Allosteric control in Limulus polyphemus hemocyanin: functional relevance of interactions between hexamers

Hemocyanin of the horseshoe crab Limulus polyphemus is composed of 48 oxygen-binding subunits, which are arranged in eight hexameric building blocks. Allosteric interactions in this oligomeric protein have been examined by measurement of high-precision oxygen-equilibrium curves, using an automated Imai cell. Several models were compared in numerical analysis of the data. A number of conclusions can be drawn with confidence. (1) Oxygen binding by Limulus hemocyanin cannot satisfactorily be described by the two-state MWC model [Monod, J., Wyman, J., & Changeux, J.P. (1965) J. Mol. Biol. 12, 88-118] for allosteric transitions with either the hexamer or dodecamer as the allosteric unit. (2) Of the models tested, the data sets can be best described by an extended MWC model that allows for an equilibrium, within the 48-subunit ensemble, between cooperative hexamers and cooperative dodecamers. The model invokes T and R states for both hexamers (T6 and R6) and dodecamers (T12 and R12). Allosteric effectors modulate oxygen affinity and cooperativity by affecting the R to T equilibria within hexamers and dodecamers and by shifting the equilibria between hexamers and dodecamers. (3) The fitted model parameters show that under most conditions the intersubunit contacts within T-state hexamers are more constrained than those within T-state dodecamers. (4) The oxygen affinities of the hexameric and dodecameric R states are the same, but under all conditions examined the conformation of the fully oxygenated molecule is that of the dodecameric R state. (5) Between pH 7.4 and pH 8.5 the dodecameric T state has a higher affinity for oxygen than the hexameric T state, allowing for "T-state cooperativity".(ABSTRACT TRUNCATED AT 250 WORDS)     

Residues in Cdc42 that specify binding to individual CRIB effector proteins

Cdc42 is a member of the Rho family of small G proteins. Signal transduction events emanating from Cdc42 lead to cytoskeletal rearrangements, cell proliferation, and cell differentiation. Many effector proteins have been identified for Cdc42; however, it is not clear how certain effectors specifically recognize and bind to Cdc42, as opposed to Rac or Rho, or in many cases, which effector controls what cellular events. Mutations were introduced into Cdc42 at residues: Met1, Val8, Phe28, Tyr32, Val33, Thr35, Val36, Phe37, Asp38, Tyr40, Val42, Met45, Ile46, Glu127, Ala130, Asn132, Gln134, Lys135, and Leu174. Measurements were made of their equilibrium binding constants to the Cdc42 binding domains of the CRIB effectors ACK, PAK, and WASP and to the GTPase-activating protein Rho GAP. Generally, mutations in the effector loop have an equally deleterious effect on binding to all CRIB proteins tested, though the F37A mutation resulted in significant selectivity. Residues outside the effector loop were found to be important for binding of Cdc42 to CRIB containing proteins and also to contribute to selectivity. Mutations such as V42A and L174A resulted in large, selective changes in binding to specific CRIB effectors. Neither mutation resulted in alteration in PAK binding, whereas both severely disrupt binding to ACK and only L174A disrupted binding to WASP. These mutations are interpreted using the structures of the Cdc42/ACK and Cdc42/WASP complexes to give insight into how effectors can specifically recognize Cdc42. Those mutations in Cdc42 that inhibit certain interactions, while retaining others, should aid investigations of the role of specific effectors in Cdc42 signaling in vivo.     

A model for L-lactate binding to Cancer magister hemocyanin

L-Lactate raises the oxygen affinity of Cancer magister hemocyanin. The L-lactate analogs, D-lactate, glycolate and 2-methyl-lactate cause smaller increases in an oxygen binding affinity. Other analogs have no detectable effect. These data suggest that L-lactate binds to the hemocyanin at all four positions around the chiral carbon. The carboxyl and hydroxyl groups are required for activity. The protein can only partially distinguish between the methyl group and hydrogen atom.     

