Tetrapyrrole binding affinity of the murine and human p22HBP heme-binding proteins

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 3, 2010, Pages 396-405

  Micaelo, Nuno M ^a,c   Macedo, Anjos L ^b   Goodfellow, Brian J ^a   Félix, Vítor ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

^b UNIVERSIDADE NOVA DE LISBOA   (Portugal)

^c UNIVERSITY OF MINHO   (Portugal)

Author keywords

Binding constant; Docking; Heme binding protein; Molecular dynamics; Tetrapyrrole

Indexed keywords

BINDING ENERGY; DOCKING; MOLECULAR DYNAMICS; PROTEINS;

BINDING CONSTANT; HEME BINDING; MOLECULAR MODELING STUDIES; MOLECULAR RECOGNITION MECHANISM; NONBONDED INTERACTION; PREFERENTIAL SOLVATION; RELATIVE BINDING AFFINITY; TETRAPYRROLES;

PORPHYRINS;

BINDING PROTEIN; COPROPORPHYRIN; HEME; HEME BINDING PROTEIN; IRON PROTOPORPHYRIN IX; PORPHYRIN DERIVATIVE; PROTOPORPHYRIN; TETRAPYRROLE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BIOSYNTHESIS; HUMAN; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; MOUSE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN INTERACTION; SOLVATION; STRUCTURE ANALYSIS;

MURINAE;

EID: 78649506540     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.07.008     Document Type: Article

References (36)

