Tris(2,2'-bipyridyl-N,N')nickel(II) thiosulfate heptahydrate
Explore the source record for details and available documents.
Journal Article↗
Biomedical subjects
E Freire
Publications and source records attributed to E Freire.
Bis(1,10-phenanthroline-N,N')(thiosulfato-O, S)nickel(II)-water-methanol (1/0.92/1.4) and bis(2,2'-bipyridyl-N, N')(thiosulfato-O,S)nickel(II)-water-methanol (1/2/0.55)
The title compounds, [Ni(S(2)O(3))(C(12)H(8)N(2))(2)].0.92H(2)O.1. 4CH(4)O and [Ni(S(2)O(3))(C(10)H(8)N(2))(2)].2H(2)O.0.55CH(4)O, are monomeric, containing nickel(II) in a distorted octahedral coordination environment provided by the four N atoms of two bidentate bipy or phen groups and one S and one O atom from a chelating thiosulfate anion. The crystals are highly unstable outside their mother liquors and are stabilized in solution by a not fully determined number of water and methanol solvate molecules. The phenanthroline structure includes two independent moieties related by a non-crystallographic inversion center. The thiosulfate anions display the usual S-O lengthening found when the anion acts in a bidentate mode.
Journal Article↗
Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor.
KNI-272 is a powerful HIV-1 protease inhibitor with a reported inhibition constant in the picomolar range. In this paper, a complete experimental dissection of the thermodynamic forces that define the binding affinity of this inhibitor to the wild-type and drug-resistant mutant V82F/184V is presented. Unlike other protease inhibitors, KNI-272 binds to the protease with a favorable binding enthalpy. The origin of the favorable binding enthalpy has been traced to the coupling of the binding reaction to the burial of six water molecules. These bound water molecules, previously identified by NMR studies, optimize the atomic packing at the inhibitor/protein interface enhancing van der Waals and other favorable interactions. These interactions offset the unfavorable enthalpy usually associated with the binding of hydrophobic molecules. The association constant to the drug resistant mutant is 100-500 times weaker. The decrease in binding affinity corresponds to an increase in the Gibbs energy of binding of 3-3.5 kcal/mol, which originates from less favorable enthalpy (1.7 kcal/mol more positive) and entropy changes. Calorimetric binding experiments performed as a function of pH and utilizing buffers with different ionization enthalpies have permitted the dissection of proton linkage effects. According to these experiments, the binding of the inhibitor is linked to the protonation/deprotonation of two groups. In the uncomplexed form these groups have pKs of 6.0 and 4.8, and become 6.6 and 2.9 in the complex. These groups have been identified as one of the aspartates in the catalytic aspartyl dyad in the protease and the isoquinoline nitrogen in the inhibitor molecule. The binding affinity is maximal between pH 5 and pH 6. At those pH values the affinity is close to 6 x 10(10) M(-1) (Kd = 16 pM). Global analysis of the data yield a buffer- and pH-independent binding enthalpy of -6.3 kcal/mol. Under conditions in which the exchange of protons is zero, the Gibbs energy of binding is -14.7 kcal/mol from which a binding entropy of 28 cal/K mol is obtained. Thus, the binding of KNI-272 is both enthalpically and entropically favorable. The structure-based thermodynamic analysis indicates that the allophenylnorstatine nucleus of KNI-272 provides an important scaffold for the design of inhibitors that are less susceptible to resistant mutations.
Calorimetry, Differential Scanning↗
The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme.
