Transduction of binding energy into hemoglobin cooperativity

Derivation and numerical profile analysis of a hierarchically formulated microscopic model of hemoglobin oxygen binding

To address complex thermodynamic systems with multiple interacting events, we have developed the concept of hierarchical thermodynamic interactions. In this study, this concept is extended to protein-ligand systems with similar but not identical protein subunits, and applied to the analysis of previously published NMR and UV-vis monitored hemoglobin oxygen binding data. Non-linear regression provided estimated errors for statistically significant parameters, but not for null (zero) valued parameters. A numerical/graphical profiling approach was therefore used to assess confidence intervals and correlations for both the statistically significant and nulled valued parameters in this model. Individual parameters were set to fixed values around their best-fit value, and the subset of statistically significant parameters re-minimized against hemoglobin oxygen binding data. Plots provide a graphical representation of parameter confidence intervals and correlations, and demonstrate how the two different data types - UV-vis and NMR - constrain the range of values for each parameter. This analysis further illustrates the value of hierarchically formulated models for the analysis of complex state systems, and illuminates the complexity of parameter space around the derived minimum microscopic model of hemoglobin oxygen binding.

Allosteric communication pathways and thermal rectification in PDZ-2 protein: a computational study

Allosteric communication in proteins is a fundamental and yet unresolved problem of structural biochemistry. Previous findings, from computational biology ( Ota, N.; Agard, D. A. J. Mol. Biol. 2005 , 351 , 345 - 354 ), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures: heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (∼2.85 Å) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (∼2.60 Å), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science.

Positive cooperativity induces multimodal site and thermodynamic affinity distributions in multivalent proteins

The characterization of the stoichiometric and site-affinity distributions for the reaction of hemoglobin with O(2) and CO is presented as an example of a multivalent receptor system which exhibits positive site-site interactions. The distributions of stoichiometric constants, T(i)(K(i))'s, are obtained assuming that the distribution of site constants, N(k), is known. The importance of these distributions is that they can be directly related to quantities measured experimentally and that they represent affinity distributions for each ligation step. In hemoglobin, positive site-site interactions generate both stoichiometric and site-affinity distributions with complex and previously unrecognized multimodal patterns that are very different from the theoretical distributions obtained in the absence of interactions. These distributions are related to the generation of heterogeneity during the ligand binding process. Experimental binding data show that these complex distributions can be related to the physiological functions of uptake, transport, and release of gaseous ligands by hemoglobin.

Role of redox potential of hemoglobin-based oxygen carriers on methemoglobin reduction by plasma components

A functional requirement for all hemoglobin-based oxygen carriers (HBOCs) is the maintenance of the heme-iron in the reduced state. This is necessary for the reversible binding/release of molecular oxygen and minimization of methemoglobin (Fe+3) formation. Acellular hemoglobins are especially susceptible to oxidation and denaturation. In the absence of the intrinsic reducing systems of the red blood cell, the reduced heme-Fe+2 can be oxidized to form increasing levels of methemoglobin that can give rise to free radicals and oxidative cellular damage. If acellular HBOCs are to be utilized as red cell substitutes for oxygen delivery, these carriers must be stabilized in the plasma, the carrier medium. Normal plasma contains reducing components, such as ascorbic acid and glutathione, that can afford protection to these acellular HBOCs through electron-transfer mediated processes. For these components to provide effective reduction to an HBOC, a favorable reduction potential difference must exist between the reducing agent and the HBOC. Using a modified thin-layer spectroelectrochemical method, a determination of the formal reduction potential (vs. Ag/AgCl) of several oxygen carriers, including monomeric myoglobin, tetrameric HbA and HbS, chemically cross-linked HbXL99alpha, polymerized oxyglobin (FDA approved for canine anemia), and the natural cross-linked polymeric Lumbricus hemoglobin, have been determined. In contrast to the negative formal reduction potentials (-155 to -50 mV) obtained for Mb, HbA, HbS, HbXL99alpha, and oxyglobin, Lumbricus hemoglobin exhibited a positive formal reduction potential (approximately 100 mV). These results may help explain the greater effectiveness of the tested reducing agents to reduce met Lumbricus hemoglobin, compared to the other HBOCs, back to the required reduced form necessary for physiological binding/release of oxygen. Each reducing agent was capable of reducing met Lumbricus hemoglobin to the fully reduced state, although the kinetics of these reactions were different. HbA, HbXL99alpha, and oxyglobin were only partially reduced (10 to 37%) by glutathione, beta-NADH, and ascorbic acid under similar conditions.

The stereochemical mechanism of the cooperative effects in hemoglobin revisited

In 1970, Perutz tried to put the allosteric mechanism of hemoglobin, proposed by Monod, Wyman and Changeux in 1965, on a stereochemical basis. He interpreted their two-state model in terms of an equilibrium between two alternative structures, a tense one (T) with low oxygen affinity, constrained by salt-bridges between the C-termini of the four subunits, and a relaxed one (R) lacking these bridges. The equilibrium was thought to be governed primarily by the positions of the iron atoms relative to the porphyrin: out-of-plane in five-coordinated, high-spin deoxyhemoglobin, and in-plane in six-coordinated, low-spin oxyhemoglobin. The tension exercised by the salt-bridges in the T-structure was to be transmitted to the heme-linked histidines and to restrain the movement of the iron atoms into the porphyrin plane that is necessary for oxygen binding. At the beta-hemes, the distal valine and histidine block the oxygen-combining site in the T-structure; its tension was thought to strengthen that blockage. Finally, Perutz attributed the linearity of proton release with early oxygen uptake to the sequential rupture of salt-bridges in the T-structure and to the accompanying drop in pKa of the weak bases that form part of them. Almost every feature of this mechanism has been disputed, but evidence that has come to light more than 25 years later now shows it to have been substantially correct. That new evidence is reviewed below.