1. Taketani S., Adachi Y., Kohno H., Ikehara S., Tokunaga R., Ishii T. Molecular characterization of a newly identified heme-binding protein induced during differentiation of urine erythroleukemia cells. J. Biol. Chem. 1998, 273:31388-31394.
2. Blackmon B.J., Dailey T.A., Xiao L.C., Dailey H.A. Characterization of a human and mouse tetrapyrrole-binding protein. Arch. Biochem. Biophys. 2002, 407:196-201.
3. Migeotte I., Riboldi E., Franssen J.D., Gregoire F., Loison U., Wittamer V., Detheux M., Robberecht P., Costagliola S., Vassart G., Sozzani S., Parmentier M., Communi D. Identification and characterization of an endogenous chemotactic ligand specific for FPRL2. J. Exp. Med. 2005, 201:83-93.
4. Babusiak M., Man P., Sutak R., Petrak J., Vyoral D. Identification of heme binding protein complexes in murine erythroleukemic cells: study by a novel two-dimensional native separation - liquid chromatography and electrophoresis. Proteomics 2005, 5(2):340-350.
5. Zylka M.J., Reppert S.M. Discovery of a putative heme-binding protein family (SOUL/HBP) by two-tissue suppression subtractive hybridization and database searches. Brain Res. Mol. Brain Res. 1999, 74(1-2):175-181.
6. Sato E., Sagami I., Uchida T., Sato A., Kitagawa T., Igarashi J., Shimizu T. SOUL in mouse eyes is a new hexameric heme-binding protein with characteristic optical absorption, resonance Raman spectral, and heme-binding properties. Biochemistry 2004, 43:14189-14198.
7. Szigeti A, Hocsak E., Rapolti E., Racz B., Boronkai A., Pozsgai E., Debreceni B., Bognar Z., Bellyei S., Sumegi B., Gallyas F., Szigeti A. Facilitation of mitochondrial outer and inner membrane permeabilization and cell death in oxidative stress by a novel Bcl-2 homology 3 domain protein. J. Biol. Chem. 2010, 285(3):2140-2151.
8. Dias J.S., Macedo A.L., Ferreira G.C., Peterson F.C., Volkman B.F., Goodfellow B.J. The first structure from the SOUL/HBP family of heme-binding proteins, murine P22HBP. J. Biol. Chem. 2006, 281:31553-31561.
9. Dias J.S., Macedo A.L., Ferreira G.C., Jeanty N., Taketani S., Goodfellow B.J., Peterson F.C., Volkman B.F. H-1, N-15 and C-13 resonance assignments of the heme-binding protein murine p22HBP. J. Biomol. NMR 2005, 32(4):338-1338.
10. Ryter S.W., Tyrrell R.M. The heme synthesis and degradation pathways: role in oxidant sensitivity - heme oxygenase has both pro- and antioxidant properties. Free Radic. Biol. Med. 2000, 28:289-309.
11. Park S.Y., Yokoyama T., Shibayama N., Shiro Y., Tame J.R.H. 1.25 angstrom resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. J. Mol. Biol. 2006, 360:690-701.
12. DeLano W.L. The PyMOL Molecular Graphics System 2002, Palo Alto, CA, USA. D. Scientific (Ed.).
13. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Gonzalez C., Pople J.A. Gaussian 03, Revision C. 02 2004, Gaussian, Inc., Wallingford, CT.
14. Bayly C.I., Cieplak P., Cornell W.D., Kollman P.A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the RESP model. J. Phys. Chem. 1993, 97:10269-10280.
15. Oostenbrink C., Villa A., Mark A.E., Van Gunsteren W.F. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25:1656-1676.
16. Rappe A.K., Casewit C.J., Colwell K.S., Goddard W.A., Skiff W.M. Uff, a full periodic-table force-field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114:10024-10035.
17. Sali A., Blundell T.L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234:779-815.
18. Laskowski R.A., Macarthur M.W., Moss D.S., Thornton J.M. PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
19. Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K., Goodsell D.S., Olson A.J. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 2009, 30(16):2785-2791.
20. Berendsen H.J.C., van der Spoel D., van Drunen R. GROMACS: a message-passing parallel molecular-dynamics implementation. Comput. Phys. Commun. 1995, 91:43-56.
21. Lindahl E., Hess B., van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7:306-317.
22. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18:1463-1472.
23. Miyamoto S., Kollman P.A. SETTLE: an analytical version of the shake and rattle algorithm for rigid water models. J. Comput. Chem. 1992, 13:952-962.
24. Smith P.E., van Gunsteren W.F. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300K. J. Chem. Phys. 1994, 100:3169-3174.
25. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Dinola A., Haak J.R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81:3684-3690.
26. Gilson M.K., Zhou H.X. Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 2007, 36:21-42.
27. Bashford D. An object-oriented programming suite for electrostatic effects in biological molecules. Scientific Computing in Object-oriented Parallel Environments, ISCOPE97 1997, 233-240. Springer, Berlin. Y. Ishikawa, R.R. Oldehoeft, J.V.W. Reynders, M. Tholburn (Eds.).
28. Demchuk E., Wade R.C. Improving the continuum dielectric approach to calculating pK(a)s of ionizable groups in proteins. J. Phys. Chem. 1996, 100:17373-17387.
29. Mohan V., Davis M.E., Mccammon J.A., Pettitt B.M. Continuum model-calculations of solvation free-energies-accurate evaluation of electrostatic contributions. J. Phys. Chem. 1992, 96:6428-6431.
30. Teixeira V.H., Cunha C.A., Machuqueiro M., Oliveira A.S.F., Victor B.L., Soares C.M., Baptista A.M. On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium. J. Phys. Chem. B 2005, 109:14691-14706.
31. Elcock A.H., Sept D., McCammon J.A. Computer simulation of protein-protein interactions. J. Phys. Chem. B 2001, 105:1504-1518.
32. Schafer H., Mark A.E., van Gunsteren W.F. Absolute entropies from molecular dynamics simulation trajectories. J. Chem. Phys. 2000, 113:7809-7817.
33. Osapay K., Case D.A. A new analysis of proton chemical-shifts in proteins. J. Am. Chem. Soc. 1991, 113:9436-9444.
34. Liu H.L., Zhou H.N., Xing W.M., Zhao H.F., Li S.X., Huang J.F., Bi R.C. 2.6 angstrom resolution crystal structure of the bacterioferritin from Azotobacter vinelandii. FEBS Lett. 2004, 573:93-98.
35. Macedo S., Romao C.V., Mitchell E., Matias P.M., Liu M.Y., Xavier A.V., LeGall J., Teixeira M., Lindley P., Carrondo M.A. The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans. Nat. Struct. Biol. 2003, 10:285-290.
36. Frolow F., Kalb A.J., Yariv J. Structure of a unique twofold symmetrical heme-binding site. Nat. Struct. Biol. 1994, 1:453-460.