Theoretical basis for differential scanning calorimetric analysis of multimeric proteins

A new general equation simulating irreversible DSC transitions of multimeric proteins was developed. The equation put forward here is the result of an improved mathematical re-elaboration of the classical Lumry-Eyring models, where no restrictive a priori assumptions are made on the kinetic constraints of the denaturation process, or on the enthalpy of the final denatured state. In order to test the wide applicability of this new effective theoretical tool, a series of DSC transitions were simulated with the aim of determining the effects of all relevant thermodynamic, kinetic or experimental parameters on the shape of DSC profiles. Moreover, the classical equations used widely in DSC investigations for the calculus in both kinetic parameters and changes of molecularity, were studied in the light of the model developed here, highlighting, in each case, their rather limited applicability. The new approach proposed in this article was applied to study the thermal denaturation of an hexameric protein (Glucosamine-6-phosphate deaminase), putting in evidence the practical applicability of the theoretical equations developed.     

Allosteric models for cooperative polymerization of linear polymers

In the cytoskeleton, unfavorable nucleation steps allow cells to regulate where, when, and how many polymers assemble. Nucleated polymerization is traditionally explained by a model in which multistranded polymers assemble cooperatively, whereas linear, single-stranded polymers do not. Recent data on the assembly of FtsZ, the bacterial homolog of tubulin, do not fit either category. FtsZ can polymerize into single-stranded protofilaments that are stable in the absence of lateral interactions, but that assemble cooperatively. We developed a model for cooperative polymerization that does not require polymers to be multistranded. Instead, a conformational change allows subunits in oligomers to associate with high affinity, whereas a lower-affinity conformation is favored in monomers. We derive equations for calculating polymer concentrations, subunit conformations, and the apparent affinity of subunits for polymer ends. Certain combinations of equilibrium constants produce the sharp critical concentrations characteristic of cooperative polymerization. In these cases, the low-affinity conformation predominates in monomers, whereas virtually all polymers are composed of high-affinity subunits. Our model predicts that the three routes to forming HH dimers all involve unstable intermediates, limiting nucleation. The mathematical framework developed here can represent allosteric assembly systems with a variety of biochemical interpretations, some of which can show cooperativity, and others of which cannot.     

Positive cooperativity in binding carbon monoxide to hemocyanin

The binding of carbon monoxide to hemocyanin from the crab $\text{Scylla serrata}$ has been studied by thin layer optical absorption and front face fluorescence techniques. The binding to the monomeric form is completely noncooperative whereas the binding to the native oligomeric form is found to be weakly but definitely cooperative. An analysis based on the MWC model of the oxygen and carbon monoxide binding curves indicates that the allosteric constant, L, describing the equilibrium between the 2 unligated forms is different for each ligand. This implies that at least 3 allosteric forms are needed to characterize the binding of oxygen and carbon monoxide to this hemocyanin.     

Allosteric interactions between muscarinic agonist binding sites and effector sites demonstrated by the use of bisquaternary pyridinium oximes

Agonist binding to muscarinic receptors from rat brain stem and cerebral cortex was studied using bisquaternary pyridinium oximes for detecting possible interactions between agonist binding sites and sites of the effector guanosine 5' (beta, gamma-imino) triphosphate (Gpp(NH)p) and Co2+. Pretreatment of either brain stem or cortical homogenates with 200 microM 1-(2-hydroxyiminoethylpyridinium) 1-(3-phenylcarboxypyridinium) dimethylether (HGG-12) reduced the affinity of muscarinic agonists. No change was observed in the relative proportions of high (RH) and low (RL) affinity agonist binding sites. However, the oxime affected the processes of interconversion between these sites. Thus, unlike in control membranes, HGG-12 treated brain stem membranes, Gpp(NH)p could not induce conversion of RH to RL, and in cortical membranes Co2+ could not induce conversion of RL to RH. These results suggest that HGG-12 inactivates a component which is involved in both processes of induced-interconversion. Induced-interconversion between RH and RL was not affected in membranes treated with HGG-12 in the presence of carbamylcholine in concentrations at which mainly RH is occupied by the agonist. The occupation of RH by carbamylcholine protected both RH and RL from the effects of the oxime. The possible role of the molecular events involved is discussed.     

