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E Freire

Publications and source records attributed to E Freire.

At least 91 records · Page 5Linked to original sources
PubMed1994

Thermodynamic prediction of structural determinants of the molten globule state of barnase.

Recently, it has been demonstrated that the enthalpy and heat capacity changes for protein folding/unfolding can be predicted rather accurately from the crystallographic or NMR solution structure of a protein. (K.P. Murphy, V. Bhakuni, D. Xie and E. Freire, Mol. Biol. 227 (1992) 293-306.) Under some conditions proteins do not unfold completely, giving rise to states in which the molecule remains in a compact configuration after denaturation. These compact denatured or molten globule states retain a hydrophobic core, exhibit residual structure and a compactness close to that of the native state. This phenomenon is reflected in the thermodynamics of the process. By using the structural parametrization of the energetics, it is possible to develop an algorithm aimed at selecting partly folded states that conform to the experimental thermodynamic constraints of the molten globule. We have applied our molten globule search algorithm to the globular protein barnase. This approach has allowed a structure based selection of a unique family of structural states that satisfy the experimental criteria of the molten globule. The prediction of the molten globule search algorithm indicates that the first helix together with most of the beta-sheet structure (beta 2, beta 3-5) and loop 5 constitute the main determinants of the molten globule intermediate, in agreement with the NMR data. These results open the prospect for an automated search of the structural determinants of the molten globule state of proteins and suggest that solvation parameters can be effectively used to probe structural states of proteins.

Algorithms↗
PubMed1994

[Tetanus].

Tetanus is a disease of safe and easy prevention, although it continues to be a frequent pathology, with variable incidence in different countries. Portugal occupies one of the top positions in European countries. The aim of this theoretic revision is a greater sensitivity to the prevention and diagnosis of the disease.

Diagnosis, Differential↗
PubMed1993

Influence of nucleotide binding site occupancy on the thermal stability of the F1 portion of the chloroplast ATP synthase.

The irreversible thermal denaturation of the F1 portion of the chloroplast ATP synthase (CF1) was examined by differential scanning calorimetry, ATPase activity loss, and release of bound nucleotides. In nearly all cases, the loss of ATPase activity closely paralleled the temperature dependence of the excess heat capacity. Although the irreversible nature of the denaturation precluded thermodynamic interpretation, a kinetic analysis was feasible. A two-state kinetic model was found to fit the calorimetric data very well. The activation energies of thermal denaturation calculated from calorimetric data were very close to those determined from Arrhenius plots of the apparent first-order rate constants of loss of ATPase activity versus reciprocal of the temperature. The nucleotide binding site occupancy profoundly influenced the temperature at which thermal denaturation occurred. In particular, the temperature at which the maximum in excess heat capacity occurs (Tm) was increased about 8 degrees C by occupancy of tight, noncatalytic ATP binding sites and by an additional 3-4 degrees C by the presence of nucleotides in the medium during heating. The thermal denaturation of CF1, an enzyme composed of nine polypeptide chains, is highly cooperative in that it obeys the simple two-step kinetic model. Since the removal of the epsilon and delta subunits has little effect on thermal denaturation, the major forces that stabilize CF1 must, thus, be between the alpha, beta, and gamma subunits.

Binding Sites↗
PubMed1993

Thermodynamic and structural analysis of the folding/unfolding transitions of the Escherichia coli molecular chaperone DnaK.

The thermal unfolding of the Escherichia coli 70 kDa heat shock protein, DnaK, exhibits three well defined transitions. At pH 7.6, these transitions are centered at 45.2, 58.0 and 73.3 degrees C. High sensitivity calorimetric scans as a function of pH indicate that the folding/unfolding behavior is well described by a four-state model which includes a delta H, tm and delta Cp for each state. Calorimetric scans of a 44 kDa N-terminal proteolytic fragment show a major transition centered at 47.5 degrees C (N1) and a minor transition at 79.4 degrees C (N2). A calorimetric scan of a 23 kDa C-terminal proteolytic fragment exhibits a low temperature peak at 58.5 degrees C (C1) and a high temperature peak at 70.6 degrees C (C2). Deconvolution analysis of the low temperature peak reveals that it is actually composed of two transitions of roughly equal delta H centered at 50.4 degrees C (C1a) and 58.2 degrees C(C1b). These experiments have allowed us to assign the transitions of the intact protein as follows. The low temperature transition of DnaK can be assigned to the N-terminal region on the basis of the similarity between the delta H and tm values for the low temperature transition and those obtained for the N1 transition of the isolated N-terminal fragment. This assignment is also supported by measurements of the intrinsic fluorescence emission as a function of temperature. DnaK contains a single tryptophan localized at residue 102 in the N-terminal domain of the protein. Additionally, calorimetric scans show that the tm of the low temperature transition increases by 9.2 degrees C in the presence of excess ADP, which is known to bind to the N-terminal domain. The middle transition can be assigned to the C1a and C1b transitions of the C-terminal fragment on the basis of the similarity of delta H and tm. In the intact protein C1a and C1b form a single cooperative unit; however, the cooperative interactions between these folding/unfolding domains are disrupted in the isolated fragment. The high temperature transition of the intact protein is composed of contributions from both the N-terminal and C-terminal regions of the protein. These studies have allowed us to develop a quantitative model of the folding/unfolding behavior of DnaK.