The interaction of a ligand with a protein occurs at a local site (the binding site) and involves only a few residues; however, the effects of that interaction are often propagated to remote locations. The chain of events initiated by binding provides the basis for fundamental biological phenomena such as allosterism, signal transduction, and structural-stability modification. In this paper, a structure-based statistical thermodynamic approach is presented and used to predict the propagation of the stabilization effects triggered by the binding of the monoclonal antibody D1.3 to hen egg white lysozyme. Previously, Williams et al. [Williams, D. C., Benjamin, D. C., Poljak, R. J. & Rule, G. S. (1996) J. Mol. Biol. 257, 866-876] showed that the binding of this antibody affects the stability of hen egg white lysozyme and that the binding effects propagate to a selected number of residues at remote locations from the binding epitope. In this paper, we show that this phenomenon can be predicted from structure. The formalism presented here permits the identification of the structural path followed by cooperative interactions that originate at the binding site. It is shown that an important condition for the propagation of binding effects to distal regions is the presence of a significant fraction of residues with low structural stability in the uncomplexed binding site. A survey of protein structures indicates that many binding sites have a dual character and are defined by regions of high and low structural stabilities. The low-stability regions might be involved in the transmission of binding information to other regions in the protein.
Animals↗
The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease.
The effects of the peptide inhibitor acetyl pepstatin on the structural stability of the HIV-1 protease have been measured by high sensitivity calorimetric techniques. At 25 degrees C and pH 3.6, acetyl pepstatin binds to HIV-1 protease with an affinity of 1.6 x 10(7 )M-1 and an enthalpy of 7.3 +/- 0.5 kcal/mol, indicating that binding is not favored enthalpically and that the favorable Gibbs energy originates from a large positive entropy. Since the binding of acetyl pepstatin is associated with a negative change in heat capacity (-450 cal/K*mol) the association reaction becomes enthalpically favored at temperatures higher than 40 degrees C. The presence of the inhibitor stabilizes the dimeric structure of the protease in a fashion that can be quantitatively described by a set of thermodynamic linkage equations. The combination of titration and differential scanning calorimetry provides an accurate way of determining binding constants for high affinity inhibitors that cannot be determined by titration calorimetry alone. A structure-based thermodynamic analysis of the binding process indicates that the stabilization effect is not distributed uniformly throughout the protease molecule. The binding of the inhibitor selectively stabilizes those conformational states in which the binding site is formed, triggering a redistribution of the state probabilities in the ensemble of conformations populated under native conditions. As a result, the stability constants for individual residues do not exhibit the same change in magnitude upon inhibitor binding. Residues in certain areas of the protein are affected significantly whereas residues in other areas are not affected at all. In particular, inhibitor binding has a significant effect on those regions that define the binding site, especially the flap region which becomes structurally stable as a result of the additional binding free energy. The induced stabilization propagates to regions not in direct contact with the inhibitor, particularly to the strand between residues Pro9 and Ala22 and the helix between Arg87 and Gly94. On the other hand, the stability of the strand between Asp60 and Leu76 is not significantly affected by inhibitor binding. The structural distribution of binding effects define cooperative pathways within the protease molecule. Proteins 1999;36:147-156.
Algorithms↗
The native state conformational ensemble of the SH3 domain from alpha-spectrin.
The folding/unfolding equilibrium of the alpha-spectrin SH3 domain has been measured by NMR-detected hydrogen/deuterium exchange and by differential scanning calorimetry. Protection factors against exchange have been obtained under native conditions for more than half of the residues in the domain. Most protected residues are located at the beta-strands, the short 3(10) helix, and part of the long RT loop, whereas the loops connecting secondary structure elements show no measurable protection. Apparent stability constants per residue and their corresponding Gibbs energies have been calculated from the exchange experiments. The most stable region of the SH3 domain is defined by the central portions of the beta-strands. The peptide binding region, on the other hand, is composed of a highly stable region (residues 53-57) and a highly unstable region, the loop between residues 34-41 (n-Src loop). All residues in the domain have apparent Gibbs energies lower than the global unfolding Gibbs energy measured by differential scanning calorimetry, indicating that under our experimental conditions the amide exchange of all residues in the SH3 domain occurs primarily via local unfolding reactions. A structure-based thermodynamic analysis has allowed us to predict correctly the thermodynamics of the global unfolding of the domain and to define the ensemble of conformational states that quantitatively accounts for the observed pattern of hydrogen exchange protection. These results demonstrate that under native conditions the SH3 domain needs to be considered as an ensemble of conformations and that the hydrogen exchange data obtained under those conditions cannot be interpreted by a two-state equilibrium. The observation that specific regions of a protein are able to undergo independent local folding/unfolding reactions indicates that under native conditions the scale of cooperative interactions is regional rather than global.
Calorimetry, Differential Scanning↗
A simple method to measure the absolute heat capacity of proteins.
Explore the source record for details and available documents.
Animals↗
The structural stability of the HIV-1 protease.
The most common strategy in the development of HIV-1 protease inhibitors has been the design of high affinity transition state analogs that effectively compete with natural substrates for the active site. A second approach has been the development of compounds that inactivate the protease by destabilizing its quaternary or tertiary structure. A successful optimization of these strategies requires an accurate knowledge of the energetics of structural stabilization and binding, and the identification of those regions in the protease molecule that are critical to stability and function. Here the energetics of stabilization of the HIV-1 protease has been measured for the first time by high sensitivity differential scanning calorimetry. These studies have permitted the evaluation of the different components of the Gibbs energy of stabilization (the enthalpy, entropy and heat capacity changes). The stability of the protease is pH-dependent and due to its dimeric nature is also concentration-dependent. At pH 3.4 the Gibbs energy of stabilization is close to 10 kcal/mol at 25 degreesC, consistent with a dissociation constant of 5x10(-8) M. The stability of the protease increases at higher pH values. At pH 5, the Gibbs energy of stabilization is 14.5 kcal/mol at 25 degreesC, consistent with a dissociation constant of 2.3x10(-11) M. The pH dependence of the Gibbs energy of stabilization indicates that between pH 3.4 and pH 5 an average of 3-4 ionizable groups per dimer become protonated upon unfolding. A structure-based thermodynamic analysis of the protease molecule indicates that most of the Gibbs energy of stabilization is provided by the dimerization interface and that the isolated subunits are intrinsically unstable. The Gibbs energy, however, is not uniformly distributed along the dimerization interface. The dimer interface is characterized by the presence of clusters of residues (hot spots) that contribute significantly and other regions that contribute very little to subunit association. At the dimerization interface, residues located at the carboxy and amino termini contribute close to 75% of the total Gibbs energy (Cys95, Thr96, Leu97, Asn98 and Phe99 and Pro1, Ile3, Leu5). Residues Thr26, Gly27 and Asp29 located at the base of the active site are also important, and to a lesser extent Gly49, Ile50, Gly51 located at the tip of the flap region. The structure-based thermodynamic analysis also predicts the existence of regions of the protease with only marginal stability and a high propensity to undergo independent local unfolding. In particular, the flap region occupies a very shallow energy minimum and its conformation can easily be affected by relatively small perturbations. This property of the protease can be related to the ability of some mutations to elicit resistance towards certain inhibitors.
Calorimetry, Differential Scanning↗
The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble.
Cooperative interactions link the behavior of different amino acid residues within a protein molecule. As a result, the effects of chemical or physical perturbations to any given residue are propagated to other residues by an intricate network of interactions. Very often, amino acids "sense" the effects of perturbations occurring at very distant locations in the protein molecule. In these studies, we have investigated by computer simulation the structural distribution of those interactions. We show here that cooperative interactions are not intrinsically bi-directional and that different residues play different roles within the intricate network of interactions existing in a protein. The effect of a perturbation to residue j on residue k is not necessarily equal to the effect of the same perturbation to residue k on residue j. In this paper, we introduce a computer algorithm aimed at mapping the network of cooperative interactions within a protein. This algorithm exhaustively performs single site thermodynamic mutations to each residue in the protein and examines the effects of those mutations on the distribution of conformational states. The algorithm has been applied to three different proteins (lambda repressor fragment 6-85, chymotrypsin inhibitor 2, and barnase). This algorithm accounts well for the observed behavior of these proteins.
Algorithms↗
Partially unfolded proteins efficiently penetrate cell membranes--implications for oral drug delivery.