Testing models for transport systems dependent on periplasmic binding proteins.

A carrier model in which transport across the cytoplasmic membrane is mediated by a periplasmic binding protein (Krupka, R.M. (1992) Biochim. Biophys. Acta 1110, 1-10) is shown to account for many of the properties of these systems: (i) Michaelis-Menten kinetics; (ii) seemingly irreversible uptake; (iii) the absence of exchange transport and counter-transport; (iv) substrate half-saturation constants that in different systems may be lower or higher than the dissociation constant of the binding protein; (v) the high concentration of the binding protein in the periplasm and its weak association with the membrane component. The binding protein appears to function as a valve or rectifier that permits the substrate to enter the cell, but blocks exit in both the energized and de-energized states. The asymmetry depends on both the abruptness and the extent of the conformational change in the binding protein. Characteristically, these systems build up steep gradients across the membrane, circumstances in which such a valve might be important. In agreement with the mechanism, (a) the binding protein is missing in members of the same family of transporters that function in export of the substrate rather than import; and (b) in Gram-positive organisms, which have no periplasmic space, binding proteins function while anchored to the cytoplasmic membrane.     

Chain-selective isotopic labeling for NMR studies of large multimeric proteins: application to hemoglobin

Multidimensional, multinuclear NMR has the potential to elucidate the mechanisms of allostery and cooperativity in multimeric proteins under near-physiological conditions. However, NMR studies of proteins made up of non-equivalent subunits face the problem of severe resonance overlap, which can prevent the unambiguous assignment of resonances, a necessary step in interpreting the spectra. We report the application of a chain-selective labeling technique, in which one type of subunit is labeled at a time, to carbonmonoxy-hemoglobin A (HbCO A). This labeling method can be used to extend previous resonance assignments of key amino acid residues, which are important to the physiological function of hemoglobin. Among these amino acid residues are the surface histidyls, which account for the majority of the Bohr effect. In the present work, we report the results of two-dimensional heteronuclear multiple quantum coherence (HMQC) experiments performed on recombinant (15)N-labeled HbCO A. In addition to the C2-proton (H epsilon(1)) chemical shifts, these spectra also reveal the corresponding C4-proton (H delta(2)) resonances, correlated with the N epsilon(2) and N delta(1) chemical shifts of all 13 surface histidines per alpha beta dimer. The HMQC spectrum also allows the assignment of the H delta(1), H epsilon(1), and N epsilon(1) resonances of all three tryptophan residues per alpha beta dimer in HbCO A. These results indicate that heteronuclear NMR, used with chain-selective isotopic labeling, can provide resonance assignments of key regions in large, multimeric proteins, suggesting an approach to elucidating the solution structure of hemoglobin, a protein with molecular weight 64.5 kDa.     

Oxygen binding to hemocyanin: a resonance Raman spectroscopic study

Oxygenation of hemocyanin gives rise to resonance Raman peaks at 742 and 282 cm^?1. The 742 cm^?1 peak which is in resonance with the 575 nm charge transfer band shifts to 704 cm^?1 when ¹⁸O₂ is substituted for ¹⁶O₂. Our results establish that the bound oxygen is in the form of peroxide (O₂^2?). The 282 cm^?1 peak which is in resonance with the 340 nm optical transition is insensitive to isotopic substitution, suggesting that the 282 cm^?1 peak corresponds to a vibration involving the magnetically-coupled Cu(II)··Cu(II) centers.     

NMR methods for structural studies of large monomeric and multimeric proteins

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Measuring the effect of ligand binding on the interface stability of multimeric proteins using dynamic light scattering

We have demonstrated that an approach using guanidine hydrochloride at low concentrations to progressively disrupt protein-protein interactions can be quantitated using dynamic light scattering. This approach is sensitive enough to detect ligand-induced changes of subunit-subunit interactions for homo-hexameric glutamate dehydrogenase, allowing ΔΔG of reversible subunit dissociation to be calculated. The use of dynamic light scattering makes this approach generally applicable to soluble proteins to monitor the relative strength of protein-protein interactions with a particular emphasis on assessing the impact of ligand binding on such interfaces.     

