Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55-Å Resolution

Shibayama, Naoya; Miura, Shogo; Tame, J.R.H.; Yonetani, Takashi; Park, Sam-Yong

doi:10.1074/jbc.m205461200

Cited by 52 publications

(59 citation statements)

References 34 publications

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“…This observation may be correlated with the effector-induced structural changes found by X-ray crystallography, i.e., shortened distance between the heme-Fe and the distal histidine (27). It should be noted that the structural variation at the ·-heme pocket is also one of the key features associated with the T-R allosteric transition, according to Perutz' stereochemistry model (13).…”

Section: Conformational Fluctuation Of Hbco a Upon Ihp Bindingmentioning

confidence: 93%

Effector-Induced Structural Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States of Hemoglobin

Song

Simplăceanu

et al. 2008

Biochemistry

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The present study reports distinct dynamic consequences for the T-and R-states of human normal adult hemoglobin (Hb A) due to the binding of a heterotropic allosteric effector, inositol hexaphosphate (IHP). A nuclear magnetic resonance (NMR) technique based on modified transverse relaxation optimized spectroscopy (TROSY) has been used to investigate the effect of conformational exchange of Hb A in both deoxy and CO forms, in the absence and presence of IHP, at 14.1 and 21.1 T, and at 37 °C. Our results show that the majority of the polypeptide backbone amino acid residues of deoxy-and carbonmonoxy-forms of Hb A in the absence of IHP is not mobile on the ·s-ms time scale, with the exception of several amino acid residues, that is, · 109Val and · 132Lys in deoxy-Hb A, and R40Lys in HbCO A. The mobility of R40Lys in HbCO A can be explained by the crystallographic data showing that the H-bond between R40Lys and · 146His in deoxy-Hb A is absent in HbCO A. However, the conformational exchange of ·109Val, which is located in the intradimer (R 1 · 1 or R 2 · 2 ) interface, is not consistent with the crystallographic observations that show rigid packing at this site. IHP binding appears to rigidify R40Lys in HbCO A, but does not significantly affect the flexibility of · 109Val in deoxy-Hb A. In the presence of IHP, several amino acid residues, especially those at the interdimer (R 1 · 2 or R 2 · 1 ) interface of HbCO A, exhibit significant conformational exchange. The affected residues include the proximal ·92His in the ·-heme pocket, as well as some other residues located in the flexible joint (·C helix-RFG corner) and switch (RC helix-·FG corner) regions that play an important role in the dimer-dimer rotation of Hb during the oxygenation process. These findings suggest that, upon IHP binding, HbCO A undergoes a conformational fluctuation near the R-state but biased toward the T-state, apparently along the trajectory of its allosteric transition, accompanied by structural fluctuations in the heme pocket of the ·-chain. In contrast, no significant perturbation of the dynamic features on the ms-·s time scale has been observed upon IHP binding to deoxy-Hb A. We propose that the allosteric effector-induced quaternary structural fluctuation may contribute to the reduced ligand affinity of ligated hemoglobin. Conformational exchange mapping of the ·-chain of HbCO A observed at 21.1 T shows significantly increased scatter in the chemical exchange contribution to the transverse relaxation rate (R ex ) values, relative to those at lower fields, due to the enhanced effect of the local chemical shift anisotropy (CSA) fluctuation. A spring-on-scissors model is proposed to interpret the dynamic phenomena induced by the heterotropic effector, IHP.

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Section: Conformational Fluctuation Of Hbco a Upon Ihp Bindingmentioning

confidence: 93%

Effector-Induced Structural Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States of Hemoglobin

Song

Simplăceanu

et al. 2008

Biochemistry

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“…The difficulty of growing good quality crystals of R-state human hemoglobin bound to effectors is well-known [24,25]. To date, the only X-ray structure reported for a R-state Hb bound to an effector is that of horse hemoglobin complexed to BZF [26]. However, the sequence homology of horse and human Hb differs by 18%, hence the appropriateness of a computational approach to investigate the molecular basis of effector binding to HbA.…”

Section: Introductionmentioning

confidence: 99%

R‐state hemoglobin bound to heterotropic effectors: models of the DPG, IHP and RSR13 binding sites

