T state hemoglobin binds oxygen noncooperatively with allosteric effects of protons, inositol hexaphosphate, and chloride

Unfolding time distribution of GFP by single molecule fluorescence spectroscopy

We have studied the unfolding of single molecules of GFP-mut2 mutant trapped in wet silica gels in a wide range of GuHCl concentration. After the addition of denaturant, the number of fluorescent molecules decreases with unfolding rates (of the order of 0.01 min(-1)) that are in very good agreement with bulk fluorescence and circular dichroism data. Unexpectedly, single molecule experiments show rare fluctuations in the number of fluorescent proteins at equilibrium. On the other hand, although a first approximate description of the number decays can be reasonably performed by single exponential functions, the distributions of the single molecule unfolding times show a maximum at times congruent with 50-100 min up to the denaturation midpoint concentration of [GuHCl] congruent with 2.5 M. A theoretical analysis of the distributions indicates that this feature is a fingerprint of the competition between unfolding and refolding processes when the protein is very far from the midpoint denaturant concentration.

Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy

Spectrally resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and -hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of approximately 100 fs to several picoseconds, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to that of aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of picoseconds), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to that in aqueous solutions. A comparison of the sol-gel experimental results to viscosity-dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel-encapsulated MbCO exhibits dynamics that are the equivalent of the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.

Modulation of reactivity and conformation within the T-quaternary state of human hemoglobin: the combined use of mutagenesis and sol-gel encapsulation

A range of conformationally distinct functional states within the T quaternary state of hemoglobin are accessed and probed using a combination of mutagenesis and sol-gel encapsulation that greatly slow or eliminate the T --> R transition. Visible and UV resonance Raman spectroscopy are used to probe the proximal strain at the heme and the status of the alpha(1)beta(2) interface, respectively, whereas CO geminate and bimolecular recombination traces in conjunction with MEM (maximum entropy method) analysis of kinetic populations are used to identify functionally distinct T-state populations. The mutants used in this study are Hb(Nbeta102A) and the alpha99-alpha99 cross-linked derivative of Hb(Wbeta37E). The former mutant, which binds oxygen noncooperatively with very low affinity, is used to access low-affinity ligated T-state conformations, whereas the latter mutant is used to access the high-affinity end of the distribution of T-state conformations. A pattern emerges within the T state in which ligand reactivity increases as both the proximal strain and the alpha(1)beta(2) interface interactions are progressively lessened after ligand binding to the deoxy T-state species. The ligation and effector-dependent interplay between the heme environment and the stability of the Trp beta37 cluster in the hinge region of the alpha(1)beta(2) interface appears to determine the distribution of the ligated T-state species generated upon ligand binding. A qualitative model is presented, suggesting that different T quaternary structures modulate the stability of different alphabeta dimer conformations within the tetramer.

Exploring the pyridoxal 5′-phosphate-dependent enzymes

Pyridoxal 5'-phosphate (PLP)-dependent enzymes represent about 4% of the enzymes classified by the Enzyme Commission. The versatility of PLP in carrying out a large variety of reactions exploiting the electron sink effect of the pyridine ring, the conformational changes accompanying the chemical steps and stabilizing distinct catalytic intermediates, and the spectral properties of the different coenzyme-substrate derivatives signaling the reaction progress, are some of the features that have attracted our interest to investigate the structure-dynamics-function relationships of PLP-dependent enzymes. To this goal, an integrated approach combining biochemical, biophysical, computational, and molecular biology methods was used. The extensive work carried out on two enzymes, tryptophan synthase and O-acetylserine sulfhydrylase, is presented and discussed as representative of other PLP-dependent enzymes we have investigated. Finally, perspectives of PLP-dependent enzymes functional genomics and drug targeting highlight the continuous novelty of an "old" class of enzymes.

Effect of sol–gel encapsulation on the unfolding of ferric horse heart cytochrome c

Electronic absorption and resonance Raman spectra of ferric cytochrome c embedded in wet silica gels, in the presence of guanidine HCl as unfolding agent, between pH 0.35 and 7.0 are presented. The data clearly show that the ferric form of the protein encapsulated in sol-gel preserves its active site conformation. However, the spectra of the unfolded embedded protein are different from the corresponding spectra in solution suggesting that a strong interaction between the protein and the sol-gel takes place upon unfolding. The unfolding process mainly depends on the interaction between the exposed positive charges of the unfolded protein and the negatively charged functional groups of the silica surfaces. While this interaction partially stabilizes the protein in its native structure even at very acidic pH, in the presence of denaturants it has the opposite effect, causing mainly the weakening of both the heme-protein and the heme-ligand interactions.

Spectroscopic markers of the T<-->R quaternary transition in human hemoglobin

In this work, we use a sol-gel protocol to trap and compare the R and T quaternary states of both the deoxygenated (deoxyHb) and carbonmonoxide (HbCO) derivatives of human hemoglobin. The near infrared optical absorption band III and the infrared CO stretching band are used to detect the effect of quaternary structure on the spectral properties of deoxyHb and HbCO; comparison with myoglobin allows for an assessment of tertiary and quaternary contributions to the measured band shifts. The R<-->T transition is shown to cause a blue shift of the band III by approximately 35 cm(-1) for deoxyHb and a red shift of the CO stretching band by only approximately 0.3 cm(-1) for HbCO. This clearly shows that quaternary structure changes are transmitted to the heme pocket and that effects on deoxyHb are much larger than on HbCO, at least as far as the band energies are concerned. Experiments performed in the ample temperature interval of 300-10K show that the above quaternary structure effects are "static" and do not influence the dynamic properties of the heme pocket, at least as probed by the temperature dependence of band III and of the CO stretching band. The availability of quaternary structure sensitive spectroscopic markers and the quantitative measurement of the quaternary structure contribution to band shifts will be of considerable help in the analysis of flash-photolysis experiments on hemoglobin. Moreover, it will enable one to characterize the dynamic properties of functionally relevant hemoglobin intermediates and to study the kinetics of both the T-->R and R-->T quaternary transitions through time-resolved spectroscopy.

