Skip to main content
SpringerLink
Log in

Molecular dynamics simulation of a carboxy murine neuroglobin mutated on the proximal side: heme displacement and concomitant rearrangement in loop regions

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Neuroglobin, a member of vertebrate globin family, is distributed primarily in the brain and retina. Considerable evidence has accumulated regarding its unique ligand-binding properties, neural-specific distribution, distinct expression regulation, and possible roles in processes such as neuron protection and enzymatic metabolism. Structurally, neuroglobin enjoys unique features, such as bis-histidyl coordination to heme iron in the absence of exogenous ligand, heme orientational heterogeneity, and a heme sliding mechanism accompanying ligand binding. In the present work, molecular dynamics (MD) simulations were employed to reveal functional and structural information in three carboxyl murine neuroglobin mutants with single point mutations F106Y, F106L and F106I, respectively. The MD simulation indicates a remarkable proximal effect on detectable displacement of heme and a larger tunnel in the protein matrix. In addition, the mutation at F106 confers on the CD region a very sensitive mobility in all three model structures. The dynamic features of neuroglobin demonstrate rearrangement of the inner space and highly active loop regions in solution. These imply that the conserved residue at the G5 site plays a key role in the physiological function of this unusual protein.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Abbreviations

Ngb:

Neuroglobin

Hb:

Hemoglobin

Mb:

Myoglobin

MD:

Molecular dynamics

CO:

Carbon monoxide

F106LNgb:

F106L neuroglobin mutant

NgbCO:

Carboxy neuroglobin

F106YNgbCO:

Carboxy neuroglobin of F106Y mutant

F106LNgbCO:

Carboxy neuroglobin of F106L mutant

F106INgbCO:

Carboxy neuroglobin of F106I mutant

References

  1. Trent JT, Hargrove MS (2002) A ubiquitously expressed human hexacoordinate hemoglobin. J Biol Chem 277(22):19538–19545

    Article  CAS  Google Scholar 

  2. Kugelstadt D, Haberkamp M, Hankeln T, Burmester T (2004) Neuroglobin, cytoglobin, and a novel, eye-specific globin from chicken. Biochem Biophys Res Commun 325(3):719–725

    Article  CAS  Google Scholar 

  3. Roesner A, Fuchs C, Hankeln T, Burmester T (2005) A globin gene of ancient evolutionary origin in lower vertebrates: evidence for two distinct globin families in animals. Mol Biol Evol 22(1):12–20

    Article  CAS  Google Scholar 

  4. Burmester T, Weich B, Reinhardt S, Hankein T (2000) A vertebrate globin expressed in the brain. Nature 407(6803):520–523

    Article  CAS  Google Scholar 

  5. Pesce A, Bolognesi M, Bocedi A, Ascenzi P, Dewilde S, Moens L, Hankeln T, Burmester T (2002) Neuroglobin and cytoglobin—fresh blood for the vertebrate globin family. EMBO Rep 3(12):1146–1151

    Article  CAS  Google Scholar 

  6. Brunori M, Vallone B (2007) Neuroglobin, seven years after. Cell Mol Life Sci 64(10):1259–1268

    Article  CAS  Google Scholar 

  7. Brunori M, Vallone B (2006) A globin for the brain. FASEB J 20(13):2192–2197

    Article  CAS  Google Scholar 

  8. Fuchs C, Burmester T, Hankeln T (2006) The amphibian globin gene repertoire as revealed by the Xenopus genome. Cytogenet Genome Res 112(3–4):296–306

    Article  CAS  Google Scholar 

  9. Geuens E, Brouns I, Flamez D, Dewilde S, Timmermans J-P, Moens L (2003) A globin in the nucleus! J Biol Chem 278(33):30417–30420

    Article  CAS  Google Scholar 

  10. Hankeln T, Ebner B, Fuchs C, Gerlach F, Haberkamp M, Laufs TL, Roesner A, Schmidt M, Weich B, Wystub S, Saaler-Reinhardt S, Reuss S, Bolognesi M, De Sanctis D, Marden MC, Kiger L, Moens L, Dewilde S, Nevo E, Avivi A, Weber RE, Fago A, Burmester T (2005) Neuroglobin and cytoglobin in search of their role in the vertebrate globin family. J Inorg Biochem 99(1):110–119

