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Licensed Unlicensed Requires Authentication Published by De Gruyter December 23, 2017

Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure

  • Magdalena Ptak , Mateusz Banach , Zdzisław Wiśniowski , Leszek Konieczny and Irena Roterman EMAIL logo

Abstract

Heme binding by proteins and protein-protein complexation are the processes strongly related to the biological activity of proteins. The mechanism of these processes has not been still recognised. These phenomena are presented using haemoglobin as the example. Half of the mature haemoglobin (one α-chain and one β-chain) treated as a dissociation step in haemoglobin degradation reveals a specific change in heme binding after dissociation. This phenomenon is the object of analysis that interprets the structure of both complexes (tetramer and dimer) with respect to their hydrophobic core structure. The results suggest the higher stability of the complex in the form of one α-chain and one β-chain with respect to the hydrophobic core.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: The work was financially supported by Jagiellonian University Medical College (Funder Id: 10.13039/100009045, grant systems K/ZDS/006363 and K/ZDS/006366).

  3. Employment or leadership: None declared.

  4. Honorarium: None declared.

  5. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

References

1. Vasseur C, Baudin-Creuza V. Role of alpha-hemoglobin molecular chaperone in the hemoglobin formation and clinical expression of some hemoglobinopathies. Transfus Clin Biol 2015;22:49–57.10.1016/j.tracli.2015.01.002Search in Google Scholar PubMed

2. Visscher KM, Kastritis PL, Bonvin AM. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins 2015;83:445–58.10.1002/prot.24741Search in Google Scholar PubMed

3. Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein-protein complex. Mol Biosyst 2014;10:437–45.10.1039/C3MB70249ASearch in Google Scholar PubMed

4. Yura K, Hayward S. The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics 2009;25:3108–13.10.1093/bioinformatics/btp563Search in Google Scholar PubMed PubMed Central

5. Cameron DL, Jakus J, Pauleta SR, Pettigrew GW, Cooper A. Pressure perturbation calorimetry and the thermodynamics of noncovalent interactions in water: comparison of protein-protein. protein-heme. and cyclodextrin-adamantane complexes. J Phys Chem B 2010;114:16228–35.10.1021/jp107110tSearch in Google Scholar PubMed

6. Bougouffa S, Warwicker J. Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces. BMC Bioinformatics 2008;9:448.10.1186/1471-2105-9-448Search in Google Scholar PubMed PubMed Central

7. Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447–52.10.1073/pnas.0505425102Search in Google Scholar PubMed PubMed Central

8. Ehrlich LP, Nilges M, Wade RC. The impact of protein flexibility on protein-protein docking. Proteins 2005;58:126–33.10.1002/prot.20272Search in Google Scholar PubMed

9. Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate binding primes human tryptophan 2,3-dioxygenase for heme binding. J Phys Chem B 2017;121:7412–20.10.1021/acs.jpcb.7b03463Search in Google Scholar PubMed

10. Falk JE, Phillips JN, Perrin DD, O’Hagan JE. Binding of haem to protein in haemoglobin and myoglobin. Nature 1959;184:1651–2.10.1038/1841651b0Search in Google Scholar PubMed

11. Keilin J. Nature of the haem-binding groups in native and denatured haemoglobin and myoglobin. Nature 1960;187:365–71.10.1038/187365a0Search in Google Scholar PubMed

12. Benesch R. The molecular origin of the control mechanisms in haemoglobin. Bibl Haematol 1968;29:1049–55.10.1159/000384738Search in Google Scholar PubMed

13. Bunn HF, Jandl JH. Exchange of heme among hemoglobins and between haemoglobin and albumin. J Biol Chem 1968;243:465–75.10.1016/S0021-9258(18)93628-8Search in Google Scholar PubMed

14. Krinsky MM, Alexander NM. Thyroid peroxidase. Nature of the heme binding to apoperoxidase. J Biol Chem 1971;246:4755–8.10.1016/S0021-9258(18)62000-9Search in Google Scholar PubMed

