Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases

Proteins: Structure, Function and Genetics

Volumn 68, Issue 2, 2007, Pages 480-487

  Martí, Marcelo A ^a   Capece, Luciana ^a   Bikiel, Damián E ^a   Falcone, Bruno ^a   Estrin, Darío A ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

Heme protein; Hydrogen bond; Ligand binding; Molecular dynamics; QM MM; Structure

Indexed keywords

CARBON MONOXIDE; HEMOGLOBIN; LEGHEMOGLOBIN; NITRIC OXIDE; OXYGEN;

ARTICLE; COMPUTER SIMULATION; ENTHALPY; HYDROGEN BOND; MOLECULAR DYNAMICS; MUTATION; NONHUMAN; OXYGEN AFFINITY; PARAMECIUM CAUDATUM; PRIORITY JOURNAL; PROTEIN CONFORMATION; QUANTUM CHEMISTRY; SOYBEAN;

ANIMALS; BINDING SITES; COMPUTER SIMULATION; HEMOGLOBINS; KINETICS; LEGHEMOGLOBIN; MODELS, MOLECULAR; OXYGEN; PARAMECIUM CAUDATUM; PLANT PROTEINS; PROTEIN CONFORMATION; PROTOZOAN PROTEINS; SOYBEANS;

GLYCINE MAX; PARAMECIUM CAUDATUM;

EID: 34250821654     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21454     Document Type: Article

References (36)

1. Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Gough J, Dewilde S, Moens L, Vanfleteren JR. A phylogenomic profile of globins. BMC Evol Biol 2006;6:1-17.
2. Jain R, Chan MK. Mechanisms of ligand discrimination by heme proteins. J Biol Inorg Chem 2003;8:1-11.
3. 2 entry into and exit from myoglobin. J Biol Chem 2001;276:5177-5188.
4. Marti MA, Crespo A, Capece L, Boechi L, Bikiel DE, Scherlis DA, Estrin DA. Dioxygen affinity in heme proteins investigated by computer simulation. J Inorg Biochem 2006;100:761-770.
5. Pesce A, Nardini M, Dewilde S, Geuens E, Yamauchi K, Ascenzi P, Riggs AF, Moens L, Bolognesi M. The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the α-helical globin fold. Structure 2002;10:725-735.
6. 2 affinity in Cerebratulus lacteus mini-hemoglobin. J Biol Chem 2004;279:33662-33672.
7. Milani M, Pesce A, Nardini M, Ouellet H, Ouellet Y, Dewilde S, Bocedi A, Ascenzi P, Guertin M, Moens L, Friedman JM, Wittenberg JB, Bolognesi M. Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins. J Inorg Biochem 2005;99:97-109.
8. Yeh SR, Couture M, Ouellet Y, Guertin M, Rousseau DL. A cooperative oxygen binding hemoglobin from Mycobacterium tuberculosis. Stabilization of heme ligands by a distal tyrosine residue. J Biol Chem 2000;275:1679-1684.
9. Marti MA, Bikiel DE, Crespo A, Nardini M, Bolognesi M, Estrin DA. Two distinct heme distal site states define Cerebratulus lacteus mini-hemoglobin oxygen affinity. Proteins 2006;62:641-648.
10. Kundu S, Trent JT, III, Hargrove MS. Plants, humans and hemoglobins. Trends Plant Sci 2003;8:387-393.
11. Wittenberg JB, Bergersen FJ, Appleby CA, Turner GL. Facilitated oxygen diffusion. The role of leghemoglobin in nitrogen fixation by bacteroids isolated from soybean root nodules. J Biol Chem 1974;249:4057-4066.
12. Hargrove MS, Barry JK, Brucker EA, Berry MB, Phillips GN, Jr, Olson JS, Arredondo-Peter R, Dean JM, Klucas RV, Sarath G. Characterization of recombinant soybean leghemoglobin a and apolar distal histidine mutants. J Mol Biol 1997;266:1032-1042.
13. Kundu S, Blouin GC, Premer SA, Sarath G, Olson JS, Hargrove MS. Tyrosine B10 inhibits stabilization of bound carbon monoxide and oxygen in soybean leghemoglobin. Biochemistry 2004;43:6241-6252.
14. Quillin ML, Arduini RM, Olson JS, Phillips GN, Jr. High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin. J Mol Biol 1993;234:140-155.
15. Das TK, Weber RE, Dewilde S, Wittenberg JB, Wittenberg BA, Yamauchi K, Van Hauwaert ML, Moens L, Rousseau DL. Ligand binding in the ferric and ferrous states of Paramecium hemoglobin. Biochemistry 2000;39:14330-14340.
16. Pesce A, Couture M, Dewilde S, Guertin M, Yamauchi K, Ascenzi P, Moens L, Bolognesi M. A novel two-over-two α-helical sandwich fold is characteristic of the truncated hemoglobin family. EMBO J 2000;19:2424-2434.
17. Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, Ascenzi P, Guertin M, Bolognesi M. Heme-ligand tunneling in group I truncated hemoglobins. J Biol Chem 2004;279:21520-21525.
18. Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem 2003;66:27-85.
19. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, III, DeBolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
20. Berendsen HJC, Postma JPM, Van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
21. Crespo A, Marti MA, Kalko SG, Morreale A, Orozco M, Gelpi JL, Luque FJ, Estrin DA. Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism. J Am Chem Soc 2005;127:4433-4444.
22. Leach AR. Molecular modelling principles and applications, 2nd ed. Edinburgh Gate, England: Pearson Education; 2001.
23. Soler JM, Artacho E, Gale JD, García A, Junquera J, Ordejón P, Sánchez-Portal D. The SIESTA method for ab initio order-N materials simulation. J Phys: Condens Matter 2002;14:2745-2779.
24. Crespo A, Scherlis DA, Marti MA, Ordejón P, Roitberg AE, Estrin DA. A DFT-based QM-MM approach designed for the treatment of large molecular systems: application to chorismate mutase. J Phys Chem B 2003;107:13728-13736.
25. Marti MA, Capece L, Crespo A, Doctorovich F, Estrin DA. Nitric oxide interaction with cytochrome c′ and its relevance to guanylate cyclase. Why does the iron histidine bond break? J Am Chem Soc 2005;127:7721-7728.
26. Capece L, Marti MA, Crespo A, Doctorovich F, Estrin DA. Heme protein oxygen affinity regulation exerted by proximal effects. J Am Chem Soc 2006;128:12455-12461.
27. Marti MA, Scherlis DA, Doctorovich FA, Ordejon P, Estrin DA. Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase. J Biol Inorg Chem 2003;8:595-600.
28. Troullier N, Martins JL. Phys Rev B 1991;43:1993-2006.
29. Louie SG, Froyen S, Cohen ML. Phys Rev B 1982;26:1738-1742.
30. Perdew JP, Burke K, Ernzerhof M. Generalized gradient approximation made simple. Phys Rev Lett 1996;77:3865-3868.
31. Eichinger M, Tavan P, Hutter J, Parrinello M. A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields. J Chem Phys 1999;110:10452-10467.
32. Rovira C, Schulze B, Eichinger M, Evanseck JD, Parrinello M. Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. Biophys J 2001;81:435-445.
33. Moens L, Vanfleteren J, Van De Peer Y, Peeters K, Kapp O, Czeluzniak J, Goodman M, Blaxter M, Vinogradov S. Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. Mol Biol Evol 1996;13:324-333.
34. Couture M, Das TK, Lee HC, Peisach J, Rousseau DL, Wittenberg BA, Wittenberg JB, Guertin M. Chlamydomonas chloroplast ferrous hemoglobin: heme pocket structure and reactions with ligands. J Biol Chem 1999;274:6898-6910.
35. Couture M, Yeh SR, Wittenberg BA, Wittenberg JB, Ouellet Y, Rousseau DL, Guertin M. A cooperative oxygen-binding hemoglobin from Mycobacterium tuberculosis. Proc Natl Acad Sci USA 1999;96:11223-11228.
36. Hvitved AN, Trent JT, III, Premer SA, Hargrove MS. Ligand binding and hexacoordination in Synechocystis hemoglobin. J Biol Chem 2001;276:34714-34721.