Bacterial Proteins↗
PubMed1993

Are the molten globule and the unfolded states of apo-alpha-lactalbumin enthalpically equivalent?

Recently, the absence of a thermally induced transition has been offered as proof that the unfolded and the molten globule states of apo-alpha-lactalbumin are enthalpically equivalent. In this paper we demonstrate that that argument is thermodynamically incorrect. In addition, it is shown that the absence of a thermally induced transition at extremely low salt concentrations can be accounted for in terms of the known ionic strength dependence of the transition temperature and the thermodynamic parameters associated with the unfolding of apo-alpha-lactalbumin.

Apoproteins↗
PubMed1993

Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4.

The thermal stability of a 56 amino acid fragment of GCN4 has been studied by high-sensitivity differential scanning calorimetry and circular dichroism spectroscopy. This fragment contains the leucine zipper and part of the basic region. The thermal unfolding of GCN4-56 is a reversible process and can be well represented by a reaction of the form N2<-->2U, indicating that the unfolding of the leucine zipper is a two-state process in which the helices are only stable when they are in the coiled-coil conformation. As expected, the transition temperature is concentration dependent. At pH 7.06 and a protein concentration of 5 x 10(-4) M the transition temperature is close to 70 degrees C while at 5 x 10(-6) M it is close to 50 degrees C. The enthalpy change for unfolding is 31.5 kcal mol-1 at 70 degrees C. Since the isolated helices are unstable, interactions at the interface between the two helices play a key role in the stabilization of the native dimer. These interactions primarily involve the burial of apolar surface from the solvent (hydrophobic effect) and electrostatic interactions. Structural thermodynamic calculations have permitted a dissection of the magnitude of the various contributions to the total Gibbs free energy of stabilization.

Amino Acid Sequence↗
PubMed1993

Structural energetics of peptide recognition: angiotensin II/antibody binding.

The ability to predict the strength of the association of peptide hormones or other ligands with their protein receptors is of fundamental importance in the fields of protein engineering and rational drug design. To form a tight complex between a flexible peptide hormone and its receptor, the largeloss of configurational entropy must be overcome. Recently, the crystallographic structure of the complex between angiotensin II and the Fab fragment of a high affinity monoclonal antibody has been determined (Garcia, K.C., Ronco, P.M., Verroust, P.J., Brünger, A.T., Amzel, L.M. Three-dimensional structure of an angiotensin II-Fab complex at 3 A: Hormone recognition by an anti-idiotypic antibody. Science 257:502-507, 1992). In this paper we present a study of the thermodynamics of the association by high sensitivity isothermal titration calorimetry. The results of the experiments indicate that at 30 degrees C the binding is characterized by (1) a delta H of -8.9 +/- 0.7 kcal mol-1, (2) a delta Cp of -240 +/- 20 cal K-1 mol-1, and (3) the release of 1.1 +/- 0.1 protons per binding site in the pH range 6.0-7.3. Using these values and the previously determined binding constant in phosphate buffer, delta G at 30 degrees C is estimated as -11 kcal mol-1 and delta S as 6.9 cal K-1 mol-1. The calorimetric data indicate that binding is favored both enthalpically and entropically. These results have been complemented by structural thermodynamic calculations. The calculated and experimentally determined thermodynamic quantities are in good agreement.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1993

Structural energetics of the molten globule state.

Certain partly ordered protein conformations, commonly called "molten globule states," are widely believed to represent protein folding intermediates. Recent structural studies of molten globule states of different proteins have revealed features which appear to be general in scope. The emerging consensus is that these partly ordered forms exhibit a high content of secondary structure, considerable compactness, nonspecific tertiary structure, and significant structural flexibility. These characteristics may be used to define a general state of protein folding called "the molten globule state," which is structurally and thermodynamically distinct from both the native state and the denatured state. Despite extensive knowledge of structural features of a few molten globule states, a cogent thermodynamic argument for their stability has not yet been advanced. The prevailing opinion of the last decade was that there is little or no enthalpy difference or heat capacity difference between the molten globule state and the unfolded state. This view, however, appears to be at variance with the existing database of protein structural energetics and with recent estimates of the energetics of denaturation of alpha-lactalbumin, cytochrome c, apomyoglobin, and T4 lysozyme. We discuss these four proteins at length. The results of structural studies, together with the existing thermodynamic values for fundamental interactions in proteins, provide the foundation for a structural thermodynamic framework which can account for the observed behavior of molten globule states. Within this framework, we analyze the physical basis for both the high stability of several molten globule states and the low probability of other potential folding intermediates. Additionally, we consider, in terms of reduced enthalpy changes and disrupted cooperative interactions, the thermodynamic basis for the apparent absence of a thermally induced, cooperative unfolding transition for some molten globule states.

Amino Acid Sequence↗
PubMed1993

Molecular basis of cooperativity in protein folding. IV. CORE: a general cooperative folding model.

The cooperative nature of the protein folding process is independent of the characteristic fold and the specific secondary structure attributes of a globular protein. A general folding/unfolding model should, therefore, be based upon structural features that transcend the peculiarities of alpha-helices, beta-sheets, and other structural motifs found in proteins. The studies presented in this paper suggest that a single structural characteristic common to all globular proteins is essential for cooperative folding. The formation of a partly folded state from the native state results in the exposure to solvent of two distinct regions: (1) the portions of the protein that are unfolded; and (2) the "complementary surfaces," located in the regions of the protein that remain folded. The cooperative character of the folding/unfolding transition is determined largely by the energetics of exposing complementary surface regions to the solvent. By definition, complementary regions are present only in partly folded states; they are absent from the native and unfolded states. An unfavorable free energy lowers the probability of partly folded states and increases the cooperativity of the transition. In this paper we present a mathematical formulation of this behavior and develop a general cooperative folding/unfolding model, termed the "complementary region" (CORE) model. This model successfully reproduces the main properties of folding/unfolding transitions without limiting the number of partly folded states accessible to the protein, thereby permitting a systematic examination of the structural and solvent conditions under which intermediates become populated. It is shown that the CORE model predicts two-state folding/unfolding behavior, even though the two-state character is not assumed in the model.

Apolipoproteins↗
PubMed1993

Structural thermodynamics: prediction of protein stability and protein binding affinities.

The relationships between the structure of a protein and the thermodynamic parameters that determine its stability constitute the focus of attention of an increasing number of research laboratories. Advances in this area have reached the point in which accurate protein stability predictions and interaction energetics based on crystallographic information appear to be within reach. The purpose of this article is to summarize these developments and discuss future goals and trends.

Drug Stability↗
PubMed1993

Analysis of thermally induced protein folding/unfolding transitions using free solution capillary electrophoresis.

It is shown that free solution capillary electrophoresis (FSCE) can be used to monitor the temperature-dependent folding/unfolding transitions of proteins. Furthermore, analysis of the data obtained by FSCE can be used to estimate the apparent thermodynamic parameters (enthalpy change (delta HvH), entropy change (delta S), and transition temperature (Tm)) associated with the folding/unfolding transition. In addition to mobility changes associated with the transition, FSCE analysis is unique in its ability to provide access to the population distribution of mobility states. This is demonstrated by the temperature-dependent change in the electrophoretic peak width and by the appearance of multiple peaks for very slow equilibrium or irreversible processes. Moreover, by comparing the mobility of the denatured state to that of unstructured model peptides, it is possible to characterize the relative degree of structure present in the unfolded state of a protein. This methodology has been applied to the analysis of the thermally induced unfolding of lysozyme at low pH. It is shown that the mobility of thermally denatured lysozyme can be described by the same function that describes unstructured, fully solvated peptides. On the contrary, the mobility of the native lysozyme is significantly higher than the value predicted by the same function. The accuracy of the apparent thermodynamic parameters obtained by this methodology compare within error with values obtained by direct calorimetric measurements using differential scanning calorimetry.

Amino Acid Sequence↗
PubMed1993

Cardiorespiratory alterations produced by pharmacological agents applied to the ventrolateral medulla (intermediate area) of the cat. Effect of exercise condition on glycine-induced inhibition.

1. To study the action of the intermediate area (IA), coextensive with the rostral ventrolateral medulla, on the neurophysiological mechanisms involved in the regulation of respiration, in terms of inspiratory drive and respiratory timing, cats were submitted to topical application of sodium pentobarbital (30 mg/ml), leptazol (200 mg/ml), glutamate (50 mg/ml) and glycine (100 and 50 mg/ml) to the IA. The effects of electrically induced exercise on the ventilatory response and oxygen uptake (VO2) obtained by topical application of glycine (50 mg/ml) to the IA were also studied. 2. Leptazol reduced minute ventilation (VE) and inspiratory drive (VT/TI) and changed the timing mechanism. Glutamate only increased tidal volume (VT), VE and VT/TI. Arterial blood pressure (AP) increased and heart rate (HR) did not change with either drug. 3. Sodium pentobarbital reduced VT and changed the timing mechanism. Glycine only reduced VE, VT and VT/TI. AP decreased and HR did not change with either drug. 4. The depressor effects of glycine on respiratory pattern, VO2 and CO2 production (VCO2) tended to be attenuated by exercise. 5. The fall in AP due to glycine application did not differ between resting and exercise conditions. 6. Our results indicate that at least two different nervous structures are involved in the IA: one responsible for the respiratory drive and sensitive to glycine and glutamate, and the other responsible for the regulation of the timing mechanism and sensitive to sodium pentobarbital and leptazol.

Animals↗
PubMed1992

Microcalorimetric study of wheat germ agglutinin binding to N-acetylglucosamine and its oligomers.

The energetics of association of wheat germ agglutinin (WGA) with N-acetylglucosamine (GlcNAc) and its beta(1,4) oligomers have been measured using isothermal titration calorimetry. Association constants of 0.4, 5.3, 11.1, 12.3, and 19.1 mM-1 and enthalpies of binding of -6.1, -15.6, -19.4, -19.3, and -18.2 kcal mol-1 were obtained at 26 degrees C for the titration of WGA with GlcNAc, (GlcNAc)2, (GlcNAc)3, (GlcNAc)4, and (GlcNAc)5, respectively. The term T delta S was always of negative value, indicating that the binding process is enthalpically driven. Titrations of WGA performed at pH 4.5 did not differ significantly from those performed at pH 7.0, suggesting that no groups with a pKa in this range are directly involved in the binding event. Also, performing the titration in a buffer system with a higher enthalpy of protonation did not change the enthalpy of binding confirming that there is no net protonation or deprotonation when WGA binds GlcNAc residues at pH 7. A model of four independent binding sites was found to adequately describe the binding curves, except in the case of (GlcNAc)4 which exhibited positive cooperativity. The energetic values are discussed within the context of the structure of the WGA-(GlcNAc)2 complex.

Acetylglucosamine↗
PubMed1992

Temperature and guanidine hydrochloride dependence of the structural stability of ribonuclease T1.

The thermal unfolding of ribonuclease T1 has been studied by high-sensitivity differential scanning calorimetry as a function of temperature, [GuHCl], and scanning rate. The destabilizing effect of GuHCl has revealed that the kinetics of the unfolding transition become extremely slow as the transition temperature decreases. At pH 5.3 and zero GuHCl, the unfolding transition is centered at 59.1 degrees C; upon increasing the GuHCl concentration, the transition occurs at lower temperatures and exhibits progressively slower kinetics; so, for example, at 3 M GuHCl, the transition temperature is 40.6 degrees C and is characterized by a time constant close to 10 min. Under all conditions studied (pH 5.3, pH 7.0, [GuHCl] < 3 M), the transition is thermodynamically reversible. The slow kinetics of the transition induce significant distortions in the shape of the transition profiles that can be mistakenly interpreted as deviations from a two-state mechanism. Determination of the thermodynamic parameters from the calorimetric data has required the development of an analytical formalism that explicitly includes the thermodynamics as well as the kinetics of the transition. Using this formalism, it is shown that a two-state slow-kinetics model is capable of accurately describing the structural stability of ribonuclease T1 as a function of temperature, GuHCl concentration, and scanning rate. Multidimensional analysis of the calorimetric data has been used to estimate the intrinsic thermodynamic parameters for protein stability, the interaction parameters with GuHCl, and the time constant for the unfolding transition and its temperature dependence.

Aspergillus↗
PubMed1992

On the origin of the enthalpy and entropy convergence temperatures in protein folding.

Temperature dependence of the thermodynamics of folding/unfolding for cytochrome c has been determined as a function of moderate [0-10% (vol/vol)] concentrations of methanol. Heat capacity change (delta Cp) for unfolding decreases with increased concentrations of methanol, consistent with a higher solvent hydrophobicity. For a given transition temperature, this effect results in higher experimental enthalpy (delta H) and entropy (delta S) changes with increased methanol concentrations. When the enthalpy or entropy data sets obtained at different methanol concentrations are plotted as a function of temperature, they are seen to converge and assume common values around 100 degrees C for delta H and 112 degrees C for delta S. These convergence temperatures are similar to those obtained for different proteins in aqueous solution when delta H and delta S are normalized with respect to number of residues. It has been previously hypothesized that these convergence temperatures correspond to the temperatures at which the hydrophobic contributions to delta H and delta S are zero; the results presented here agree with this viewpoint.

Calorimetry, Differential Scanning↗
PubMed1992

Molecular basis of co-operativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates.

The hierarchical partition function formalism for protein folding developed earlier has been extended through the use of three-dimensional polar and apolar contact plots. For each amino acid residue in the protein, these plots indicate the apolar and polar surfaces that are buried from the solvent, the identity of all amino acid residues that contribute to this shielding, and the magnitude of their contributions. These contact plots are then used to examine the distribution of the free energy of stabilization throughout the protein molecule. Analysis of these data allows identification of co-operative folding units and their hierarchical levels, and the identification of partially folded intermediates with a significant probability of being populated. The overall folding/unfolding thermodynamics of 12 globular proteins, for which crystallographic and experimental thermodynamics are available, is predicted within error. An energetic classification of partially folded intermediates is presented and the results compared to those cases for which structural and thermodynamic experimental information is available. Four different types of partially folded states and their structural energies are considered. (1) Local intermediates, in which only a local region of the protein loses secondary and tertiary interactions, while the rest of the protein remains intact. (2) Global intermediates, corresponding to the standard molten globule definition, in which significant secondary structure is maintained but native-like tertiary structure contacts are disrupted. (3) Extended intermediates characterized by the existence of secondary structure elements (e.g. alpha-helices) exposed to solvent. (4) Folding intermediates in proteins with two structural domains. The structure and energetics of folding intermediates of apo-myoglobin, alpha-lactalbumin, phosphoglycerate kinase and arabinose-binding protein are considered in detail.

Crystallography↗
PubMed1992

Fuc-GM1 ganglioside mimics the receptor function of GM1 for cholera toxin.

The ability of Fuc-GM1 ganglioside to mimic the receptor function of GM1 for cholera toxin (CT) has been investigated. For this purpose, rat glioma C6 cultured cells were enriched with Fuc-GM1 and the responsiveness to CT was compared with that of cells enriched with GM1 ganglioside. Fuc-GM1 was taken up by cells as rapidly and to the same extent as GM1. When comparable amounts of ganglioside were associated, the cells enriched with Fuc-GM1 bound the same amount of 125I-CT as did cells enriched with GM1. Under conditions in which GM1- and Fuc-GM1-enriched cells bound comparable amounts of CT, the Fuc-GM1-treated cells accumulated virtually the same amount of cyclic AMP as did GM1-treated cells, and activation of adenylate cyclase was also similar. The lag time preceding the CT-induced cAMP accumulation was the same in Fuc-GM1- and GM1-enriched cells. High-sensitivity isothermal titration calorimetry (ITC) experiments showed that the association constants of CT with Fuc-GM1 or GM1 ganglioside were comparable (4 x 10(7) M-1 and 1.9 x 10(7) M-1, respectively, at 25 degrees C). Also, the association constants of the B-subunit pentamer with Fuc-GM1 or GM1 ganglioside were comparable (about 3 x 10(7) M-1 and 7 x 10(7) M-1, respectively, at 25 degrees C).

Adenylyl Cyclases↗