15. Nagel RL, Gibson QH, Jenkins T. Heme binding in haemoglobin J Capetown. J Mol Biol 1971;58:643–50.10.1016/0022-2836(71)90029-5Search in Google Scholar PubMed

16. Uchida H, Heystek J, Klapper MH. Effect of structural perturbations on the heme-binding properties of human methemoglobin A. J Biol Chem 1971;246:6843–8.10.1016/S0021-9258(19)45923-1Search in Google Scholar

17. Gersonde K. Interaction between heme group and protein structure. Hamatol Bluttransfus 1972;10:183–90.Search in Google Scholar PubMed

18. Fox JB Jr, Dymicky M, Wasserman AE. Heme-protein-heme interactions. Adv Exp Med Biol 1974;48:97–108.10.1007/978-1-4684-0943-7_5Search in Google Scholar PubMed

19. Caughey WS, Smythe GA, O’Keeffe DH, Maskasky JE, Smith MI. Heme A of cytochrome c oxidase. Structure and properties: comparisons with hemes B, C, and S and derivatives. J Biol Chem 1975;250:7602–22.10.1016/S0021-9258(19)40860-0Search in Google Scholar PubMed

20. Alberding N, Austin RH, Beeson KW, Chan SS, Eisenstein L, Frauenfelder H, et al. Tunneling in heme binding to heme proteins. Science 1976;192:1002–4.10.1126/science.1273579Search in Google Scholar PubMed

21. Goddard WA 3rd, Olafson BD. Theoretical studies of oxygen binding. Ann N Y Acad Sci 1981;367:419–33.10.1111/j.1749-6632.1981.tb50582.xSearch in Google Scholar PubMed

22. Rai J. Mini heme-proteins: designability of structure and diversity of functions. Curr Protein Pept Sci 2017;18:1132–40.10.2174/1389203718666170515144037Search in Google Scholar PubMed

23. Lukin JA, Kontaxis G, Simplaceanu V, Yuan Y, Bax A, Ho C. Quaternary structure of hemoglobin in solution. Proc Natl Acad Sci USA 2003;100:517–20.10.1073/pnas.232715799Search in Google Scholar

24. Swapna LS, Mahajan S, de Brevern AG, Srinivasan N. Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC Struct Biol 2012;12:6.10.1186/1472-6807-12-6Search in Google Scholar PubMed

25. Konieczny L, Brylinski M, Roterman I. Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 2006;6:15–22.Search in Google Scholar PubMed

26. Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17:1477–507.10.3390/e17031477Search in Google Scholar

27. Yi J, Thomas LM, Musayev FN, Safo MK, Richter-Addo GB. Crystallographic trapping of heme loss intermediates during the nitrite-induced degradation of human haemoglobin. Biochemistry 2011;50:8323–32.10.1021/bi2009322Search in Google Scholar PubMed

28. Seixas FA, de Azevedo WF Jr, Colombo MF. Crystallization and x-ray diffraction data analysis of human deoxyhaemoglobin A(0) fully stripped of any anions. Acta Crystallogr D Biol Crystallogr 1999;55(Pt 11):1914–6.10.1107/S0907444999009750Search in Google Scholar

29. Brás NF, Fernandes PA, Ramos MJ. Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complex. Chem Biol Drug Des 2014;83:427–39.10.1111/cbdd.12258Search in Google Scholar PubMed

30. Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J 2007;92:1891–9.10.1529/biophysj.106.092122Search in Google Scholar PubMed

31. Bonet J, Caltabiano G, Khan AK, Johnston MA, Corbí C, Gómez A, et al. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study. Proteins 2006;63:65–77.10.1002/prot.20791Search in Google Scholar PubMed

32. Schreiber G. Kinetic studies of protein-protein interactions. Curr Opin Struct Biol 2002;12:41–7.10.1016/S0959-440X(02)00287-7Search in Google Scholar PubMed

Received: 2017-10-30
Accepted: 2017-11-22
Published Online: 2017-12-23
Published in Print: 2017-12-20

©2017 Walter de Gruyter GmbH, Berlin/Boston

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