Tracking unfolding and refolding of single GFPmut2 molecules

The unfolding and refolding kinetics of >600 single GFPmut2 molecules, entrapped in wet nanoporous silica gels, were followed by monitoring simultaneously the fluorescence emission of the anionic and neutral state of the chromophore, primed by two-photon excitation. The rate of unfolding, induced by guanidinium chloride, was determined by counting the number of single molecules that disappear in fluorescence images, under conditions that do not cause bleaching or photoinduced conversion between chromophore protonation states. The unfolding rate is of the order of 0.01 min(-1), and its dependence on denaturant concentration is very similar to that previously reported for high protein load gels. Upon rinsing the gels with denaturant-free buffer, the GFPmut2 molecules refold with rates >10 min(-1), with an apparently random distribution between neutral and anionic states, that can be very different from the preunfolding equilibrium. A subsequent very slow (lifetime of approximately 70 min) relaxation leads to the equilibrium distribution of the protonation states. This mechanism, involving one or more native-like refolding intermediates, is likely rate limited by conformational rearrangements that are undetectable in circular dichroism experiments. Several unfolding/refolding cycles can be followed on the same molecules, indicating full reversibility of the process and, noticeably, a bias of denaturated molecules toward refolding in the original protonation state.

Confinement and crowding effects on tryptophan synthase alpha2beta2 complex

Biological molecules experience in vivo a highly crowded environment. The investigation of the functional properties of the tryptophan synthase alpha(2)beta(2) complex either entrapped in wet nanoporous silica gels or in the presence of the crowding agents dextran 70 and ficoll 70 indicates that the rates of the conformational transitions associated to catalysis and regulation are reduced, and an open and less catalytically active conformation is stabilized.

Cross-linking with O-raffinose lowers oxygen affinity and stabilizes haemoglobin in a non-cooperative T-state conformation

O-R-polyHbA(0) is an intra- and intermolecularly O-raffinose cross-linked derivative of deoxygenated human haemoglobin developed as an oxygen therapeutic. When compared with its native protein (HbA(0)), O-R-polyHbA(0) was found to be locked in the T (tense) quaternary conformation with a lower oxygen affinity, a reduced Bohr effect (50% of HbA(0)) and no measurable cooperativity (h=1). The kinetics of oxygen and CO binding to the protein indicate lower 'on' rates and faster 'off' rates than HbA(0) and the absence of effects of inositol hexaphosphate (IHP) on the kinetics. Other properties consistent with a T-like conformation are inaccessibility of the betaCys-93 thiol group of O-R-polyHbA(0), the hyperfine splitting from nitrogen in the EPR spectrum of the Fe(II)NO complex of O-R-polyHbA(0) and decreased flexibility in the distal haem pocket, as indicated by low-spin bis-histidine complexes detected by EPR of oxidized chains. A comparison of the properties of O-R-polyHbA(0) with those of HbA(0) with and without IHP, as well as the reaction of nitrite with deoxygenated haemoglobin, provide additional insights into the variations in the conformation of T-state haemoglobin in solution (modifications of the T state produced by adding organic phosphates, like IHP and 2,3-diphosphoglycerate). Although the physiological ramifications of locking HbA(0) in the T conformation with the O-raffinose are still unknown, valuable insights into haemoglobin function are provided by these studies of O-R-polyHbA(0).

Unfolding of Green Fluorescent Protein mut2 in wet nanoporous silica gels

Many of the effects exerted on protein structure, stability, and dynamics by molecular crowding and confinement in the cellular environment can be mimicked by encapsulation in polymeric matrices. We have compared the stability and unfolding kinetics of a highly fluorescent mutant of Green Fluorescent Protein, GFPmut2, in solution and in wet, nanoporous silica gels. In the absence of denaturant, encapsulation does not induce any observable change in the circular dichroism and fluorescence emission spectra of GFPmut2. In solution, the unfolding induced by guanidinium chloride is well described by a thermodynamic and kinetic two-state process. In the gel, biphasic unfolding kinetics reveal that at least two alternative conformations of the native protein are significantly populated. The relative rates for the unfolding of each conformer differ by almost two orders of magnitude. The slower rate, once extrapolated to native solvent conditions, superimposes to that of the single unfolding phase observed in solution. Differences in the dependence on denaturant concentration are consistent with restrictions opposed by the gel to possibly expanded transition states and to the conformational entropy of the denatured ensemble. The observed behavior highlights the significance of investigating protein function and stability in different environments to uncover structural and dynamic properties that can escape detection in dilute solution, but might be relevant for proteins in vivo.

Single molecule spectroscopic characterization of GFP-MUT2 mutant for two-photon microscopy applications

Green Fluorescent Protein (GFP) mutants are extensively used in optical microscopy studies of in vivo biological processes in cells. Nonetheless, blinking and bleaching of the GFP chromophore at the single molecule level greatly limits its usefulness. We have worked out what we think are the best experimental conditions for the use of the GFP mutant, GFP-mut2, as a single molecule marker in two-photon excitation measurements. We have measured molecular brightness, excited state lifetime, blinking and photo-bleaching times versus the two-photon excitation intensity on proteins embedded in silica gel matrices versus the excitation wavelength in the range 700-1,000 nm. Our results indicate that GFPmut2 can be employed as a long-lived reporter of biological processes.

Tyrosine phenol-lyase and tryptophan indole-lyase encapsulated in wet nanoporous silica gels: Selective stabilization of tertiary conformations

The pyridoxal 5'-phosphate-dependent enzymes tyrosine phenol-lyase and tryptophan indole-lyase were encapsulated in wet nanoporous silica gels, a powerful method to selectively stabilize tertiary and quaternary protein conformations and to develop bioreactors and biosensors. A comparison of the enzyme reactivity in silica gels and in solution was carried out by determining equilibrium and kinetic parameters, exploiting the distinct spectral properties of catalytic intermediates and reaction products. The encapsulated enzymes exhibit altered distributions of ketoenamine and enolimine tautomers, increased values of inhibitors dissociation constants, slow attaining of steady-state in the presence of substrate and substrate analogs, modified steady-state distribution of catalytic intermediates, and a sixfold-eightfold decrease of specific activities. This behavior can be rationalized by a reduced conformational flexibility for the encapsulated enzymes and a selective stabilization of either the open (inactive) or the closed (active) form of the enzymes. Despite very similar structures and catalytic mechanisms, the influence of encapsulation is more pronounced for tyrosine phenol-lyase than tryptophan indole-lyase. This finding indicates that subtle structural and dynamic differences can lead to distinct interactions of the protein with the gel matrix.

New insights into allosteric mechanisms from trapping unstable protein conformations in silica gels

To understand why the classical two-state allosteric model of Monod, Wyman, and Changeux explains cooperative oxygen binding by hemoglobin but does not explain changes in oxygen affinity by allosteric inhibitors, we have investigated the kinetic properties of unstable conformations transiently trapped by encapsulation in silica gels. Conformational trapping reveals that after nanosecond photodissociation of carbon monoxide a large fraction of the subunits of the T quaternary structure has kinetic properties almost identical to those of subunits of the R quaternary structure. Addition of allosteric inhibitors reduces both the fraction of R-like subunits and the oxygen affinity of the T quaternary structure. These kinetic and equilibrium results are readily explained by a recently proposed generalization of the Monod-Wyman-Changeux model in which a pre-equilibrium between two functionally different tertiary, rather than quaternary, conformations plays the central role.

Viscosity-dependent Relaxation Significantly Modulates the Kinetics of CO Recombination in the Truncated Hemoglobin TrHbN from Mycobacterium tuberculosis

Kinetic traces were generated for the nanosecond and slower rebinding of photodissociated CO to trHbN in solution and in porous sol-gel matrices as a function of viscosity, conformation, and mutation. TrHbN is one of the two truncated hemoglobins from Mycobacterium tuberculosis. The kinetic traces were analyzed in terms of three distinct phases. These three phases are ascribed to rebinding: (i) from the distal heme pocket, (ii) from the adjacent apolar tunnel prior to conformational relaxation, and (iii) from the apolar tunnel subsequent to conformational relaxation. The fractional content of each of these phases was shown to be a function of the viscosity and, in the case of the sol-gel-encapsulated samples, sample preparation history. The observed kinetic patterns support a model consisting of the following elements: (i) the viscosity and conformation-sensitive dynamics of the Tyr(B10) side chain facilitate diffusion of the dissociated ligand from the distal heme pocket into the adjacent tunnel; (ii) the distal heme pocket architecture determines ligand access from the tunnel back to the heme iron; (iii) the distal heme pocket architecture is governed by a ligand-dependent hydrogen bonding network that limits the range of accessible side chain positions; and (iv) the apolar tunnel linking the heme site to the solvent biases the competition between water and ligand for occupancy of the vacated polar distal heme pocket greatly toward the nonpolar ligand. Implications of these finding with respect to biological function are discussed.

Ferricytochrome c encapsulated in silica nanoparticles: Structural stability and functional properties

Using a modified sol-gel technique, we have succeeded in encapsulating ferric cytochrome c in silica nanoparticles obtained from hydrolysis and polycondensation of tetramethylorthosilicate. Particles dimensions have been determined with dynamic light scattering; this technique yields an hydrodynamic radius of about 100 nm, each nanoparticle containing about 10(2)-10(3) proteins. If stored in the cold at low ionic strength, nanoparticles are stable for more than one week, even if a slow radius increase with time is observed. CD measurements show that encapsulated proteins exhibit substantially increased stability against guanidinium hydrochloride induced denaturation. Reduction kinetics of encapsulated ferric cytochrome c by sodium dithionite, measured with standard stopped flow techniques, are slower by a factor of ten with respect to those measured in solution. Analogous experiments with myoglobin suggest that this slowing down is due to the diffusion time of dithionite within the silica matrix. Indeed, if a smaller ligand like CO is used, the intrinsic kinetic properties of encapsulated proteins are found to be unaltered even in the millisecond time range. The reported data show that our nanoparticles are extremely useful both for basic research, to study the stability and functions of encapsulated proteins, and for their potential biotechnological applications.

Distal heme pocket conformers of carbonmonoxy derivatives of Ascaris hemoglobin: evidence of conformational trapping in porous sol-gel matrices

We report the ligand dependence of the conformer distribution in the distal heme pocket of Ascaris suum hemoglobin (Hb) studied by resonance Raman spectroscopy. The heme-bound CO is used as a spectroscopic antenna to probe the original distribution of conformers in the dioxygen derivative of Ascaris Hb, by utilizing sol-gel encapsulation. The first step is to encapsulate the dioxygen derivative in the porous sol-gel and let the gel age, thus trapping the equilibrium conformational distribution of Ascaris dioxygen Hb. In the second step, the dioxygen ligand is replaced by CO. The sol-gel environment impedes any large scale movements, drastically slowing down the conformational relaxation triggered by the ligation change, essentially "locking in" the initial quaternary and even tertiary structure of the protein. Studying the Fe-CO frequencies of the latter sample allows evaluation of the distribution of the distal heme pocket conformers that was originally associated with the dioxygen derivative. Extending the study to the Ascaris mutants allows for examination of the effect of specific residues in the distal pocket on the conformational distribution. The choice of mutants was largely based on the anticipated variation in hydrogen bonding patterns. The results show that the sol-gel encapsulation can slow or prevent re-equilibration within the distal heme pocket of Ascaris Hb and that the distribution of distal heme pocket conformers for the CO derivative of Ascaris Hb in the sol-gel is highly dependent on the history of the sample. Additionally, we report a detailed study of the CO complex of the mutants in solution for assignment of the various heme pocket conformers, and we present a comparison of the sol-gel data with solution data. The results support a picture in which the dioxygen derivative biases the population strongly toward a tightly packed configuration that favors the network of strong hydrogen bonding interactions, and suggest that Ascaris Hb is uniquely designed for dioxygen capture.

Structure and dynamics of proteins encapsulated in silica hydrogels by Trp phosphorescence

This report establishes the conditions for monitoring the intrinsic Trp phosphorescence of proteins encapsulated in silica hydrogels and demonstrates the usefulness of the delayed emission for examining potential perturbations of protein structure-dynamics by the silica matrix. Phosphorescence measurements were conducted both in low temperature (140 K) glasses and at ambient temperature on the proteins apo- and Cd-azurin, alkaline phosphatase and liver alcohol dehydrogenase together with the complexes of liver alcohol dehydrogenase with coenzyme analogs ADPR and H(2)NADH. While spectral shifts and broadening indicate that alterations of the Trp microenvironment are more marked on superficial regions of the macromolecule the decay kinetics of deeply buried chromophores show that the internal flexibility of the polypeptide in two out of three cases is significantly affected by silica entrapment. Both the intrinsic lifetime and the bimolecular acrylamide quenching constant confirm that, relative to the aqueous solution, in hydrogels the globular fold is more rigid with azurin, looser with alcohol dehydrogenase and substantially unaltered with alkaline phosphatase. It was also noted that large amplitude structural fluctuations, as those involved in coenzyme binding to alcohol dehydrogenase or thermally activated in alkaline phosphatase, were not restricted by gelation. Common features of the three silica entrapped proteins are pronounced conformational heterogeneity and immobilization of rotational motions of the macromolecule in the long time scale of seconds.

Binding and release of iron by gel-encapsulated human transferrin: evidence for a conformational search

Human transferrin is a single-chain bilobal protein with each of the two similar but not identical lobes in turn composed of two domains. Each lobe may assume one of two stable structural conformations, open or closed, determined by a rigid rotation of the domains with respect to each other. In solution, the transformation of a lobe between open and closed conformations is associated with the release or binding of an Fe(III) ion. The results of the present study indicate that encapsulation of transferrin within a porous sol-gel matrix allows for a dramatic expansion, to days or weeks, of this interconversion time period, thus providing an opportunity to probe heretofore inaccessible transient intermediates. Sol-gel-encapsulated iron-free transferrin samples are prepared by using two protocols. In the first protocol, the equilibrium form of apotransferrin is encapsulated in the sol-gel matrix, whereas in the second protocol holotransferrin is first encapsulated and then iron is removed from the protein. Results of kinetic and spectroscopic studies allow for distinguishing between two models for iron binding. In the first, iron is assumed to bind to amino acid ligands of one domain, inducing a rigid rotation of the second domain to effect closure of the interdomain cleft. In the second, iron undertakes a conformational search among the thermally accessible states of the lobe, "choosing" the state which most nearly approximates the stable closed state when iron is bound. Our experimental results support the second mechanism.

Ferricytochrome c encapsulated in silica hydrogels: correlation between active site dynamics and solvent structure

Ferricytochrome c encapsulated in silica hydrogels has been prepared by the sol-gel technique following, with some modifications, the procedure originally developed by Zink et al. A suitable preparation of hydrogels enables to have both 'wet' and 'dry' samples. Wet samples have a high water content: as the temperature is lowered below approximately 260 K water freezes and the samples crack. On the contrary, dry samples have a low water content (hydration h approximately 0.35): in these conditions water does not freeze even at cryogenic temperatures and the samples remain transparent and non-cracking. The dynamics of ferricytochrome c and its dependence on the surrounding medium have been studied by optical absorption spectroscopy in the temperature range 10-300 K. At each temperature, spectra were collected both in the Soret region and in the near infrared at approximately 1.45 microm (the water overtone band); this enables to probe the local dynamics of the protein active site as well as the 'structure' of water molecules present in the sample. The data show that sol-gel encapsulation 'per se' does not alter the protein active site dynamics, but rather introduces an increased local heterogeneity. At difference, we find a correlation between active site dynamics and water structure: in the wet hydrogel, freezing of water quenches the ensemble of soft modes linearly coupled to the Soret transition; while, in the dry hydrogel, water does not freeze, and an active site dynamic behavior-similar to the non-freezing water/glycerol solution-is observed.

Ferricytochrome c encapsulated in silica hydrogels: correlation between active site dynamics and solvent structure

Ferricytochrome c encapsulated in silica hydrogels has been prepared by the sol-gel technique following, with some modifications, the procedure originally developed by Ellerby et al. (Science 255 1113 (1992)). A suitable preparation of hydrogels enables having both 'wet' and 'dry' samples. Wet samples have a high water content: as the temperature is lowered below approximately 260 K, water freezes and the samples crack. On the contrary, dry samples have a low water content (hydration h approximately equal 0.35): in these conditions water does not freeze even at cryogenic temperatures and the samples remain transparent and non-cracking. The dynamics of ferricytochrome c and its dependence on the surrounding medium have been studied by optical absorption spectroscopy in the temperature range 10-300 K. At each temperature, spectra were collected both in the Soret region and in the near infrared at approximately 1.45 microm (the water overtone band); this enables probing the local dynamics of the protein active site as well as the 'structure' of water molecules present in the sample. The data show that sol-gel encapsulation 'per se' does not alter the protein active site dynamics, but rather introduces an increased local heterogeneity. We find a correlation between active site dynamics and water structure: in the wet hydrogel, freezing of water quenches the ensemble of soft modes linearly coupled to the Soret transition; while, in the dry hydrogel, water does not freeze and an active site dynamic behavior--similar to the non-freezing water/glycerol solution--is observed.

Crystal structure of horse carbonmonoxyhemoglobin-bezafibrate complex at 1.55-A resolution. A novel allosteric binding site in R-state hemoglobin

Bezafibrate, an antilipidemic drug, is known as a potent allosteric effector of hemoglobin. The previously proposed mechanism for the allosteric potency of this drug was that it stabilizes and constrains the T-state of hemoglobin by specifically binding to the large central cavity of the T-state. Here we report a new allosteric binding site of fully liganded R-state hemoglobin for this drug. The high resolution crystal structure of horse carbonmonoxyhemoglobin in complex with bezafibrate reveals that the bezafibrate molecule lies near the surface of the E-helix of each alpha subunit and the complex maintains the quaternary structure of the R-state. Binding is caused by the close fit of bezafibrate into the binding pocket, which is composed of some hydrophobic residues and the heme edge, suggesting the importance of hydrophobic interactions. Upon binding of bezafibrate, the distance between Fe and the N epsilon(2) of distal His E7(alpha 58) is shortened by 0.22 A in the alpha subunit, whereas no significant structural changes are transmitted to the beta subunit. Oxygen equilibrium studies of R-state-locked hemoglobin with bezafibrate in a wet porous sol-gel indicate that bezafibrate selectively lowers the oxygen affinity of one type of subunit within the R-state, consistent with the structural data. These results disclose a new allosteric mechanism of bezafibrate and offer the first demonstration of how the allosteric effector interacts with R-state hemoglobin.

Spectroscopically and kinetically distinct conformational populations of sol-gel-encapsulated carbonmonoxy myoglobin. A comparison with hemoglobin

We have used sol-gel encapsulation protocols to trap kinetically and spectroscopically distinct conformational populations of native horse carbonmonoxy myoglobin. The method allows for direct comparison of functional and spectroscopic properties of equilibrium and non-equilibrium populations under the same temperature and viscosity conditions. The results implicate tertiary structure changes that include the proximal heme environment in the mechanism for population-specific differences in the observed rebinding kinetics. Differences in the resonance Raman frequency of nu(Fe-His), the iron-proximal histidine stretching mode, are attributed to differences in the positioning of the F helix. For myoglobin, the degree of separation between the F helix and the heme is assigned as the conformational coordinate that modulates both this frequency and the innermost barrier controlling CO rebinding. A comparison with the behavior of encapsulated derivatives of human adult hemoglobin indicates that these CO binding-induced conformational changes are qualitatively similar to the tertiary changes that occur within both the R and T quaternary states. Protein-specific differences in the time scale for the proposed F helix relaxation are attributed to variations in the intra-helical hydrogen bonding patterns that help stabilize the position of the F helix.

A tertiary two-state allosteric model for hemoglobin

The two-state allosteric model of Monod, Wyman, and Changeux (MWC) provides an excellent description of homotropic effects in a vast array of equilibrium and kinetic measurements on cooperative ligand binding by hemoglobin. However, in contrast to experimental observations, the model does not allow for alteration of the ligand affinity of the T quaternary structure by allosteric effectors. This failure to explain heterotropic effects has been appreciated for over 30 years, and it has been generally assumed to result from tertiary conformational changes in the absence of a quaternary change. Here we explore a model that preserves the essential MWC idea that binding without a quaternary conformational change is non-cooperative, but where tertiary conformations of individual subunits play the primary role instead of the quaternary conformations. In this model, which we call the 'tertiary two-state (TTS) model', the two affinity states correspond to two tertiary conformations of individual subunits rather than the two quaternary conformations of the MWC two-state allosteric model. Ligation and the R quaternary structure bias the subunit population toward the high affinity tertiary conformation, while deligation and the T quaternary structure favor the low affinity tertiary conformation. We show that the model is successful in quantitatively explaining a demanding set of kinetic data from nanosecond carbon monoxide photodissociation experiments at times longer than approximately 1 micros. Better agreement between the model and the submicrosecond kinetic data may result from detailed considerations of the distribution and dynamics of conformational substates of the two tertiary conformations. The model is consistent with the results of solution, gel, and single crystal oxygen binding studies, but underestimates the population of doubly-liganded molecules determined in low-temperature electrophoresis experiments.

Dynamics of green fluorescent protein mutant2 in solution, on spin-coated glasses, and encapsulated in wet silica gels

Single-molecule experiments are performed by investigating spectroscopic properties of molecules either diffusing in and out of the observation volume or fixed in space by different immobilization procedures. To evaluate the effect of immobilization methods on the structural and dynamic properties of proteins, a highly fluorescent mutant of the green fluorescent protein, GFPmut2, was spectroscopically characterized in bulk solutions, dispersed on etched glasses, and encapsulated in wet, nanoporous silica gels. The emission spectrum, the fluorescence lifetimes, the anisotropy, and the rotational correlation time of GFPmut2, encapsulated in silica gels, are very similar to those obtained in solution. This finding indicates that the gel matrix does not alter the protein conformation and dynamics. In contrast, the fluorescence lifetimes of GFPmut2 on glasses are two-to fourfold higher and the fluorescence anisotropy decays yield almost no phase shifts. This indicates that the interaction of the protein with the bare glass surface induces a significant structural perturbation and severely restricts the rotational motion. Single molecules of GFPmut2 on glasses or in silica gels, identified by confocal image analysis, show a significant stability to illumination with bleaching times of the order of 90 and 60 sec, respectively. Overall, these data indicate that silica gels represent an ideal matrix for following biologically relevant events at a single molecule level.