We have previously reported on the biological activity of members of a library of low molecular weight compounds (carriers) that enable the oral delivery of proteins (Milstein, Proceedings of the 1995 Miami Bio/Technology Winter Symposium on Protein Engineering and Structural Biology, IRL Press at Oxford University Press, 1995, p. 13; Leone-Bay et al., J. Med. Chem. 38 (1995) 4263-4269; Leone-Bay et al., J. Med. Chem. 39 (1996) 2571-2578; [1-3]). When rats or primates are orally administered a solution of carrier and either recombinant human alpha-interferon (rhIFN), insulin or recombinant human growth hormone (rhGH) significant serum concentrations of the proteins are detectable. The transport activity of these compounds is positively correlated with their structural effects on the protein molecules. Direct measurement of the interaction of these carrier molecules with the proteins indicates that they reversibly destabilize the native state of the molecule favoring a partially unfolded conformation. Apparently these intermediate protein conformations are transport competent and are able to be absorbed through the intestinal tissue and into the bloodstream. Since the measured binding of the carriers to the partially unfolded proteins is relatively weak (Kb = 100 M(-1)) and the systemic activity of the proteins appears to be unaffected, the changes in the structure of the proteins are manifestly reversible.
Administration, Oral↗
Molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis.
The binding thermodynamics of the HIV-1 protease inhibitor acetyl pepstatin and the substrate Val-Ser-Gln-Asn-Tyr-Pro-Ile-Val-Gln, corresponding to one of the cleavage sites in the gag, gag-pol polyproteins, have been measured by direct microcalorimetric analysis. The results indicate that the binding of the peptide substrate or peptide inhibitor is entropically driven; i.e., it is characterized by an unfavorable enthalpy and a favorable entropy change, in agreement with a structure-based thermodynamic analysis based upon an empirical parameterization of the energetics. Dissection of the binding enthalpy indicates that the intrinsic interactions are favorable and that the unfavorable enthalpy originates from the energy cost of rearranging the flap region in the protease molecule. In addition, the binding is coupled to a negative heat capacity change. The dominant binding force is the increase in solvent entropy that accompanies the burial of a significant hydrophobic surface. Comparison of the binding energetics obtained for the substrate with that obtained for synthetic nonpeptide inhibitors indicates that the major difference is in the magnitude of the conformational entropy change. In solution, the peptide substrate has a higher flexibility than the synthetic inhibitors and therefore suffers a higher conformational entropy loss upon binding. This higher entropy loss accounts for the lower binding affinity of the substrate. On the other hand, due to its higher flexibility, the peptide substrate is more amenable to adapt to backbone rearrangements or subtle conformational changes induced by mutations in the protease. The synthetic inhibitors are less flexible, and their capacity to adapt is more restricted. The expected result is a more pronounced effect of mutations on the binding affinity of the synthetic inhibitors. On the basis of the thermodynamic differences in the mode of binding of substrate and synthetic inhibitors, it appears that a key factor to understanding resistance is given by the relative balance of the different forces that contribute to the binding free energy and, in particular, the balance between conformational and solvation entropy.
Binding Sites↗
The conformational equilibrium of human growth hormone.
The structural stability of recombinant human growth hormone (rhGH) has been studied by differential scanning calorimetry, circular dichroism and by following the tyrosine and histidine chemical shifts in the 1H NMR spectrum. These studies demonstrate that the folding/unfolding equilibrium of rhGH involves a partially folded dimeric intermediate. The formation of this dimeric intermediate is a reversible process. At acid pH (pH 3) the conformational equilibrium is reversible even at high protein concentrations (10 mg/ml). At neutral pH reversibility is observed only at low protein concentrations (<0.5 mg/ml). The free energy of this intermediate conformation is only approximately 3 kcal/mol apart from the native state indicating that the conformational equilibrium can be effectively modulated by changes in solvent composition or physical conditions. According to the spectroscopic and thermodynamic results, the formation of the dimeric intermediate occurs without a major loss in helical content and is driven by the formation of substantial hydrophobic contacts between two partially folded molecules. A thermodynamic model that accounts quantitatively for the experimental data has been developed. These studies demonstrate that partially folded conformations of certain proteins are able to form stoichiometric complexes, and that the formation of these complexes provide a significant source of stabilizing Gibbs energy for conformational states that, otherwise, will be characterized by extremely unfavorable free energies.
