Collective Dynamics Underlying Allosteric Transitions in Hemoglobin

PLoS Computational Biology

Volumn 9, Issue 9, 2013, Pages

  Vesper, Martin D ^a   de Groot, Bert L ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHAINS; HYDROGEN BONDS; MOLECULAR DYNAMICS;

ALLOSTERIC MECHANISMS; ALLOSTERIC PROTEINS; ALLOSTERIC TRANSITION; ATOMISTIC LEVELS; CHAIN MOTIONS; COLLECTIVE DYNAMICS; COMPUTATIONAL TECHNIQUE; COOPERATIVITY; DYNAMICS SIMULATION; HAEMOGLOBINS;

HEMOGLOBIN;

HEMOGLOBIN; OXYGEN;

ALLOSTERISM; ARTICLE; ATOM; BINDING SITE; BOHR EFFECT; CHEMICAL REACTION; CONFORMATIONAL TRANSITION; COOPERATION; CRYSTAL STRUCTURE; HYDROGEN BOND; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; OXYGEN AFFINITY; PH; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; PROTEIN TRANSPORT; PROTON TRANSPORT; STRUCTURE ANALYSIS;

ALLOSTERIC REGULATION; HEMOGLOBINS; HISTIDINE; MOLECULAR DYNAMICS SIMULATION;

EID: 84884688109     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003232     Document Type: Article

References (32)

1. Perutz MF, Wilkinson A, Paoli M, Dodson G, (1998) The stereochemical mechanism of the cooperative effects in hemoglobin revisited. Annu Rev Biophys Biomol Struct 27: 1-34.
2. Eaton W, Henry E, Hofrichter J, Bettati S, Viappiani C, et al. (2007) Evolution of allosteric models for hemoglobin. IUBMB Life 59: 586-599.
3. Shadrina MS, English AM, Peslherbe GH, (2012) Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in t-state deoxyhemoglobin. J Am Chem Soc 134: 11177-11184.
4. Lepeshkevich SV, Biziuk SA, Lemeza AM, Dzhagarov BM, (2011) The kinetics of molecular oxygen migration in the isolated α chains of human hemoglobin as revealed by molecular dynamics simulations and laser kinetic spectroscopy. Biochim Biophys Acta 1814: 1279-1288.
5. Ramadas N, Rifkind J, (1999) Molecular Dynamics of Human Methemoglobin: The Transmission of Conformational Information between Subunits in an αβ Dimer. Biophys J 76: 1796-1811.
6. Mouawad L, Perahia D, Robert CH, Guilbert C, (2002) New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations. Biophys J 82: 3224-3245.
7. Hub J, Kubitzki M, de Groot B, (2010) Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation. PLoS Comput Biol 6: e1000774.
8. Fischer S, Olsen KW, Nam K, Karplus M, (2011) Unsuspected pathway of the allosteric transition in hemoglobin. Proc Natl Acad Sci U S A 108: 5608-5613.
9. Yusuff OK, Babalola JO, Bussi G, Raugei S, (2012) Role of the subunit interactions in the conformational transitions in adult human hemoglobin: An explicit solvent molecular dynamics study. J Phys Chem B 116: 11004-11009.
10. Lehmann H, Carrell R, (1969) Variations in the structure of human haemoglobin with particular reference to the unstable haemoglobins. Br Med Bull 25: 14-23.
11. Balakrishnan G, Case M, Pevsner A, Zhao X, Tengroth C, et al. (2004) Time-resolved absorption and UV resonance Raman spectra reveal stepwise formation of T quaternary contacts in the allosteric pathway of hemoglobin. J Mol Biol 340: 843-856.
12. Benesch R, Benesch R, (1961) The chemistry of the Bohr effect. J Biol Chem 236: 405-410.
13. Ho C, Russu I, (1987) How much do we know about the Bohr effect of hemoglobin? Biochemistry 26: 6299-6305.
14. Hub J, de Groot B, (2009) Detection of functional modes in protein dynamics. PLoS Comput Biol 5: e1000480.
15. Krivobokova T, Briones R, Hub J, Munk A, de Groot B, (2012) Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1. Biophys J 103: 786-796.
16. Perutz M, (1965) Structure and function of haemoglobin: I. a tentative atomic model of horse oxyhaemoglobin. J Mol Biol 13: 646- IN2.
17. Fernandez E, Abad-Zapatero C, Olsen K, (2000) Crystal structure of lysβ182-lysβ182 crosslinked hemoglobin: A possible allosteric intermediate. J Mol Biol 296: 1245-1256.
18. Park SY, Shibayama N, Hiraki T, Tame J, (2004) Crystal structures of unliganded and half-liganded human hemoglobinderivatives cross-linked between lys 82β1 and lys 82β2. Biochemistry 43: 8711-8717.
19. Kovalevsky A, Chatake T, Shibayama N, Park S, Ishikawa T, et al. (2010) Direct determination of protonation states of histidine residues in a 2 Å neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect. J Mol Biol 398: 276-291.
20. Wajcman H, Kister J, Galactéros F, Spielvogel A, Lin M, et al. (1996) Hb Montefiore (α126 (H9) Asp→Tyr) High Oxygen Affnity and Loss of Cooperativity Secondary to C-Terminal Disruption. J Biol Chem 271: 22990-22998.
21. Baldwin J, Chothia C, (1979) Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism. J Mol Biol 129: 175-220.
22. MacKerell AD, Banavali N, Foloppe N, (2000) Development and current status of the charmm force field for nucleic acids. Biopolymers 56: 257-265.
23. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65: 712-725.
24. Fermi G, Perutz M, Shaanan B, Fourme R, (1984) The crystal structure of human deoxyhaemoglobin at 1.74 å resolution. J Mol Biol 175: 159-174.
25. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A, et al. (2005) Gromacs: fast, exible, and free. J Comput Chem 26: 1701-1718.
26. Hess B, Kutzner C, Van Der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for highly effcient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4: 435-447.
27. van Gunsteren W, Billeter S, Eising AA, Hünenberger P, Krüger P, et al. (1996) Biomolecular Simulation: The GROMOS96 manual and user guide.
28. Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JR, (2006) 1.25 Å resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. J Mol Biol 360: 690-701.
29. de Groot B, van Aalten D, Scheek R, Amadei A, Vriend G, et al. (1997) Prediction of protein conformational freedom from distance constraints. Proteins 29: 240-251.
30. Blau C, Grubmüller H, (2013) g_contacts: Fast contacts search in biomolecular ensemble data. Computer Physics Communications [epub ahead of print] available: http://www.sciencedirect.com/science/article/pii/S0010465513002464.
31. Reed C, Hampson R, Gordon S, Jones R, Novy M, et al. (1968) Erythrocytosis secondary to increased oxygen affnity of a mutant hemoglobin, hemoglobin kempsey. Blood 31: 623.
32. Bunn H, Wohl R, Bradley T, Cooley M, Gibson Q, (1974) Functional properties of hemoglobin kempsey. J Biol Chem 249: 7402-7409.