Geminate rebinding in trehalose-glass embedded myoglobins reveals residue-specific control of intramolecular trajectories

It is becoming increasingly apparent that hydrophobic cavities (also referred to as xenon cavities) within proteins have significant functional implications. The potential functional role of these cavities in modulating the internal dynamics of carbon monoxide in myoglobin (Mb) is explored in the present study by using glassy matrices derived from trehalose to limit protein dynamics and to eliminate ligand exchange between the solvent and the protein. By varying the temperature (-15 to 65 degrees C) and humidity for samples of carbonmonoxy myoglobin embedded in trehalose-glass, it is possible to observe a hierarchy of distinct geminate recombination phases that extend from nanosecond to almost seconds that can be directly associated with rebinding from specific hydrophobic cavities. The use of mutant forms of Mb reveals the role of key residues in modulating ligand access between these cavities and the distal hemepocket.

High and low oxygen affinity conformations of T state hemoglobin

To understand the interplay between tertiary and quaternary transitions associated with hemoglobin function and regulation, oxygen binding curves were obtained for hemoglobin A fixed in the T quaternary state by encapsulation in wet porous silica gels. At pH 7.0 and 15 degrees C, the oxygen pressure at half saturation (p50) was measured to be 12.4 +/- 0.2 and 139 +/- 4 torr for hemoglobin gels prepared in the absence and presence of the strong allosteric effectors inositol hexaphosphate and bezafibrate, respectively. Both values are in excellent agreement with those found for the binding of the first oxygen to hemoglobin in solution under similar experimental conditions. The corresponding Hill coefficients of hemoglobin gels were 0.94 +/- 0.02 and 0.93 +/- 0.03, indicating, in the frame of the Monod, Wyman, and Changeux model, that high and low oxygen-affinity tertiary T-state conformations have been isolated in a pure form. The values, slightly lower than unity, reflect the different oxygen affinity of alpha- and beta-hemes. Significantly, hemoglobin encapsulated in the presence of the weak effector phosphate led to gels that show intermediate oxygen affinity and Hill coefficients of 0.7 to 0.8. The heterogeneous oxygen binding results from the presence of a mixture of the high and low oxygen-affinity T states. The Bohr effect was measured for hemoglobin gels containing the pure conformations and found to be more pronounced for the high-affinity T state and almost absent for the low-affinity T state. These findings indicate that the functional properties of the T quaternary state result from the contribution of two distinct, interconverting conformations, characterized by a 10-fold difference in oxygen affinity and a different extent of tertiary Bohr effect. The very small degree of T-state cooperativity observed in solution and in the crystalline state might arise from a ligand-induced perturbation of the distribution between the high- and low-affinity T-state conformations.

Use of silicate sol-gels to trap the R and T quaternary conformational states of pig kidney fructose-1,6-bisphosphatase

Encapsulation of the homotetrameric pig kidney fructose-1,6-bisphosphatase (FBPase) in tetramethyl orthosilicate sol-gels was used to dramatically reduce the rate of the allosteric transition of the enzyme between the T and R allosteric states. When assayed in the absence of the allosteric inhibitor AMP, the enzyme encapsulated in the T-state exhibited little activity. The enzyme encapsulated in the R-state exhibited a 4-fold lower k(cat) and V(max) than the enzyme in solution, and the apparent K(m) for this enzyme was 350-fold higher than the corresponding value for the enzyme in solution. The [Mg(2+)](0.5) for the encapsulated enzyme was only 0.1 mM, compared to 0.54 mM for the normal enzyme. Magnesium activation, under both sets of conditions, was cooperative with a Hill coefficient of approximately 2. The activity of enzyme encapsulated in the R-state decreased to about 70% of initial activity within 1 min of adding AMP, it then decreased slowly to about 40% of initial activity over the following 7 h. Under the conditions tested, the encapsulated enzyme never became completely inactivated and AMP inhibition was no longer cooperative. For enzyme encapsulated in the T-state, activity was restored over approximately 7 h after removal of the AMP. The biphasic and slow responses to changing AMP levels suggest that encapsulated enzyme can be used to study the effects of local conformational changes distinct from the global quaternary conformational changes by slowing down the ability of the enzyme to carry out global rotations. The response to AMP exhibited by the encapsulated enzyme is consistent with the ability of AMP, at least partially, to directly influence the activity of the active site within each subunit.

The Bohr effect of hemoglobin intermediates and the role of salt bridges in the tertiary/quaternary transitions

Understanding mechanisms in cooperative proteins requires the analysis of the intermediate ligation states. The release of hydrogen ions at the intermediate states of native and chemically modified hemoglobin, known as the Bohr effect, is an indicator of the protein tertiary/quaternary transitions, useful for testing models of cooperativity. The Bohr effects due to ligation of one subunit of a dimer and two subunits across the dimer interface are not additive. The reductions of the Bohr effect due to the chemical modification of a Bohr group of one and two alpha or beta subunits are additive. The Bohr effects of monoliganded chemically modified hemoglobins indicate the additivity of the effects of ligation and chemical modification with the possible exception of ligation and chemical modification of the alpha subunits. These observations suggest that ligation of a subunit brings about a tertiary structure change of hemoglobin in the T quaternary structure, which breaks some salt bridges, releases hydrogen ions, and is signaled across the dimer interface in such a way that ligation of a second subunit in the adjacent dimer promotes the switch from the T to the R quaternary structure. The rupture of the salt bridges per se does not drive the transition.

