  29. Murray L. P., Hofrichter J., Henry E. R., Ikeda-Saito M., Kitagishi K., Yonetani T., Eaton W. A. The effect of quaternary structure on the kinetics of conformational changes and nanosecond geminate rebinding of carbon monoxide to hemoglobin. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2151–2155. doi: 10.1073/pnas.85.7.2151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ogawa S., Shulman R. G. High resolution nuclear magnetic resonance spectra of hemoglobin. 3. The half-ligated state and allosteric interactions. J Mol Biol. 1972 Sep 28;70(2):315–336. doi: 10.1016/0022-2836(72)90542-6. [DOI] [PubMed] [Google Scholar]
  31. Paoli M., Liddington R., Tame J., Wilkinson A., Dodson G. Crystal structure of T state haemoglobin with oxygen bound at all four haems. J Mol Biol. 1996 Mar 8;256(4):775–792. doi: 10.1006/jmbi.1996.0124. [DOI] [PubMed] [Google Scholar]
  32. Perutz M. F. Stereochemistry of cooperative effects in haemoglobin. Nature. 1970 Nov 21;228(5273):726–739. doi: 10.1038/228726a0. [DOI] [PubMed] [Google Scholar]
  33. Perutz M. F., Wilkinson A. J., Paoli M., Dodson G. G. The stereochemical mechanism of the cooperative effects in hemoglobin revisited. Annu Rev Biophys Biomol Struct. 1998;27:1–34. doi: 10.1146/annurev.biophys.27.1.1. [DOI] [PubMed] [Google Scholar]
  34. Peterson E. S., Friedman J. M. A possible allosteric communication pathway identified through a resonance Raman study of four beta37 mutants of human hemoglobin A. Biochemistry. 1998 Mar 31;37(13):4346–4357. doi: 10.1021/bi9708693. [DOI] [PubMed] [Google Scholar]
  35. Ramadas N., Rifkind J. M. Molecular dynamics of human methemoglobin: the transmission of conformational information between subunits in an alpha beta dimer. Biophys J. 1999 Apr;76(4):1796–1811. doi: 10.1016/S0006-3495(99)77340-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Schlitter J., Engels M., Krüger P. Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J Mol Graph. 1994 Jun;12(2):84–89. doi: 10.1016/0263-7855(94)80072-3. [DOI] [PubMed] [Google Scholar]
  37. Schumacher M. A., Dixon M. M., Kluger R., Jones R. T., Brennan R. G. Allosteric transition intermediates modelled by crosslinked haemoglobins. Nature. 1995 May 4;375(6526):84–87. doi: 10.1038/375084a0. [DOI] [PubMed] [Google Scholar]
  38. Selinger D. A., Lisch D., Chandler V. L. The maize regulatory gene B-Peru contains a DNA rearrangement that specifies tissue-specific expression through both positive and negative promoter elements. Genetics. 1998 Jun;149(2):1125–1138. doi: 10.1093/genetics/149.2.1125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Shaanan B. Structure of human oxyhaemoglobin at 2.1 A resolution. J Mol Biol. 1983 Nov 25;171(1):31–59. doi: 10.1016/s0022-2836(83)80313-1. [DOI] [PubMed] [Google Scholar]
  40. Shibayama N., Imai K., Morimoto H., Saigo S. Oxygen equilibrium properties of nickel(II)-iron(II) hybrid hemoglobins cross-linked between 82 beta 1 and 82 beta 2 lysyl residues by bis(3,5-dibromosalicyl)fumarate: determination of the first two-step microscopic Adair constants for human hemoglobin. Biochemistry. 1995 Apr 11;34(14):4773–4780. doi: 10.1021/bi00014a035. [DOI] [PubMed] [Google Scholar]
  41. Shibayama N., Yonetani T., Regan R. M., Gibson Q. H. Mechanism of ligand binding to Ni(II)-Fe(II) hybrid hemoglobins. Biochemistry. 1995 Nov 14;34(45):14658–14667. doi: 10.1021/bi00045a006. [DOI] [PubMed] [Google Scholar]
  42. Silva M. M., Rogers P. H., Arnone A. A third quaternary structure of human hemoglobin A at 1.7-A resolution. J Biol Chem. 1992 Aug 25;267(24):17248–17256. [PubMed] [Google Scholar]
  43. Smith F. R., Lattman E. E., Carter C. W., Jr The mutation beta 99 Asp-Tyr stabilizes Y--a new, composite quaternary state of human hemoglobin. Proteins. 1991;10(2):81–91. doi: 10.1002/prot.340100202. [DOI] [PubMed] [Google Scholar]
  44. Srinivasan R., Rose G. D. The T-to-R transformation in hemoglobin: a reevaluation. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11113–11117. doi: 10.1073/pnas.91.23.11113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Tsai C. H., Fang T. Y., Ho N. T., Ho C. Novel recombinant hemoglobin, rHb (beta N108Q), with low oxygen affinity, high cooperativity, and stability against autoxidation. Biochemistry. 2000 Nov 14;39(45):13719–13729. doi: 10.1021/bi001116a. [DOI] [PubMed] [Google Scholar]
  46. Tsai C. H., Shen T. J., Ho N. T., Ho C. Effects of substitutions of lysine and aspartic acid for asparagine at beta 108 and of tryptophan for valine at alpha 96 on the structural and functional properties of human normal adult hemoglobin: roles of alpha 1 beta 1 and alpha 1 beta 2 subunit interfaces in the cooperative oxygenation process. Biochemistry. 1999 Jul 6;38(27):8751–8761. doi: 10.1021/bi990286o. [DOI] [PubMed] [Google Scholar]
  47. Unzai S., Eich R., Shibayama N., Olson J. S., Morimoto H. Rate constants for O2 and CO binding to the alpha and beta subunits within the R and T states of human hemoglobin. J Biol Chem. 1998 Sep 4;273(36):23150–23159. doi: 10.1074/jbc.273.36.23150. [DOI] [PubMed] [Google Scholar]
  48. Waller D. A., Liddington R. C. Refinement of a partially oxygenated T state human haemoglobin at 1.5 A resolution. Acta Crystallogr B. 1990 Jun 1;46(Pt 3):409–418. doi: 10.1107/s0108768190000313. [DOI] [PubMed] [Google Scholar]
  49. Zhou Y. X., Feng Y. P., Takashi Y. Proton nuclear magnetic resonance and electron paramagnetic resonance investigation of alpha-alpha cross-linked Fe-Co hybrid hemoglobins. Sci China B. 1991 Jul;34(7):850–858. [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES