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Biomedical subjects

E Freire

Publications and source records attributed to E Freire.

At least 19 recordsLinked to original sources
PubMed1996

Thermodynamic studies of the core histones: pH and ionic strength effects on the stability of the (H3-H4)/(H3-H4)2 system.

The self-associative behavior and the thermal stability of the H3/H4 histone complex was studied in low-ionic strength conditions by several physicochemical techniques, including differential scanning calorimetry and circular dichroism spectroscopy. At neutrality, the major molecular species present in solution is the (H3-H4)2 tetramer. Its thermodynamic properties cannot be studied directly though, since its thermal denaturation is completely irreversible even at the lowest salt concentrations. However, a complete thermodynamic analysis can be performed at low ionic strength and pH 4.5, where the (H3-H4)2 tetramer is quantitatively dissociated into two H3-H4 dimers and where almost complete reversibility of the thermal transitions is attained. The unfolding transition temperature of the 26.5 kDa H3-H4 dimer increases as a function of both the ionic strength of the solvent and the total protein concentration. The thermal denaturation of the H3-H4 dimer is characterized by the presence of a single calorimetric peak, centered at 58 degrees C, with a corresponding enthalpy change of 25 kcal/mol of a 13 kDa monomer unit and a change in heat capacity upon unfolding of about 0.6 kcal/(K mol of 13 kDa monomer unit). The complex between histones H3 and H4 (tetramer or dimer) is stable between pH 9.5 and 3.0. At pH 1.5, the system is almost completely unfolded at all temperatures. At low ionic strengths and pH values between 5.0 and 2.5, the H3-H4 dimer behaves as a highly cooperative system, melting as a single unit; i.e. individual H3 and H4 folded monomers are not detectable during the treatment. The two-state mechanism accounting for the unfolding of the H3-H4 dimer at pH 4.5 is the same as that described for the H2A-H2B dimer at neutrality. Just like for the H2A and H2B histones, the H3 and H4 polypeptides are properly folded only when assembled as H3-H4 dimers or in higher-order histone assemblies. Therefore, coupling along the interfaces of the two chains within the heterodimer is the major factor contributing to the stabilization of the secondary and tertiary structures of the chains as well as of the histone dimers.

Animals↗
PubMed1995

Precise scanning calorimeter for studying thermal properties of biological macromolecules in dilute solution.

A precise scanning calorimeter for studying the heat capacity of liquids in a broad temperature range has been developed. By its design and capabilities this calorimeter is the first of a new generation for this type of instrument. This new scanning calorimeter operates differentially, is equipped with a pair of gold capillary cells and semiconductor sensors, and is able to scan up and down in temperature at user-selected rates. This instrument is completely operated by an integrated computer which also provides a full thermodynamic analysis of the results. Its construction does not involve the use of organic compounds, thus eliminating a source of baseline noise that has affected previous calorimeters. The operational temperature range of the instrument can be varied between 0 and 120 degrees C. The gold capillary cells (operational volume 0.8 ml) minimize temperature gradients in the heated/cooled liquid sample and permit easy washing and reloading without air bubbles. These features are crucial for the accuracy of difference heat capacity measurements and determination of the absolute value of the partial heat capacity of solute molecules. The measurements can be performed under an excess constant pressure (up to 3 atm) to prevent formation of gas bubbles and boiling of aqueous solutions above 100 degrees C. The noise level of the recorded heating/cooling power difference is below 50 x 10(-9) W (i.e., below 10 ncal/s) with a response half-time of 5 s. The reproducibility of the baseline without refilling the capillary cells is on the order of 0.5 x 10(-6) W. Reproducibility of the baseline upon refilling the cell is of the same order of magnitude. This provides an accuracy in difference heat capacity determination on the order of 10 mu cal/degrees Kml at a heating rate of 1 degree K/min.