Direct observation of two distinct affinity conformations in the T state human deoxyhemoglobin

The main features of cooperative oxygenation of human hemoglobin have been described by assuming the equilibrium between two affinity conformations of the entire molecule, T and R. However, the molecular basis for explaining the wide variation in the O(2) affinities of the deoxy T state has remained obscure. We address this long-standing issue by trapping the conformational states of deoxyhemoglobin molecules within wet porous transparent silicate sol-gels. The equilibrium O(2) binding measurements of the encapsulated deoxyhemoglobin samples showed that deoxyhemoglobin free of anions coexists in two conformations that differ in O(2) affinity by 40 times or more, and addition of inositol hexaphosphate to this anion-free deoxyhemoglobin brings about a very slow redistribution of these affinity conformations. These results are the first, direct demonstration of the existence of equilibrium between two (at least two) functionally distinguishable conformational states in the T state deoxyhemoglobin.

Confirmation of a unique intra-dimer cooperativity in the human hemoglobin alpha(1)beta(1)half-oxygenated intermediate supports the symmetry rule model of allosteric regulation

The contribution of the alpha(1)beta(1)half-oxygenated tetramer [alphabeta:alphaO(2)betaO(2)] (species 21) to human hemoglobin cooperativity was evaluated using cryogenic isoelectric focusing. The cooperative free energy of binding, reflecting O(2)-driven protein structure changes, was measured as (21)DeltaG(c) = 5.1 +/- 0. 3 kcal for the Zn/FeO(2) analog. For the Fe/FeCN analog, (21)DeltaG(c) was estimated as 4.0 kcal after correction for a CN ligand rearrangement artifact, demonstrating that ligand rearrangement does not invalidate previous conclusions regarding this species. In the context of the entire Hb cooperativity cascade, which includes eight intermediate species, the 21 tetramer is highly abundant relative to the other doubly-ligated species, providing strong support for the previously determined consensus partition function of O(2) binding and for the Symmetry Rule model of hemoglobin cooperativity (Ackers et al., Science 1992;255:54-63). Cooperativity of normal human hemoglobin is shown to depend on site-configuration, and not solely the number of O(2) bound, nor the occupancy of alpha vs. beta subunits. Verification of a unique contribution from the alpha(1)beta(1)doubly-oxygenated species to the equilibrium O(2) binding curve strongly reinforces the Symmetry Rule interpretation that the alpha(1)beta(1)dimer acts both as a structural and functional element in cooperative O(2) binding.

Homotropic cooperative binding of organic solvent vapors by solid trypsin

Homotropic cooperative binding was observed at vapor sorption of organic solvents (acetonitrile, propionitrile, ethanol, 1-propanol, 2-propanol, nitroethane) by dried solid trypsin from porcine pancreas (0.05 g H2O/g protein). The vapor sorption isotherms were obtained by the static method of gas chromatographic headspace analysis at 298 K for 'vapor solvent+solid trypsin' systems in the absence of the liquid phase. All isotherms have a sigmoidal shape with significant sorbate uptake only above the threshold of sorbate thermodynamic activity. On the sorption isotherms of non-hydroxylic sorbates the saturation of trypsin by organic solvent was observed above the sorbate threshold activity. The formation of inclusion compounds with phase transition between solvent-free and solvent-saturated trypsin is supposed. Approximation of obtained isotherms by the Hill equation gives the inclusion stoichiometry S, inclusion free energy, and the Hill constant N of clathrates. The inclusion stoichiometry S depends significantly on the size and shape of sorbate molecules and changes from S=31 mol of sorbate per mol of trypsin for ethanol to S=6 for nitroethane. The inclusion free energies determined for the standard states of pure liquid sorbate and infinitely dilute solution in toluene are in the range from -0.5 to -1.2 kJ/mol and from -3.1 to -8.1 kJ/mol, respectively, per 1 mol of sorbate. The Hill constants are relatively high: from N=5.6 for 1-propanol to N approximately equal to 10(3) for nitroethane. The implication of the obtained results for the interpretation of solvent effects on the enzyme activity and stability in low-water medium is discussed.

Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals

Oxygen binding by hemoglobin fixed in the T state either by crystallization or by encapsulation in silica gels is apparently noncooperative. However, cooperativity might be masked by different oxygen affinities of alpha and beta subunits. Metal hybrid hemoglobins, where the noniron metal does not bind oxygen, provide the opportunity to determine the oxygen affinities of alpha and beta hemes separately. Previous studies have characterized the oxygen binding by alpha(Ni2+)2beta(Fe2+)2 crystals. Here, we have determined the three-dimensional (3D) structure and oxygen binding of alpha(Fe2+)2beta(Ni2+)2 crystals grown from polyethylene glycol solutions. Polarized absorption spectra were recorded at different oxygen pressures with light polarized parallel either to the b or c crystal axis by single crystal microspectrophotometry. The oxygen pressures at 50% saturation (p50s) are 95 +/- 3 and 87 +/- 4 Torr along the b and c crystal axes, respectively, and the corresponding Hill coefficients are 0.96 +/- 0.06 and 0.90 +/- 0.03. Analysis of the binding curves, taking into account the different projections of the alpha hemes along the optical directions, indicates that the oxygen affinity of alpha1 hemes is 1.3-fold lower than alpha2 hemes. Inspection of the 3D structure suggests that this inequivalence may arise from packing interactions of the Hb tetramer within the monoclinic crystal lattice. A similar inequivalence was found for the beta subunits of alpha(Ni2+)2beta(Fe2+)2 crystals. The average oxygen affinity of the alpha subunits (p50 = 91 Torr) is about 1.2-fold higher than the beta subunits (p50 = 110 Torr). In the absence of cooperativity, this heterogeneity yields an oxygen binding curve of Hb A with a Hill coefficient of 0.999. Since the binding curves of Hb A crystals exhibit a Hill coefficient very close to unity, these findings indicate that oxygen binding by T-state hemoglobin is noncooperative, in keeping with the Monod, Wyman, and Changeux model.

