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Effects of active site mutations in haemoglobin I from Lucina pectinata: a molecular dynamic study

By Eunice Ramirez, Anthony Cruz, Diana Rodriguez, Lilen Uchima, Ruth Pietri, Alberto Santana, Juan López-Garriga and Gustavo E. López

Abstract

Haemoglobin I from Lucina pectinata is a monomeric protein consisting of 142 amino acids. Its active site contains a peculiar arrangement of phenylalanine residues (PheB10, PheCD1 and PheE11) and a distal Gln at position E7. Active site mutations at positions B10, E7 and E11 were performed in deoxy haemoglobin I (HbI), followed by 10 ns molecular dynamic simulations. The results showed that the mutations induced changes in domains far from the active site producing more flexible structures than the native HbI. Distance analyses revealed that the heme pocket amino acids at positions E7 and B10 are extremely sensitive to any heme pocket residue mutation. The high flexibility observed by the E7 position suggests an important role in the ligand binding kinetics in ferrous HbI, while both positions play a major role in the ligand stabilisation processes. Furthermore, our results showed that E11Phe plays a pivotal role in protein stability

Topics: Original Article
Publisher: Taylor & Francis
OAI identifier: oai:pubmedcentral.nih.gov:2657002
Provided by: PubMed Central
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    Citations

    1. (1997). Am yoglobins mutant desingned to mimict he oxygen-avid ascaris suum hemoglobin: Elucidation of the distal hydrogen bonding network by solution NMR,B iophys.
    2. andM .B runori, Extended subnanoseconds tructural dynamics of myoglobinr evealedb yL auec rystallography,P roc.
    3. (1995). As mooth particle mesh Ewald method,J .C hem.
    4. (1996). Biomolecular Simulation:
    5. (1999). Cyanide binding to Lucina pectinata haemoglobin Ia nd to sperm whale myoglobin: An X-ray crystallographic study,B iophys.
    6. (1979). Dynamics of ligand binding to heme proteins,J
    7. (2006). Haemoglobin If rom Lucina pectinata:Amodel for distal heme-ligand control,B iochim.
    8. (1991). Haemoglobin of eukaryote/prokaryote symbioses,i n Structurea nd Function
    9. (1990). Haemoglobin of Lucina pectinata bacterials ymbiosis. I. Molecularp roperties, kinetics and equilibria of reactions with ligands,J
    10. (1994). Haemoglobins from bacteria to man: Evolution of different patterns of gene expression,J
    11. Interaction models for water in relation to protein hydration,i n Intermolecular Forces,B
    12. (1995). Interactions amongr esiduesC D3,E 7, E10, and E11i nm yoglobins: Attemptt os imulatet he liganb inding properties of aplysiam yoglobin,B
    13. (2003). Kinetic modulationi nc arbonmonoxy derivatives of truncated haemoglobins: The role of distal heme pocket residues and extended apolar tunnel,J .B iol.
    14. (1997). LINCS: Al inear constraint solver for molecular simulations,
    15. (1989). Mechanisms of ligand recognition in myoglobin ,C hem.
    16. (2005). Molecular dynamics simulation of sperm whale myoglobin:Effects of mutationsand trapped CO on the structure and dynamics of cavities,B iophys.
    17. (1984). Moleculard ynamics with coupling to an external bath,J .C hem.
    18. (1998). Myoglobin and haemoglobin: Role of distal residues in reactions with heme ligands,T rends
    19. (1997). Myoglobin discriminates between O 2 ,N Oa nd CO by electrostatic interaction with the bound ligand,
    20. (2001). Myoglobin-CO conformational substate dynamics: Steric effects of isoleusina 107(G8)
    21. (2002). New insights into thea llosteric mechanism of human haemoglobin from molecular dynamics simulations,B iophys.
    22. (1997). Nonvertebrae haemoglobins: Structural bases for reactivity,P rog.
    23. (2001). Nonvertebrate haemoglobins: Functions and molecular adaptations,P hysiol.
    24. (1983). Oxygen transport in the blood,i n The Biology of the Crustacean: Internal Anatomy and Physiological Regulation
    25. pez-Garriga, Reaction of gaseous ligands with hemoglobin Im utants from Lucina pectinata provide insight into the reduction of Fe III-H2 Si ronc enter in hemeproteins,m anuscripti np reparation
    26. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithmsf or rigid water models,J .C omp.
    27. (1996). Structural bases fors ulfider ecognition in Lucina pectinata haemoglobin
    28. (2005). Structural dynamics of the lac repressor-DNAc omplexr evealed by am ulti scale simulation,P roc.
    29. (2006). Sulfide-binding haemoglobins: Effects of mutations on active-site flexibility,B iophys.
    30. (1997). Swiss-model and the Swiss pdbviewer: An environment for comparative protein modelling,E
    31. (2005). The position 68(E11) side chain in myoglobin regulates ligand capture, bond formation with heme iron, and internal movement into the xenon cavities
    32. (2003). Thec DNA-deriveda mino acid sequence of haemoglobin
    33. (1995). v an derS poel,a nd R. vanD runen, GROMACS: Am essage-passingp arallel moleculard ynamics implementation,C omp.
    34. (1996). VMD –v isual molecular dynamics,J

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