Calorimetry, Differential Scanning↗
PubMed1995

Subunit III of cytochrome c oxidase influences the conformation of subunits I and II: an infrared study.

The secondary structure of wild-type Paracoccus denitrificans cytochrome c oxidase obtained by decomposition of the infrared amide I band contains 44% alpha-helix, 18% beta-sheet, 14% beta-turns, 18% loops, and 6% nonordered segments. The mutant lacking subunit III presents a small but significant increase (from 18% to 24%) in the percentage of loops and slight differences in the other components. Using band/area ratios and tyrosine side chain absorption as an inner standard, it is shown that in the absence of subunit III the structure of subunits I and II is altered although no changes in their alpha-helix or beta-sheet content are observed. In the bacterial oxidase, thermal infrared studies show a complex denaturation pattern characterized by the presence of a partially denatured intermediate state. Of the seven predicted subunit III alpha-helices, only four are resistant toward the thermal challenge and behave as expected for typical transmembrane helices. The observation that the absence of subunit III influences the conformation of loop regions in the two other subunits suggests that part of the interaction surface between subunit III and the catalytic subunits might be located outside the lipid bilayer.

Electron Transport Complex IV↗
PubMed1995

The unfolding thermodynamics of c-type lysozymes: a calorimetric study of the heat denaturation of equine lysozyme.

The energetics of the temperature-induced unfolding of equine lysozyme was studied calorimetrically and compared with that of two structurally homologous proteins: hen egg white lysozyme and alpha-lactalbumin. The structure of each of these proteins is characterized by the presence of a deep cleft that divides the molecule into two regions called the alpha and beta domains. In equine lysozyme and alpha-lactalbumin the latter domain specifically binds Ca2+. It is shown that, in contrast to hen egg white lysozyme in which the alpha and beta domains unfold as a single cooperative unit, in equine lysozyme the two domains unfold in two separate cooperative stages even in the presence of excess Ca2+. The calcium binding beta-domain unfolds at a lower temperature and with more extensive heat absorption than the alpha-domain. Binding of Ca2+ increases the stability of the beta-domain, but even in the holo form it is less stable than the alpha-domain. The thermodynamic characteristics of Ca2+ binding have been determined, and indicate that it is an entropically driven process. The unfolding of equine lysozyme largely resembles the unfolding of alpha-lactalbumin, which also unfolds in two stages, but in the latter case the second stage is much less cooperative and proceeds with a smaller and diffuse heat absorption. As a result, the total enthalpy of unfolding of equine lysozyme is significantly larger than that of alpha-lactalbumin, being almost of the same magnitude as the enthalpy of egg white lysozyme unfolding, which proceeds as a single two-state transition. Analyses of the unfolding enthalpy function of various lysozymes, which bind or do not bind Ca2+, and unfold in one or two stages, have led us to the conclusion that the main reason for the loss of interdomain cooperativity in equine lysozyme is not the cluster of negative charges forming the calcium binding site, but the difference in atomic packing in the interior and at the interface between the alpha and beta domains.

Animals↗
PubMed1995

Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin.

The discovery that the protease from the human immunodeficiency virus (HIV) belongs to the aspartic protease family has generated renewed interest in this class of proteins. In this paper, the interactions of endothiapepsin, an aspartic proteinase from the fungus Endothia parasitica, with the inhibitor pepstatin A have been studied by high-sensitivity calorimetric techniques. These experiments have permitted a complete characterization of the temperature and pH-dependence of the binding energetics. The binding reaction is characterized by negative intrinsic binding enthalpy and negative heat capacity changes. The association constant is maximal at low pH (2 x 10(9) M-1 at pH 3) but decreases upon increasing pH (8.1 x 10(6) M-1 at pH 7). The binding of the inhibitor is coupled to the protonation of one of the aspartic moieties in the Asp dyad of the catalytic site of the protein. This phenomenon is responsible for the decrease in the apparent affinity of the inhibitor for the enzyme upon increasing pH. The experimental results presented here indicate that the binding of the inhibitor is favored both enthalpically and entropically. While the favorable enthalpic contribution is intuitively expected, the favorable entropic contribution is due to the large gain in solvent-related entropy associated with the burial of a large hydrophobic surface, that overcompensates the loss in conformational and translational/rotational degrees of freedom upon complex formation. The characteristics of the molecular recognition process have been evaluated by means of structure-based thermodynamic analysis. Three regions in the protein contribute significantly to the free energy of binding: the residues surrounding the Asp dyad (Asp32 in the N-terminal lobe and Asp215 in the C-terminal domain) and the flap region (Ile73 to Asp77). In addition, the rearrangement of residues that are not in immediate contact with the inhibitor provides close to 40% of the protease contribution to the binding free energy. On the other hand, the two statine residues provide more than half of the inhibitor contributions to the total free energy of binding. It is demonstrated that a previously developed empirical structural parametrization of the thermodynamic parameters that define the Gibbs energy, accurately accounts for the binding energetics and its temperature and pH-dependence.

Aspartic Acid Endopeptidases↗
PubMed1995

Forces and factors that contribute to the structural stability of membrane proteins.

While a considerable amount of literature deals with the structural energetics of water-soluble proteins, relatively little is known about the forces that determine the stability of membrane proteins. Similarly, only a few membrane protein structures are known at atomic resolution, although new structures have recently been described. In this article, we review the current knowledge about the structural features of membrane proteins. We then proceed to summarize the existing literature regarding the thermal stability of bacteriorhodopsin, cytochrome-c oxidase, the band 3 protein, Photosystem II and porins. We conclude that a fundamental difference between soluble and membrane proteins is the high thermal stability of intrabilayer secondary structure elements in membrane proteins. This property manifests itself as incomplete unfolding, and is reflected in the observed low enthalpies of denaturation of most membrane proteins. By contrast, the extramembranous parts of membrane proteins may behave much like soluble proteins. A brief general account of thermodynamics factors that contribute to the stability of water soluble and membrane proteins is presented.

Amino Acid Sequence↗
PubMed1995

Thermodynamic studies of the core histones: ionic strength and pH dependence of H2A-H2B dimer stability.

The thermal stability of the core histone dimer H2A-H2B has been studied by high-sensitivity differential scanning calorimetry and circular dichroism spectroscopy. The unfolding transition temperature of the 28 kDa H2A-H2B dimer increases as a function of both the ionic strength of the solvent and the total protein concentration. At neutral pH and physiological ionic strength, the thermal denaturation is centered at about 50 degrees C with a corresponding enthalpy change of about 40 kcal/mol of 14 kDa monomer unit and an excess heat capacity of about 1.4 kcal/(K.mol) of 14 kDa monomer unit. The H2A-H2B dimer is stable mainly between pH 5.5 and 10.5. Below pH 4.0, the system is unfolded at all temperatures. The thermodynamic analysis is performed at low ionic strength where almost complete reversibility is attained, since higher salt conditions seem to promote aggregation and irreversibility of the transitions. Analysis of the data shows that at low ionic strength and pH values between 6.5 and 8.5, the H2A-H2B dimer behaves as a highly cooperative system, melting as a single unit without any detectable intermediates of dissociated, yet folded, H2A and H2B monomers. This is consistent with the observed protein concentration dependence of the midpoint of the thermal denaturation. The two-state unfolding process can be described by the general scheme AB-->2U, indicating that the individual H2A and H2B polypeptides are folded, stable entities only when complexed as the H2A-H2B dimer and that the major contribution to the stabilization of the dimer derives from the coupling between the H2A and H2B interfaces.

Animals↗
PubMed1995

Thermodynamic analysis of the structural stability of the tetrameric oligomerization domain of p53 tumor suppressor.