    Article  CAS  Google Scholar 

  11. Laufs TL, Wystub S, Reuss S, Burmester T, Saaler-Reinhardt S, Hankeln T (2004) Neuron-specific expression of neuroglobin in mammals. Neurosci Lett 362(2):83–86

    Article  CAS  Google Scholar 

  12. Schmidt M, Giessl A, Laufs T, Hankeln T, Wolfrum U, Burmester T (2003) How does the eye breathe? Evidence for neuroglobin-mediated oxygen supply in the mammalian retina. J Biol Chem 278(3):1932–1935

    Article  CAS  Google Scholar 

  13. Sun Y, Jin K, Mao XO, Zhu Y, Greenberg DA (2001) Neuroglobin is up-regulated by and protects neurons from hypoxic-ischemic injury. Proc Natl Acad Sci USA 98(26):15306–15311

    Article  CAS  Google Scholar 

  14. Sun Y, Jin K, Peel A, Mao XO, Xie L, Greenberg DA (2003) Neuroglobin protects the brain from experimental stroke invivo. Proc Natl Acad Sci USA 100(6):3497–3500

    Article  CAS  Google Scholar 

  15. Wolfrum U, Giessl A, Schmidt M, Laufs T, Hankeln T, Burmester T (2003) How does the eye breathe? Evidence for neuroglobin-mediated oxygen supply in the mammalian retina. Invest Ophthalmol Vis Sci 44(5):3266

    Google Scholar 

  16. Brunori M, Giuffre A, Nienhaus K, Nienhaus GU, Scandurra FM, Vallone B (2005) Neuroglobin, nitric oxide, and oxygen: functional pathways and conformational changes. Proc Natl Acad Sci USA 102(24):8483–8488

    Article  CAS  Google Scholar 

  17. Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Guertin M, Gough J, Dewilde S, Moens L, Vanfleteren JR (2005) Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc Natl Acad Sci USA 102(32):11385–11389

    Article  CAS  Google Scholar 

  18. Wittenberg BA, Wittenberg JB (1989) Transport of oxygen in muscle. Annu Rev Physiol 51(1):857–878

    Article  CAS  Google Scholar 

  19. Ostojic J, Sakaguchi DS, de Lathouder Y, Hargrove MS, Trent JT, Kwon YH, Kardon RH, Kuehn MH, Betts DM, Grozdanic S (2006) Neuroglobin and cytoglobin: oxygen-binding proteins in retinal neurons. Invest Ophthalmol Visual Sci 47(3):1016–1023

    Article  Google Scholar 

  20. Burmester T, Hankeln T (2004) Neuroglobin: a respiratory protein of the nervous system. News Physiol Sci 19:110–113

    CAS  Google Scholar 

  21. Fordel E, Thijs L, Moens L, Dewilde S (2007) Neuroglobin and cytoglobin expression in mice—evidence for a correlation with reactive oxygen species scavenging. FEBS J 274(5):1312–1317

    Article  CAS  Google Scholar 

  22. Wakasugi K, Nakano T, Morishima I (2003) Oxidized human neuroglobin acts as a heterotrimeric G alpha protein guanine nucleotide dissociation inhibitor. J Biol Chem 278(38):36505–36512

    Article  CAS  Google Scholar 

  23. Kitatsuji C, Kurogochi M, Nishimura S, Ishimori K, Wakasugi K (2007) Molecular basis of guanine nucleotide dissociation inhibitor activity of human neuroglobin by chemical cross-linking and mass spectrometry. J Mol Biol 368(1):150–160

    Article  CAS  Google Scholar 

  24. Nayak GH, Milton SL, Prentice HM (2007) Neuroglobin is upregulated by hypoxia and anoxia in the brain of the anoxia-tolerant turtle Trachemys scripta. FASEB J 21(6):A924–A924