Laberge¹,

Kovesi²,

Yonetani³

et al. 2004

FEBS Letters

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We performed a docking study followed by a 500-ps molecular dynamics simulation of R-state human adult hemoglobin (HbA) complexed to different heterotropic effectors [2,3-diphosphoglycerate (DPG), inositol hexaphosphate (IHP), and 2-[4-[(3,5-dichlorophenylcarbamoyl)-]methyl]-phenoxy]-2-methylpropionic acid (RSR13)) to propose a molecular basis for recently reported interactions of effectors with oxygenated hemoglobin. The simulations were carried out with counterions and explicit solvation. As reported for T-state HbA, the effector binding sites are also located in the central cavity of the R-state and differ depending on effector anionic character. DPG and IHP bind between the a-subunits and the RSR13 site spans the a 1 -, a 2 -and b 2 -subunits. The generated models provide the first report of the molecular details of R-state HbA bound to heterotropic effectors.

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“…These tertiary effects then lead to the detected changes in oxygen association (18,19). Until now, no structural data have been published for the complex of R-state human HbA with allosteric effectors; the only available structure is that of horse HbA complexed to CO (20). Recently, however, a docking and molecular dynamics simulation study in our laboratory (21) proposed models for the structure of HbA bound with the allosteric effectors DPG, IHP, and 2-{4-{(3,5-dichlorophenylcarbamoyl)-{methyl}-phenoxy}-2-methylpropionoc acid.…”

mentioning

confidence: 99%

Allosteric Effectors Influence the Tetramer Stability of Both R- and T-states of Hemoglobin A

Schay

Smeller

Tsuneshige

et al. 2006

Journal of Biological Chemistry

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The contribution of heterotropic effectors to hemoglobin allostery is still not completely understood. With the recently proposed global allostery model, this question acquires crucial significance, because it relates tertiary conformational changes to effector binding in both the R-and T-states. In this context, an important question is how far the induced conformational changes propagate from the binding site(s) of the allosteric effectors. We present a study in which we monitored the interdimeric interface when the effectors such as Cl ؊ , 2,3-diphosphoglycerate, inositol hexaphosphate, and bezafibrate were bound. We studied oxy-Hb and a hybrid form (␣FeO 2 ) 2 -(␤Zn) 2 as the T-state analogue by monitoring heme absorption and Trp intrinsic fluorescence under hydrostatic pressure. We observed a pressure-dependent change in the intrinsic fluorescence, which we attribute to a pressure-induced tetramer to dimer transition with characteristic pressures in the 70 -200-megapascal range. The transition is sensitive to the binding of allosteric effectors. We fitted the data with a simple model for the tetramer-dimer transition and determined the dissociation constants at atmospheric pressure. In the R-state, we observed a stabilizing effect by the allosteric effectors, although in the T-analogue a stronger destabilizing effect was seen. The order of efficiency was the same in both states, but with the opposite trend as inositol hexaphosphate > 2,3-diphosphoglycerate > Cl ؊ . We detected intrinsic fluorescence from bound bezafibrate that introduced uncertainty in the comparison with other effectors. The results support the global allostery model by showing that conformational changes propagate from the effector binding site to the interdimeric interfaces in both quaternary states.Hemoglobin (1) is a tetrameric protein, which plays a vital role in the transport of oxygen. It consists of two dimers of ␣ and ␤ subunits that reversibly bind and release oxygen (1). The description of this cooperative phenomenon has been most frequently derived from the Monod-Wyman-Changeux (MWC) 2 two-state allosteric model (2) that attributes cooperativity to a rapid equilibrium between two conformations of distinct oxygen affinity of the whole tetramer. These distinct states are the fully unliganded T-state and the fully ligated R-state. Szabo and Karplus (3) modified the two-state model incorporating the stereochemical mechanism suggested by Perutz (4) for the T to R switch, and introduced ligation-induced tertiary changes within the T-state. In this extended model (MWC-SK), it was proposed that cooperativity still works through a ligation-induced shift in the equilibrium of states T and R, but the model attributed importance in the conformational switch to certain changes at the inter-and intrasubunit interfaces.

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Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55-Å Resolution

Cited by 52 publications

References 34 publications

Effector-Induced Structural Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States of Hemoglobin

Effector-Induced Structural Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States of Hemoglobin

R‐state hemoglobin bound to heterotropic effectors: models of the DPG, IHP and RSR13 binding sites

Allosteric Effectors Influence the Tetramer Stability of Both R- and T-states of Hemoglobin A

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