The structural stability of an amino acid fragment containing the oligomerization domain (residues 303-366) of the tumor suppressor p53 has been studied using high-precision differential scanning calorimetry (DSC) and circular dichroism spectroscopy (CD). Previous NMR solution structural determinations have revealed that the fragment forms a symmetric 29.8 kDa tetramer composed of a dimer of dimers (p53tet) [Lee, W., Harvey, T. S., Yin, Y., Yau, P., Litchfield, D., & Arrowsmith, C. H. (1994) Nature Struct. Biol. 1, 877-890]. Thermal unfolding of the tetramer is reversible and can be described as a two-state transition in which the folded tetramer is converted directly to unfolded monomers (N4<==>4U). According to the DSC and CD data, the population of intermediate species consisting of folded monomers or dimers is insignificant, indicating that isolated dimeric or monomeric structures have a much lower stability than the dimer and do not become populated during thermal denaturation under the conditions studied. The transition temperature of unfolding is found to be highly dependent on protein concentration and to follow the expected behavior for a tetramer that dissociates upon unfolding. Experiments conducted at pH 4.0 in 25 mM sodium acetate at a tetramer concentration of 145.8 microM have a transition temperature (Tm) of 75.3 degrees C while at 0.5 microM the value drops to 39.2 degrees C. The enthalpy change of unfolding at 60 degrees C is 26 kcal (mol of monomer)-1 with a heat capacity change of 387 cal (K.mol of monomer)-1. The stability of p53tet is dependent on pH and salt concentration.(ABSTRACT TRUNCATED AT 250 WORDS)

Calorimetry, Differential Scanning↗
PubMed1995

Forces and factors that contribute to the structural stability of membrane proteins.

While a considerable amount of literature deals with the structural energetics of water-soluble proteins, relatively little is known about the forces that determine the stability of membrane proteins. Similarly, only a few membrane protein structures are known at atomic resolution, although new structures have recently been described. In this article, we review the current knowledge about the structural features of membrane proteins. We then proceed to summarize the existing literature regarding the thermal stability of bacteriorhodopsin, cytochrome-c oxidase, the band 3 protein, Photosystem II and porins. We conclude that a fundamental difference between soluble and membrane proteins is the high thermal stability of intrabilayer secondary structure elements in membrane proteins. This property manifests itself as incomplete unfolding, and is reflected in the observed low enthalpies of denaturation of most membrane proteins. By contrast, the extramembranous parts of membrane proteins may behave much like soluble proteins. A brief general account of thermodynamics factors that contribute to the stability of water soluble and membrane proteins is presented.

Amino Acid Sequence↗
PubMed1995

GroES and the chaperonin-assisted protein folding cycle: GroES has no affinity for nucleotides.

The E. coli chaperonin proteins, GroEL and GroES, assist in folding newly synthesized proteins. GroES is necessary for GroEL-assisted folding under conditions where the substrate protein cannot spontaneously fold. On the basis of photolabelling of GroES with 8-azido-ATP, a role for nucleotide binding to GroES in chaperonin function was suggested [Martin, et al., Nature, 366 (1993) 279-282]. We confirm the photolabeling of GroES with 8-azido-ATP. However, other proteins not known to contain nucleotide binding sites also became photolabeled suggesting that labeling is non-specific. Using rigorous physical methods, isothermal calorimetry and equilibrium binding, no interaction between GroES and nucleotides could be detected. We conclude that GroES has no nucleotide binding site.

Adenosine Triphosphate↗
PubMed1995

A calorimetric characterization of the salt dependence of the stability of the GCN4 leucine zipper.