    Google Scholar 

  25. Yu Z, Fan X, Lo EH, Wang X (2009) Neuroprotective roles and mechanisms of neuroglobin. Neurol Res 31(2):122–127

    Article  CAS  Google Scholar 

  26. Burmester T, Hankeln T (2009) What is the function of neuroglobin? J Exp Biol 212(10):1423–1428

    Article  CAS  Google Scholar 

  27. Zhou GY, Zhou SN, Lou ZY, Zhu CS, Zheng XP, Hu XQ (2008) Translocation and neuroprotective properties of transactivator-of-transcription protein-transduction domain-neuroglobin fusion protein in primary cultured cortical neurons. Biotechnol Appl Biochem 49:25–33

    Article  CAS  Google Scholar 

  28. Liu J, Yu Z, Guo S, Lee SR, Xing C, Zhang C, Gao Y, Nicholls DG, Lo EH, Wang X (2009) Effects of neuroglobin overexpression on mitochondrial function and oxidative stress following hypoxia/reoxygenation in cultured neurons. J Neurosci Res 87(1):164–170

    Article  CAS  Google Scholar 

  29. Yu Z, Liu J, Guo S, Xing C, Zhu H, Yuan JC, Lo EH, Wang X (2008) Neuroglobin-overexpression alters hypoxic response gene expression in primary neuron culture following oxygen glucose deprivation. Stroke 39(2):676–676

    Google Scholar 

  30. Wang XY, Liu JX, Zhu HH, Tejima E, Tsuji K, Murata Y, Atochin DN, Huang PL, Zhang CG, Lo EH (2008) Effects of neuroglobin overexpression on acute brain injury and long-term outcomes after focal cerebral ischemia. Stroke 39(6):1869–1874

    Article  CAS  Google Scholar 

  31. Duong TT, Witting PK, Antao ST, Parry SN, Kennerson M, Lai B, Vogt S, Lay PA, Harris HH (2009) Multiple protective activities of neuroglobin in cultured neuronal cells exposed to hypoxia re-oxygenation injury. J Neurochem 108(5):1143–1154

    Article  CAS  Google Scholar 

  32. Yu Z, Liu J, Guo S, Xing C, Fan X, Ning M, Yuan JC, Lo EH, Wang X (2009) Neuroglobin-overexpression alters hypoxic response gene expression in primary neuron culture following oxygen glucose deprivation. Neuroscience 162(2):396–403

    Article  CAS  Google Scholar 

  33. Pesce A, Dewilde S, Nardini M, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M (2003) Human brain neuroglobin structure reveals a distinct mode of controlling oxygen affinity. Structure 11(9):1087–1095

    Article  CAS  Google Scholar 

  34. Vallone B, Nienhaus K, Matthes A, Brunori M, Nienhaus GU (2004) The structure of carbonmonoxy neuroglobin reveals a heme-sliding mechanism for control of ligand affinity. Proc Natl Acad Sci USA 101(50):17351–17356

    Article  CAS  Google Scholar 

  35. Dewilde S, Kiger L, Burmester T, Hankeln T, Baudin-Creuza V, Aerts T, Marden MC, Caubergs R, Moens L (2001) Biochemical characterization and ligand-binding properties of neuroglobin, a novel member of the globin family. J Biol Chem 276(42):38949–38955

    Article  CAS  Google Scholar 

  36. Hamdane D, Kiger L, Dewilde S, Green BN, Pesce A, Uzan J, Burmester T, Hankeln T, Bolognesi M, Moens L, Marden MC (2003) The redox state of the cell regulates the ligand binding affinity of human neuroglobin and cytoglobin. J Biol Chem 278(51):51713–51721

    Article  CAS  Google Scholar 

  37. Smagghe BJ, Sarath G, Ross E, Hilbert JL, Hargrove MS (2006) Slow ligand binding kinetics dominate ferrous hexacoordinate hemoglobin reactivities and reveal differences between plants and other species. Biochemistry 45(2):561–570

    Article  CAS  Google Scholar 

  38. Trent JT, Watts RA, Hargrove MS (2001) Human neuroglobin, a hexacoordinate hemoglobin that reversibly binds oxygen. J Biol Chem 276(32):30106–30110

    Article  CAS  Google Scholar 

  39. Vallone B, Nienhaus K, Brunori M, Nienhaus GU (2004) The structure of murine neuroglobin: novel pathways for ligand migration and binding. Proteins Struct Funct Bioinformat 56(1):85–92

    Article  CAS  Google Scholar 

  40. Du WH, Syvitski R, Dewilde S, Moens L, La Mar GN (2003) Solution 1H NMR characterization of equilibrium heme orientational disorder with functional consequences in mouse neuroglobin. J Am Chem Soc 125(27):8080–8081

    Article  CAS  Google Scholar 

  41. Du WH, Yin GW, Li YJ, Wei Q, Li J, Fang WH (2007) Ligand binding affinity of cyanide complex of single mutant F106L murine-met-neuroglobin. Chem J Chin U 28(8):1547–1551

    CAS  Google Scholar 

  42. Capece L, Marti MA, Crespo A, Doctorovich F, Estrin DA (2006) Heme protein oxygen affinity regulation exerted by proximal effects. J Am Chem Soc 128(38):12455–12461

    Article  CAS  Google Scholar 

  43. Franzen S, Peterson ES, Brown D, Friedman JM, Thomas MR, Boxer SG (2002) Proximal ligand motions in H93G myoglobin. Eur J Biochem 269(19):4879–4886

    Article  CAS  Google Scholar 

  44. Liong EC, Dou Y, Scott EE, Olson JS, Phillips GN Jr (2001) Waterproofing the heme pocket. role of proximal amino acid side chains in preventing hemin loss from myoglobin. J Biol Chem 276(12):9093–9100

    Article  CAS  Google Scholar 

  45. Adcock SA, McCammon JA (2006) Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 106(5):1589–1615

    Article  CAS  Google Scholar 

  46. Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science 316(5828):1144–1148

    Article  CAS  Google Scholar 

  47. Bret C, Roth M, Norager S, Hatchikian EC, Field MJ (2002) Molecular dynamics study of desulfovibrio africanus cytochrome c3 in oxidized and reduced forms. Biophys J 83(6):3049–3065

    Article  CAS  Google Scholar 

  48. Park H, Lee S, Suh J (2005) Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc 127(39):13634–13642

    Article  CAS  Google Scholar 

  49. Ceccarelli M, Ruggerone P, Anedda R, Fais A, Era B, Sollaino MC, Corda M, Casu M (2006) Structure–function relationship in a variant hemoglobin: a combined computational-experimental approach. Biophys J 91(9):3529–3541

    Article  CAS  Google Scholar 

  50. Henry ER, Levitt M, Eaton WA (1985) Molecular dynamics simulation of photodissociation of carbon monoxide from hemoglobin. Proc Natl Acad Sci USA 82(7):2034–2038

    Article  CAS  Google Scholar 

  51. Bossa C, Amadei A, Daidone I, Anselmi M, Vallone B, Brunori M, Di Nola A (2005) Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Biophys J 89(1):465–474

    Article  CAS  Google Scholar 

  52. Elber R, Karplus M (1987) Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science 235(4786):318–321

    Article  CAS  Google Scholar 

  53. Hummer G, Schotte F, Anfinrud PA (2004) Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations. Proc Natl Acad Sci USA 101(43):15330–15334

    Article  CAS  Google Scholar 

  54. Nadra AD, Marti MA, Pesce A, Bolognesi M, Estrin DA (2008) Exploring the molecular basis of heme coordination in human neuroglobin. Proteins 71(2):695–705

    Article  CAS  Google Scholar 

  55. Anselmi M, Brunori M, Vallone B, Di Nola A (2007) Molecular dynamics simulation of deoxy and carboxy murine neuroglobin in water. Biophys J 93(2):434–441

    Article  CAS  Google Scholar 

  56. Anselmi M, Brunori M, Vallone B, Di Nola A (2008) Molecular dynamics simulation of the neuroglobin crystal: comparison with the simulation in solution. Biophys J 95(9):4157–4162

    Article  CAS  Google Scholar 

  57. Tripos, International. SYBYL 7.3. St. Louis, MO

  58. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1996) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 118(9):2309–2309

    Article  CAS  Google Scholar 

  59. TAD CDA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9. University of California, San Francisco

    Google Scholar 

  60. Giammona DA (1984) An examination of conformational flexibility in porphyrins and bulky-ligand binding in myoglobin. University of California, Davis, CA