Homotropic activation via the subunit interaction and allosteric symmetry revealed on analysis of hybrid enzymes of L-lactate dehydrogenase

L-Lactate dehydrogenase from Bifidobacterium longum shows homotropic activation by pyruvate as well as heterotropic activation by fructose 1,6-bisphosphate. Hybrid enzymes were produced from the wild-type subunit and a mutant subunit, whose substrate specificity was altered to that of malate dehydrogenase, and separated to analyze the substrate-induced homotropic activation mechanism. Oxamate, a competitive inhibitor of L-lactate dehydrogenase, was used to mimic the substrate-induced activation of the wild-type subunit as "a regulatory subunit." The malate dehydrogenase activity of the mutant subunit as "the catalytic subunit" of the hybrid enzymes was measured, and the activity of the mutant subunit was activated on the addition of oxamate. Thus, we directly observed the inter-subunit homotropic activation transmitted from the wild-type to the mutant subunit. Moreover, "isomeric" hybrid enzymes that have different structural subunit arrangements but identical subunit compositions showed identical kinetic natures. This indicates that the enzyme maintains its subunit symmetry during the allosteric transition.

Allosteric activation of L-lactate dehydrogenase analyzed by hybrid enzymes with effector-sensitive and -insensitive subunits

Subunit-hybrid enzymes of mutant tetrameric L-lactate dehydrogenases from Bifidobacterium longum were studied in an examination of the mechanism of allosteric activation by fructose 1,6-bisphosphate. We earlier developed an in vivo method for subunit hybridization in Escherichia coli and the hybrids formed were a mixture with different subunit compositions. The B. longum hybrids were separated by anion-exchange chromatography with a mutational tag. Hybrids formed between fructose 1,6-bisphosphate-desensitized subunits and wild-type subunits and also between fructose 1, 6-bisphosphate-desensitized subunits and catalytically inactive subunits. Kinetic analyses of the hybrid enzymes showed that (i) those residues from two symmetrically related subunits that constituted the fructose 1,6-bisphosphate-binding site could bind fructose 1,6-bisphosphate and activate the enzyme only if intact, (ii) hybrids with only one functional fructose 1, 6-bisphosphate-binding site were fully sensitive to fructose 1, 6-bisphosphate, but the allosteric equilibrium had shifted partially, and (iii) activation by fructose 1,6-bisphosphate at the fructose 1, 6-bisphosphate-binding site was transmitted to the active sites through a quaternary structural change, not through direct conformational change within a subunit. These results are evidence of the validity of the concerted allosteric model of this enzyme based on T- and R-state structures in the same crystal lattice proposed earlier.

Agonist-specific conformational changes in the yeast alpha-factor pheromone receptor

The yeast alpha-factor pheromone receptor is a member of the G-protein-coupled receptor family. Limited trypsin digestion of yeast membranes was used to investigate ligand-induced conformational changes in this receptor. The agonist, alpha-factor, accelerated cleavage in the third intracellular loop, whereas the antagonist, desTrp1,Ala3-alpha-factor, reduced the cleavage rate. Thus, the enhanced accessibility of the third intracellular loop is specific to the agonist. alpha-Factor inhibited cleavage weakly at a second site near the cytoplasmic terminus of the seventh transmembrane helix, whereas the antagonist showed a stronger inhibition of cleavage at this site and at another site in the C-terminal domain of the receptor. The alpha-factor-induced conformational changes appeared to be inherent properties of the receptor, as they were retained in G-protein-deficient mutants. Moreover, a mutant receptor (ste2-L236H) that affects the third loop and is defective for G-protein coupling retained the ability to undergo the agonist-induced conformational changes. These results are consistent with a model in which G-protein activation is limited by the availability of specific contacts between the G protein and the third intracellular loop of the receptor. The antagonist appears to promote a distinct conformational state that differs from either the unoccupied or the agonist-occupied state.

Nanosecond dynamics of the R-->T transition in hemoglobin: ultraviolet Raman studies

Pulse-probe transient Raman spectroscopy, with probe excitation at 230 nanometers, reveals changes in signals arising from tyrosine and tryptophan residues of the hemoglobin molecule as it moves from the relaxed (R) to the tense (T) state after photodeligation. Signals associated with intersubunit contacts in the T state develop in about 10 microseconds but are preceded by quite different signals, which reach maximum amplitude in about 50 nanoseconds. These signals involve the interior tryptophan residues that bridge the A and E helices by means of H bonds between the indole rings and serine or threonine side chains. Alterations of the H bond strengths, as a result of interhelix motions, can account for the signals. A model is proposed here in which loss of the ligand from the heme binding pocket is concerted with inward motion of the adjacent E helix; this motion, along with a complementary motion of the proximal F helix, transmits the energy associated with heme deligation to the subunit interfaces, leading to the T state rearrangement.