The effects of different salts (LiCl, NaCl, ChoCl, KF, KCl, and KBr) on the structural stability of a 33-residue peptide corresponding to the leucine zipper region of GCN4 have been studied by high-sensitivity differential scanning calorimetry. These experiments have allowed an estimation of the salt dependence of the thermodynamic parameters that define the stability of the coiled coil. Independent of the nature of the salt, a destabilization of the coiled coil is always observed upon increasing salt concentration up to a maximum of approximately 0.5 M, depending on the specific cation or anion. At higher salt concentrations, this effect is reversed and a stabilization of the leucine zipper is observed. The effect of salt concentration is primarily entropic, judging from the lack of a significant salt dependence of the transition enthalpy. The salt dependence of the stability of the peptide is complex, suggesting the presence of specific salt effects at high salt concentrations in addition to the nonspecific electrostatic effects that are prevalent at lower salt concentrations. The data is consistent with the existence of specific interactions between anions and peptide with an affinity that follows a reverse size order (F- > Cl- > Br-). Under all conditions studied, the coiled coil undergoes reversible thermal unfolding that can be well represented by a reaction of the form N2<==>2U, indicating that the unfolding is a two-state process in which the helices are only stable when they are in the coiled coil conformation.

Anions↗
PubMed1995

Configurational effects in antibody-antigen interactions studied by microcalorimetry.

In this paper we study the binding of two monoclonal antibodies, E3 and E8, to cytochrome c using high-sensitivity isothermal titration calorimetry. We combine the calorimetric results with empirical calculations which relate changes in heat capacity to changes in entropy which arise from the hydrophobic effect. The change in heat capacity for binding E3 is -350 +/- 60 cal K-1 mol-1 while for E8 it is -165 +/- 40 cal K-1 mol-1. This result indicates that the hydrophobic effect makes a much larger contribution for E3 than for E8. Since the total entropy change at 25 degrees C is very similar for both antibodies, it follows that the configurational entropy cost for binding E3 is much larger than for binding E8 (-77 +/- 15 vs. -34 +/- 11 cal K-1 mol-1). These results illustrate a case of entropy compensation in which the cost of restricting conformational degrees of freedom is to a large extent compensated by solvent release. We also show that the thermodynamic data can be used to make estimates of the surface area changes that occur upon binding. The results of the present study are consistent with previous hydrogen-deuterium exchange data, detected using 2D NMR, on the two antibody-antigen interactions. The NMR study indicated that protection from exchange is limited to the binding epitope for E8, but extends beyond the epitope for E3.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

The heat capacity of proteins.

The heat capacity plays a major role in the determination of the energetics of protein folding and molecular recognition. As such, a better understanding of this thermodynamic parameter and its structural origin will provide new insights for the development of better molecular design strategies. In this paper we have analyzed the absolute heat capacity of proteins in different conformations. The results of these studies indicate that three major terms account for the absolute heat capacity of a protein: (1) one term that depends only on the primary or covalent structure of a protein and contains contributions from vibrational frequencies arising from the stretching and bending modes of each valence bond and internal rotations; (2) a term that contains the contributions of noncovalent interactions arising from secondary and tertiary structure; and (3) a term that contains the contributions of hydration. For a typical globular protein in solution the bulk of the heat capacity at 25 degrees C is given by the covalent structure term (close to 85% of the total). The hydration term contributes about 15 and 40% to the total heat capacity of the native and unfolded states, respectively. The contribution of non-covalent structure to the total heat capacity of the native state is positive but very small and does not amount to more than 3% at 25 degrees C. The change in heat capacity upon unfolding is primarily given by the increase in the hydration term (about 95%) and to a much lesser extent by the loss of noncovalent interactions (up to approximately 5%).(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
PubMed1995

Thermodynamics of partly folded intermediates in proteins.

Until recently, the energetics of protein-folding intermediates eluded direct measurement by high-sensitivity microcalorimetric techniques. But during the past year, the direct measurement of thermodynamic parameters for folding intermediates of alpha-lactalbumin, apomyoglobin, cytochrome c, and staphylococcal nuclease has provided new insights on the nature of the forces involved in the stabilization of nascent protein structures. In this review, I summarize those results and discuss the structural implications of the observed thermodynamic behavior.

Algorithms↗