    Google Scholar 

  61. Wu XW, Brooks BR (2003) Self-guided Langevin dynamics simulation method. Chem Phys Lett 381(3–4):512–518

    Article  CAS  Google Scholar 

  62. Nutt DR, Meuwly M (2004) CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function. Proc Natl Acad Sci USA 101(16):5998–6002

    Article  CAS  Google Scholar 

  63. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23(3):327–341

    Article  CAS  Google Scholar 

  64. Hata M, Hirano Y, Hoshino T, Tsuda M (2001) Monooxygenation mechanism by cytochrome P-450. J Am Chem Soc 123(26):6410–6416

    Article  CAS  Google Scholar 

  65. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81(8):3684–3690

    Article  CAS  Google Scholar 

  66. Koradi R, Billeter M, Wuthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 14(1):51–55 29–32

    Article  CAS  Google Scholar 

  67. Laskowski RA (1995) Surfnet—a program for visualizing molecular-surfaces, cavities, and intermolecular interactions. J Mol Graphics 13(5):323–330 307–328

    Article  CAS  Google Scholar 

  68. Tilton RF, Kuntz ID, Petsko GA (1984) Cavities in proteins: structure of a metmyoglobin xenon complex solved to 1.9 Å. Biochemistry 23(13):2849–2857

    Article  CAS  Google Scholar 

  69. Bossa C, Anselmi M, Roccatano D, Amadei A, Vallone B, Brunori M, Di Nola A (2004) Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Biophys J 86(6):3855–3862

    Article  CAS  Google Scholar 

  70. Orlowski S, Nowak W (2007) Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. J Mol Model 13(6–7):715–723

    Article  CAS  Google Scholar 

  71. Springer BA, Sligar SG, Olson JS, Phillips GN (1994) Mechanisms of ligand recognition in myoglobin. Chem Rev 94(3):699–714

    Article  CAS  Google Scholar 

  72. Shelnutt JA, Rousseau DL, Friedman JM, Simon SR (1979) Protein–heme interaction in hemoglobin: evidence from Raman difference spectroscopy. Proc Natl Acad Sci USA 76(9):4409–4413

    Article  CAS  Google Scholar 

  73. Guallar V, Jarzecki AA, Friesner RA, Spiro TG (2006) Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. J Am Chem Soc 128(16):5427–5435

    Article  CAS  Google Scholar 

  74. Draghi F, Miele AE, Travaglini-Allocatelli C, Vallone B, Brunori M, Gibson QH, Olson JS (2002) Controlling ligand binding in myoglobin by mutagenesis. J Biol Chem 277(9):7509–7519

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We thank Prof. Roman Laskowski at European Bioinformatics Institute (Cambridge, UK) for providing the Surfnet software and for helpful discussion. This work was supported by grants from the National Natural Science Foundation of China No. 20473013 and No. 20633080, as well as the National Basic Research Program of China (No. 2004CB719900).

Author information

Authors and Affiliations

  1. Department of Chemistry, Renmin University of China, Beijing, 100872, China

    Jia Xu, Guowei Yin, Feijuan Huang & Weihong Du

  2. Institute of Physical Chemistry, Peking University, Beijing, 100871, China

    Baohuai Wang

Authors
  1. Jia Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guowei Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Feijuan Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Baohuai Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Weihong Du
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Weihong Du.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1

Root-mean-square deviation (RMSD) of the control NgbCO (a), NgbF106YCO (b), NgbF106LCO (c), and NgbF106ICO (d). (DOC 140 kb)

Fig. S2

The orientation angle between His96(F8) ring plane and heme in NgbCO (a), F106YNgbCO (b), F106LNgbCO(c), and F106INgbCO (d). (DOC 138 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xu, J., Yin, G., Huang, F. et al. Molecular dynamics simulation of a carboxy murine neuroglobin mutated on the proximal side: heme displacement and concomitant rearrangement in loop regions. J Mol Model 16, 759–770 (2010). https://doi.org/10.1007/s00894-009-0581-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-009-0581-3

Keywords

Search

Navigation