1.25 Å Resolution Crystal Structures of Human Haemoglobin in the Oxy, Deoxy and Carbonmonoxy Forms

Park, Sam-Yong; Yokoyama, Takeshi; Shibayama, Naoya; Shiro, Yoshitsugu; Tame, J.R.H.

doi:10.1016/j.jmb.2006.05.036

Cited by 283 publications

(377 citation statements)

References 68 publications

(69 reference statements)

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“…The other H bond studied spectroscopically, Trp β37-Asp α94, was determined to be formed during the early fast (2-μs time constant) transition phase in the UV measurements (24,25). Although this H bond changes very little in the transition to the R structure in the calculations and in the available X-ray structures (32)(33)(34), the main calculated change occurs during Q2. This result, together with the UV measurements, provides another indication that Q2 happens during the fast phase.…”

Section: Discussionmentioning

confidence: 93%

Unsuspected pathway of the allosteric transition in hemoglobin

Fischer

Olsen

Nam

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Large conformational transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details of the path followed in going from one end structure to the other. For the hemoglobin tetramer, the transition path between the unliganded (T) and tetraoxygenated (R) structures is not known, which limits our understanding of the cooperative mechanism in this classic allosteric system, where both tertiary and quaternary changes are involved. The conjugate peak refinement algorithm is used to compute an unbiased minimum energy path at atomic detail between the two end states. Although the results confirm some of the proposals of Perutz [Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228:726-734], the subunit motions do not follow the textbook description of a simple rotation of one αβ-dimer relative to the other. Instead, the path consists of two sequential quaternary rotations, each involving different subdomains and axes. The quaternary transitions are preceded and followed by phases of tertiary structural changes. The results explain the recent photodissociation measurements, which suggest that the quaternary transition has a fast (2 μs) as well as a slow (20 μs) component and provide a testable model for single molecule FRET experiments.conformational change | cooperativity | domain motion | protein hinges M any proteins undergo large conformational transitions that are essential for their functions (1-3). The transitions can occur in monomers such as the myosin molecular motor (4-6), in multisubunit complexes such as the chaperone GroEL (7), and in systems such as the flagellar motor of bacteria, which is composed of several hundred proteins (8). Probably the most studied example is the T (tense) to R (relaxed) transition in the vertebrate hemoglobin tetramer (Hb) (9-11), for which the conformational transition increases the efficiency of oxygen transport. Hemoglobin, which is composed of two identical α-and two identical β-subunits, is the paradigm for the development of models of cooperativity and allosteric regulation in proteins (9-13). Phenomenologically, the positive cooperativity involves the increase in the affinity for oxygen of unliganded subunits upon the successive binding of oxygen to other subunits. This is achieved by structural changes within subunits (tertiary changes) and between subunits (quaternary changes). Based on the superposition of the crystallographic structures for the deoxy unliganded T state and the fully liganded R state of the protein, the quaternary T → R transition has been described as involving primarily an approximately 15°rotation of one "dimer" (α 1 β 1 ) relative to the other (α 2 β 2 ) around a virtual axis (Fig. 1A) (9, 14). Together with a small relative translation of the αβ-dimers, this reduces the central cavity between the dimers (a channel along the C2 axis of symmetry), where the heterotropic effector 2,3-bisphosphoglycerate is bound in the T state. An important aspect of these structural ch...

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Section: Discussionmentioning

confidence: 93%

Unsuspected pathway of the allosteric transition in hemoglobin

Fischer

Olsen

Nam

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…The crystal structure for 1A3N has recently been refined and its refined structure is known as 2DN2 (21). There are several interesting questions regarding these crystal structures.…”

Section: Implications Of the Present Study For The Structure-functionmentioning

confidence: 99%

“…Thus, HbCO A exhibits a large number of R-type crystal structures, differing in structural detail, depending on a number of factors including the crystallization conditions. There are also several X-ray crystallographic structures for deoxyHb A available in the Protein Data Bank [PDB accession numbers: 1A3N (15), 4HHB (16), 1HGA (17), 1KD2 (18), 1RQ3 (19), 1XXT (6), 1BZ0 (20), 1YHR (6), and 2DN2 (21)], which were crystallized under different temperature, pH, buffer, and salt conditions. A basic assumption in correlating protein structure and function is that the structure of a protein in the crystalline state is the same as that under physiological solution conditions.…”

mentioning

confidence: 99%

Insights into the Solution Structure of Human Deoxyhemoglobin in the Absence and Presence of an Allosteric Effector