Coupling of the oxygen-linked interaction energy for inositol hexakisphosphate and bezafibrate binding to human HbA0

The energetics of signal propagation between different functional domains (i.e. the binding sites for O2, inositol hexakisphospate (IHP), and bezafibrate (BZF)) of human HbA0 was analyzed at different heme ligation states and through the use of a stable, partially heme ligated intermediate. Present data allow three main conclusions to be drawn, and namely: (i) IHP and BZF enhance each others binding as the oxygenation proceeds, the coupling free energy going from close to zero in the deoxy state to -3.4 kJ/mol in the oxygenated form; (ii) the simultaneous presence of IHP and BZF stabilizes the hemoglobin T quaternary structure at very low O2 pressures, but as oxygenation proceeds it does not impair the transition toward the R structure, which indeed occurs also under these conditions; (iii) under room air pressure (i.e. pO2 = 150 torr), IHP and BZF together induce the formation of an asymmetric dioxygenated hemoglobin tetramer, whose features appear reminiscent of those suggested for transition state species (i.e. T- and R-like tertiary conformation(s) within a quaternary R-like structure).     

Tyrosine-phosphorylated bacterial effector proteins: the enemies within

The tyrosine phosphorylation of proteins has a central role during signal transduction in eukaryotes. Recent progress shows that tyrosine phosphorylation is also a common feature of several effector proteins translocated by bacterial type III and type IV secretion systems. The involvement of these secretion systems in disease development is exemplified by a variety of pathogenic processes: pedestal formation (Tir of EPEC and Citrobacter), cell scattering (CagA of Helicobacter), invasion (Tarp of Chlamydia) and possibly proinflammatory responses and cell proliferation (BepD-F of Bartonella). The discovery that different bacterial pathogens use this common strategy to subvert host-cell function suggests that more examples will soon emerge.     

Temperature effects on hemocyanin oxygen binding in an antarctic cephalopod

The functional relevance of oxygen transport by hemocyanin of the Antarctic octopod Megaleledone senoi and of the eurythermal cuttlefish Sepia officinalis was analyzed by continuous and simultaneous recordings of changes in pH and hemocyanin oxygen saturation in whole blood at various temperatures. These data were compared to literature data on other temperate and cold-water cephalopods (octopods and giant squid). In S. officinalis, the oxygen affinity of hemocyanin changed at deltaP50/degrees C = 0.12 kPa (pH 7.4) with increasing temperatures; this is similar to observations in temperate octopods. In M. senoi, thermal sensitivity was much smaller (<0.01 kPa, pH 7.2). Furthermore, M. senoi hemocyanin displayed one of the highest levels of oxygen affinity (P50 < 1 kPa, pH 7.6, 0 degrees C) found so far in cephalopods and a rather low cooperativity (n50 = 1.4 at 0 degrees C). The pH sensitivity of oxygen binding (delta log P50/delta pH) increased with increasing temperature in both the cuttlefish and the Antarctic octopod. At low PO2 (1.0 kPa) and pH (7.2), the presence of a large venous oxygen reserve (43% saturation) insensitive to pH reflects reduced pH sensitivity and high oxygen affinity in M. senoi hemocyanin at 0 degrees C. In S. officinalis, this reserve was 19% at pH 7.4, 20 degrees C, and 1.7 kPa O2, a level still higher than in squid. These findings suggest that the lower metabolic rate of octopods and cuttlefish compared to squid is reflected in less pH-dependent oxygen transport. Results of the hemocyanin analysis for the Antarctic octopod were similar to those reported for Vampyroteuthis--an extremely high oxygen affinity supporting a very low metabolic rate. In contrast to findings in cold-adapted giant squid, the minimized thermal sensitivity of oxygen transport in Antarctic octopods will reduce metabolic scope and thereby contribute to their stenothermality.