UV resonance raman spectra of ligand binding intermediates of sol-gel encapsulated hemoglobin

We report for the first time specific conformational changes for a homogeneous population of ligand-bound adult deoxy human hemoglobin A (HbA) generated by introducing CO into a sample of deoxy-HbA with the effector, inositol hexaphosphate, encapsulated in a porous sol-gel. The preparation of ligand-bound deoxy-HbA results from the speed of ligand diffusion relative to globin conformational dynamics within the sol-gel (1). The ultraviolet resonance Raman (UVRR) difference spectra obtained reveal that E helix motion is initiated upon ligand binding, as signaled by the appearance of an alpha14beta15 Trp W3 band difference at 1559 cm(-1). The subsequent appearance of Tyr (Y8a and Y9a) and W3 (1549 cm(-1)) UVRR difference bands suggest conformational shifts for the penultimate Tyralpha140 on the F helix, the "switch" region Tyralpha42, and the "hinge" region Trpbeta37. The UVRR results expose a sequence of conformational steps leading up to the ligation-induced T to R quaternary structure transition as opposed to a single, concerted switch. More generally, this report demonstrates that sol-gel encapsulation of proteins can be used to study a sequence of specific conformational events triggered by substrate binding because the traditional limitation of substrate diffusion times is overcome.

Temperature dependent quaternary state relaxation in sol-gel encapsulated hemoglobin

Samples of human adult hemoglobin (HbA) encapsulated in a wet porous sol-gel are prepared under aerobic and anaerobic conditions. Resonance Raman spectroscopy is used to compare equilibrium deoxyHbA to the nonequilibrium deoxy species generated by deoxygenating an encapsulated oxyHbA sample. The spectra of the deoxygenated samples as a function of delay subsequent to deoxygenation reveal a marked slow down by the gel of the two phases of relaxation: the tertiary relaxation associated with the transition from the liganded R to deoxy R conformations and the quaternary relaxation associated with the deoxy R to deoxy T transition. The temperature dependence (4-80 degrees C) of the relaxation indicates that the internal viscosity of the gel is greatly enhanced at the lower temperatures. At 80 degrees C the tertiary and quaternary relaxations occur over minutes to hours, respectively, whereas at 4 degrees C both relaxations are essentially frozen. These results demonstrate the impressive potential of using sol-gel encapsulation as a means of studying substrate binding induced conformational changes in proteins.

Functional analysis of hemoglobin molecules locked in doubly liganded conformations

A controversy still exists over whether the molecular basis of hemoglobin cooperativity can be more appropriately explained by one of two classic allosteric models, the concerted and sequential models. To distinguish these two models from the viewpoint of their fundamental processes, namely, the presence or absence of conformational equilibria, we have trapped the conformations of nickel(II)-iron(II) hybrid hemoglobin molecules with two CO-bound, alpha2(Fe-CO)beta2(Ni) and alpha2(Ni)beta2(Fe-CO), by encapsulation in the water-filled pores of sol-gel-derived transparent silica-gels. In our experimental system, nickel(II) protoporphyrin binds neither O2 nor CO and mimics a fixed deoxyheme, and the gel matrix provides a means of inhibiting large-scale protein structural changes, thus enabling O2 equilibrium study of the hybrids still in their doubly liganded conformations. Results showed that two conformations of widely different O2 affinity exist together in each doubly liganded hemoglobin, providing a direct proof of the concerted mechanism versus the sequential mechanism.

Erythrocyte folate analysis: a cause for concern?

Neural tube defects can be prevented by adequate intake of periconceptional folate, and inverse associations between folate status and cardiovascular disease and various cancers have been noted. Thus, there is renewed interest in the analysis of red cell folate (RCF) as an indicator of folate deficiency risk. Assessment of the assumptions that underpin RCF assays indicates that many are false. Published literature suggests that increased deoxy-hemoglobin (which can bind RCF electrostatically) yields more assayable folate, and increased oxy-hemoglobin (which cannot bind RCF) yields less assayable folate. It is argued that as deoxy-hemoglobin picks up oxygen and switches quaternary structure, any bound folate must, on purely theoretical grounds, become physically “trapped”. Venous blood taken for analysis is 65% to 75% saturated with oxygen, and pro-rata “trapping” will lead to serious underestimation of RCF. Hence, doubt is cast over the validity of all previous RCF values. Some strategies for accurately assessing RCF are suggested.

Allosteric mechanism of haemoglobin: rupture of salt-bridges raises the oxygen affinity of the T-structure

The T-structure of human haemoglobin is linked by salt-bridges between its four subunits, formed by the C-terminal arginine residues of the alpha-subunits and the C-terminal histidine residues of the beta-subunits. In the R-structure, these salt-bridges are absent. The oxygen affinity of the T-structure is lower than that of the R-structure by the equivalent of 3.5 kcal/mol haem. This difference has been attributed to the constraints imposed upon the T-structure by the salt-bridges, which were thought to hinder the changes in tertiary structure needed for firm oxygen binding. We have subjected this postulate to a rigorous test by measuring the oxygen equilibria of T-state crystals of an abnormal human haemoglobin in which the C-terminal histidine residues of the beta-chains are replaced by leucine residues. This replacement removes the salt-bridges from the histidine imidazole groups to the neighbouring aspartate residues. The crystals have an oxygen affinity about three times greater than that of crystals of normal haemoglobin. Hill's coefficient is close to unity. The oxygen affinity is unaffected by pH, chloride or the allosteric effector bezafibrate. Equilibrium curves determined by single crystal microspectrophometry using light polarised parallel and normal to the crystallographic a-axis show no significant difference between the oxygen affinities of alpha and beta-haems. Our results show that rupture of salt-bridges raises the oxygen affinity of the T-structure even when this is clamped firmly by the crystal lattice.

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.