A Structural Model for the Kinetic Behavior of Hemoglobin (original) (raw)
Related papers
Conformational kinetics of triligated hemoglobin
Biophysical Journal, 1985
ABSTRACr We have used the method of modulated excitation (Ferrone, F. A., and J. J. Hopfield, 1976, Proc. Natl. Acad. Sci. USA. 73:4497-4501), with an improved apparatus and a revised analytical procedure, to measure the rate of conformational change between the oxy (R) and deoxy (T) conformations of triligated carboxy-hemoglobin A at pH 6.5 and 7.0. We have found the rates to be kRT = 1.2 x I03 s'-and kTR = 3.5 x 103 s' for pH 6.5, while for pH 7.0, kRT = 1.0 X 103 S-l, and kTR 3.0 x 103 s-'. The value for L3, the equilibrium constant between conformations, was virtually unchanged between pH 6.5 and 7.0. While the rates measured here differ from those obtained in the original use of this method, these new rates are fully consistent with the original data when analyzed by the revised procedures presented here. When taken with other kinetic and equilibrium data, our measurements suggest that the transition state between structures is dominated by the behavior of the T quaternary structure. Finally, a spectral feature near the HbCO Soret peak has been observed that we ascribe to an allosteric perturbation of the spectra of the liganded hemes.
Ligand and interfacial dynamics in a homodimeric hemoglobin
Structural Dynamics, 2016
The structural dynamics of dimeric hemoglobin (HbI) from Scapharca inaequivalvis in different ligand-binding states is studied from atomistic simulations on the ls time scale. The intermediates are between the fully ligandbound (R) and ligand-free (T) states. Tertiary structural changes, such as rotation of the side chain of Phe97, breaking of the Lys96-heme salt bridge, and the Fe-Fe separation, are characterized and the water dynamics along the R-T transition is analyzed. All these properties for the intermediates are bracketed by those determined experimentally for the fully ligand-bound and ligand-free proteins, respectively. The dynamics of the two monomers is asymmetric on the 100 ns timescale. Several spontaneous rotations of the Phe97 side chain are observed which suggest a typical time scale of 50-100 ns for this process. Ligand migration pathways include regions between the B/G and C/G helices and, if observed, take place in the 100 ns time scale. V
Ligand binding to heme proteins: II. Transitions in the heme pocket of myoglobin
Biophysical Journal, 1993
Phenomena occurring in the heme pocket after photolysis of carbonmonoxymyoglobin (MbCO) below about 100 K are investigated using temperature-derivative spectroscopy of the infrared absorption bands of CO. MbCO exists in three conformations (A substates) that are distinguished by the stretch bands of the bound CO. We establish connections among the A substates and the substates of the photoproduct (B substates) using Fourier-transform infrared spectroscopy together with kinetic experiments on MbCO solution samples at different pH and on orthorhombic crystals. There is no one-to-one mapping between the A and B substates; in some cases, more than one B substate corresponds to a particular A substate. Rebinding is not simply a reversal of dissociation; transitions between B substates occur before rebinding. We measure the nonequilibrium populations of the B substates after photolysis below 25 K and determine the kinetics of B substate transitions leading to equilibrium. Transitions between B substates occur even at 4 K, whereas those between A substates have only been observed above about 160 K. The transitions between the B substates are nonexponential in time, providing evidence for a distribution of substates. The temperature dependence of the B substate transitions implies that they occur mainly by quantum-mechanical tunneling below 10 K. Taken together, the observations suggest that the transitions between the B substates within the same A substate reflect motions of the CO in the heme pocket and not conformational changes. Geminate rebinding of CO to Mb, monitored in the Soret band, depends on pH. Observation of geminate rebinding to the A substates in the infrared indicates that the pH dependence results from a population shift among the substates and not from a change of the rebinding to an individual A substate. INTRODUCTION1 Myoglobin is a globular protein consisting of 153 amino acids and a heme (Fe-protoporphyrin IX) as the prosthetic group. Textbooks state that the function of Mb is the reversible binding of small ligands such as dioxygen (02) and carbon monoxide (CO) at the heme iron (Stryer, 1988). One could expect such a binding process to be simple. It was indeed originally described as a one-step process (Antonini and Brunori, 1971). Flash photolysis experiments performed over wide ranges in time and temperature imply, however, that the binding process is far from simple (Austin et al., 1975). Four phenomena, in particular, produce complexity: 1. multiple wells along the reaction coordinate, 2. confor-mational substates, 3. protein relaxation after photodissociation, and 4. thermal fluctuations. In the following, we briefly describe how these phenomena affect the ligand binding to myoglobin. Multiple wells along the reaction coordinate In the simplest model, CO in the solvent binds to the heme iron in one step. Flash photolysis data, however, show evidence for multiple processes. A model that describes the salient features of the kinetic data uses three wells (states) along the reaction coordinate, A i± B S.
A quantum-chemical picture of hemoglobin affinity
Proceedings of The National Academy of Sciences, 2007
Understanding the molecular mechanism of hemoglobin cooperativity remains an enduring challenge. Protein forces that control ligand affinity are not directly accessible by experiment. We demonstrate that computational quantum mechanics/molecular mechanics methods can provide reasonable values of ligand binding energies in Hb, and of their dependence on allostery. About 40% of the binding energy differences between the relaxed state and tense state quaternary structures result from strain induced in the heme and its ligands, especially in one of the pyrrole rings. The proximal histidine also contributes significantly, in particular, in the ␣-chains. The remaining energy difference resides in protein contacts, involving residues responsible for locking the quaternary changes. In the ␣-chains, the most important contacts involve the FG corner, at the ''hinge'' region of the ␣12 quaternary interface. The energy differences are spread more evenly among the -chain residues, suggesting greater flexibility for the than for the ␣-chains along the quaternary transition. Despite this chain differentiation, the chains contribute equally to the relaxed substitute state energy difference. Thus, nature has evolved a symmetric response to the quaternary structure change, which is a requirement for maximum cooperativity, via different mechanisms for the two kinds of chains.