et al. 2007

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We present a nuclear magnetic resonance (NMR) study in solution of the structures of human normal hemoglobin (Hb A) in the deoxy or unligated form in the absence and presence of an allosteric effector, inositol hexaphosphate (IHP), using 15 N-1 H residual dipolar coupling (RDC) measurements. There are several published crystal structures for deoxyhemoglobin A (deoxy-Hb A), and it has been reported that the functional properties of Hb A in single crystals are different from those in solution. Carbonmonoxyhemoglobin A (HbCO A) can also be crystallized in several structures. Our recent RDC studies of HbCO A in the absence and presence of IHP have shown that the solution structure of this Hb molecule is distinctly different from its classical crystal structures (R and R2). In order to have a better understanding of the structure-function relationship of Hb A under physiological conditions, we need to evaluate its structures in both ligated and unligated states in solution. Here, the intrinsic paramagnetic property of deoxy-Hb A has been exploited for the measurement of RDCs using the magnetic-field dependence of the apparent one-bond 1 H-15 N Jcouplings. Our RDC analysis suggests that the quaternary and tertiary structures of deoxy-Hb A in solution differ from its recently determined high-resolution crystal structures. Upon binding of IHP, structural changes in deoxy-Hb A are also observed and these changes are largely within the α 1 β 1 (or α 2 β 2 ) dimer itself. These new structural findings allow us to gain a deeper insight into the structure-function relationship of this interesting allosteric protein.Human normal adult hemoglobin (Hb A), a heterotetrameric protein that transports oxygen from the lungs to tissues, has served as an excellent model for investigating the structurefunction relationship in multimeric, allosteric proteins. Hb A consists of four subunits, i.e., two identical α-chains of 141 amino acid residues each and two identical β-chains of 146 amino acid residues each; each subunit contains a heme group leading to a complex with a molecular weight of ~ 64.5 kDa. The heme iron atom undergoes a spin-state change in going from a highspin paramagnetic Fe +2 (S=2) in the deoxy or unligated form to a diamagnetic Fe +2 (S=0) in the ligated form (with O 2 or CO). The oxygenation of Hb A is regulated by interactions between the O 2 -binding sites (homotropic interactions) and interactions between individual amino acid residues in the protein molecule and various solutes (heterotropic interactions). Heterotropic effectors include hydrogen ions, chloride ions, carbon dioxide, inorganic phosphate ions, and organic phosphate ions [e.g., 2,3-bisphosphoglycerate (2,3-BPG) and inositol hexaphosphate (IHP)] and are known to modulate the oxygen affinity of hemoglobin. For reviews on the NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript structure-function relationship on hemoglobin, see (1-3). Allosteric effectors, 2,3-BPG and IHP, exert a significant effect on the oxygen-binding pr...

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“…In the late 1950s, Perutz and colleagues determined the three-dimensional structure of Hb through X-ray crystallography (Perutz 1960;Perutz et al 1960). More recent studies refined this structure to high resolution (Paoli et al 1996;Park et al 2006). In addition, O 2 and other ligand-binding properties have been measured in detail for native Hb and many naturally occurring mutants.…”

Section: Basic Principles Hemoglobin Synthesis Structure and Functionmentioning

confidence: 99%

“…Bunn and Forget note five general mechanisms that destabilize Hbs: amino acid substitutions within the heme pocket, disruption of secondary structure, substitution in the hydrophobic interior of the subunit, amino acid deletions, and elongation of the subunit (Bunn and Forget 1986). More than 75% of Hb is a helical Park et al 2006). This structure is particularly susceptible to disruptions by proline substitutions (Levitt 1981).…”

Section: Selected Variants That Illustrate Important Aspects Of Hemogmentioning

confidence: 99%

Hemoglobin Variants: Biochemical Properties and Clinical Correlates

Thom

Dickson

Gell

et al. 2013

Cold Spring Harbor Perspectives in Medicine

221

182

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Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples.

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1.25 Å Resolution Crystal Structures of Human Haemoglobin in the Oxy, Deoxy and Carbonmonoxy Forms

Cited by 283 publications

References 68 publications

Unsuspected pathway of the allosteric transition in hemoglobin

Unsuspected pathway of the allosteric transition in hemoglobin

Insights into the Solution Structure of Human Deoxyhemoglobin in the Absence and Presence of an Allosteric Effector

Hemoglobin Variants: Biochemical Properties and Clinical Correlates

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