Proceedings of The National Academy of Sciences, 1976
Hemoglobin M Milwaukee (β 67E11 Val --> Glu) is a naturally occurring valency hybrid containing two permanently oxidized hemes in the β -chains. In this mutant, the two abnormal β -chains cannot combine with oxygen, whereas the two α -chains are normal and can combine with oxygen cooperatively with a Hill coefficient of approximately 1.3. High-resolution proton nuclear magnetic resonance spectroscopy at 250 MHz has been used to investigate the hyperfine shifted resonances of the abnormal ferric β -chains of Hb M Milwaukee over the spectral region from -30 to -60 parts per million from water at pD 7 and 30 degrees. These resonances are found to change as a function of oxygenation of the normal α -chains in this mutant hemoglobin. The proton resonance spectra of the ferric β -hemes of partially oxygenated Hb M Milwaukee can be described as an appropriately weighted average of the spectra of zero-, singly-, and doubly-oxygenated species. The nuclear magnetic resonance spectrum of the singly-oxygenated species has been calculated by a method employing least-squares analysis of the spectra of partially oxygenated Hb M Milwaukee at several values of oxygen saturation. It is different from that of fully deoxy or fully oxygenated Hb M Milwaukee and cannot be described as an average of the spectra of the fully deoxy and oxy species. These results are not consistent with a two-structure model for the oxygenation of this mutant protein. In view of the similarities between normal adult hemoglobin and Hb M Milwaukee, it is suggested that a two-state concerted allosteric model does not provide an adequate description of the structure-function relationships in normal hemoglobin.
An allosteric model of hemoglobin
Archives of Biochemistry and Biophysics, 1972
One assumption of the Monod, Wyman, and Changeux (MWC) allosteric model of hemoglobin is that the ligand binding energies depend only upon the conformation R or T, and are independent of the degree of ligation. Canonical values of the equilibrium and kinetic constant,s for the R and T forms are obtained from the measurements, mainly by Gibson and Roughton, of the last and first ligands binding to hemoglobin. These values, differing by a factor of ~240 in equilibrium constants, are compared wit.h the values measured for mutant and chemically modified hemoglobins which are frozen in one quaternary structure or another. From these comparisons we conclude that nearly all of the affinity differences between the R and T forms are contributed by t,he quaternary structures and that the parameters for 02 binding are to a first order independent of the degree of ligation. Kinetic and equilibrium constants of t,he mutants, Hemoglobin J Capetown and Chesapeake which appear to be intermediate between the canonical values for the R and T forms are shown to be consistent with those values by postulating an earlier switch from T to R than is observed in HbA, as was originally discussed by Edelstein.
Importance of Many-Body Effects in the Kernel of Hemoglobin for Ligand Binding
Physical Review Letters, 2013
We propose a mechanism for binding of diatomic ligands to heme based on a dynamical orbital selection process. This scenario may be described as bonding determined by local valence fluctuations. We support this model using linear-scaling first-principles calculations, in combination with dynamical mean-field theory, applied to heme, the kernel of the hemoglobin metalloprotein central to human respiration. We find that variations in Hund's exchange coupling induce a reduction of the iron 3d density, with a concomitant increase of valence fluctuations. We discuss the comparison between our computed optical absorption spectra and experimental data, our picture accounting for the observation of optical transitions in the infrared regime, and how the Hund's coupling reduces, by a factor of five, the strong imbalance in the binding energies of heme with CO and O2 ligands. arXiv:1206.0412v2 [cond-mat.str-el]
Proceedings of the National Academy of Sciences, 1986
G. Weber [(1984) Proc. NatI. Acad. Sci. USA 81,[7098][7099][7100][7101][7102] has inferred that the Monod-Wyman-Changeux (MWC) model for ligand binding by hemoglobin would require (contrary to experimental evidence) that increased ligand binding must promote stabilization of a2fi2 tetramers with respect to dissociation into av dimers. Reexamination of the MWC model, however, in the light of general linkage principles and the specific analysis by G. K. Ackers and M. L. Johnson [(1981) J. Mol. Biol. 147, 559-582] shows that the opposite relation must hold, in agreement with experiment. The T form of the tetramer, with low ligand affinity, must be destabilized and progressively dissociates into the high-affinity dimers, designated D, as ligand binding increases. Each ligand molecule bound shifts the standard Gibbs free energy AG2T for the D-T equilibrium by approximately 3 kcal/mol in favor of the dimer. Thus, T must exist in (at least) five AG levels of cooperative free energy as it becomes progressively destabilized by successive binding of ligand molecules. Dissociation of the R tetramer to dimers, in contrast, is independent of the amount of ligand bound, so long as dimers and R-state tetramers possess the same (high) affinity for ligand. While the intrinsic ligand-binding constants of the T and R states (KT and KR) remain unchanged throughout by the postulates of the model, the model should not be regarded as a strictly two-state system in view of the multiple free-energy levels indicated above. The present analysis gives approximate, though not precise, agreement with experimental findings on the dimer-tetramer equilibrium considered by Weber and provides a rationale for interpreting other recent experiments concerning this equilibrium.