Calorimetry, Differential Scanning↗
Structural thermodynamic study of the binding of renin inhibitors to endothiapepsin.
Explore the source record for details and available documents.
Angiotensinogen↗
Statistical thermodynamic linkage between conformational and binding equilibria.
Explore the source record for details and available documents.
Ligands↗
Structure-based prediction of binding affinities and molecular design of peptide ligands.
Explore the source record for details and available documents.
Aspartic Acid Endopeptidases↗
The effect of exercise on ischemic mitral regurgitation.
This study investigated the effect of dynamic exercise on mitral regurgitation (MR) as assessed by color flow Doppler imaging and tested the hypothesis that MR increases in patients with left ventricular (LV) function worsening during exercise. We studied 513 patients (390 men, 123 women:mean age [+/-1 SD] 58+/-11 years) referred for treadmill exercise echocardiography (EE) to evaluate known or suspected coronary artery disease. Normal EE was seen in 182 (36%), necrosis in 131 (25%), and ischemic response (with or without necrosis) in 200 (39%). MR assessment was performed at rest and immediately postexercise, on the basis of the mosaic area. At rest, mild MR (<3 cm2) was seen in 138; moderate (3 to 6 cm2) was seen in 21; and severe (>6 cm2) was seen in 5. Forty-two patients developed new, mild (n=35), moderate (n=6), or severe (n=1) MR during exercise. Patients were assigned to three groups: group 1--new or increased MR from rest to exercise (n=70); group 2--MR at rest unchanged or decreased (n=136); and group 3--no MR at rest and exercise (n=307). At rest, LV ejection fraction (EF) and wall motion score index (WMSI) were similar in group 1 and group 2 but improved in group 3 (EF: group 1, 51+/-11%; group 2, 53+/-10%; group 3, 56+/-8%, p<0.001 vs group 1 and group 2. WMSI: group 1, 1.3+/-0.3; group 2, 1.3+/-0.4; group 3, 1.1+/-0.2, p<0.01 vs group 1, p<0.001 vs group 2). At exercise, EF and WMSI were impaired in group 1 (EF: group 1, 52+/-14%; group 2, 58+/-15%; group 3, 64+/-11%, p<0.001 vs group 1 and group 2; p<0.05 between group 1 and group 2. WMSI: group 1, 1.5+/-0.4; group 2, 1.4+/-0.4; group 3, 1.2+/-0.3, p<0.001 vs group 1 and group 2, p<0.05 between group 1 and group 2). An ischemic response was common in group 1 (67% vs 35% in group 2 and 34% in group 3, p<0.001 between group 1 and group 3 and between group 1 and group 2). Accordingly, in group 1 patients, exercise time was diminished (7.3+/-2.7 vs 8.4+/-2.7 in group 2 and 9.3+/-2.4 in group 3, p<0.01, between group 1 and group 2, p<0.001 between group 1 and group 3, p<0.001 between group 2 and group 3) and the number of severely narrowed coronary vessels greater (2.4+/-0.9 vs 1.7+/-1.0 in group 2 and 1.7+/-1.0 in group 3). In conclusion, MR does not increase in most patients submitted to dynamic exercise echocardiography. However, if MR develops, severe LV function worsening should be suspected.
Adult↗
Structure-based thermodynamic design of peptide ligands: application to peptide inhibitors of the aspartic protease endothiapepsin.
The prediction of binding affinities from structure is a necessary requirement in the development of structure-based molecular design strategies. In this paper, a structural parameterization of the energetics previously developed in this laboratory has been incorporated into a molecular design algorithm aimed at identifying peptide conformations that minimize the Gibbs energy. This approach has been employed in the design of mutants of the aspartic protease inhibitor pepstatin A. The simplest design strategy involves mutation and/or chain length modification of the wild-type peptide inhibitor. The structural parameterization allows evaluation of the contribution of different amino acids to the Gibbs energy in the wild-type structure, and therefore the identification of potential targets for mutation in the original peptide. The structure of the wild-type complex is used as a template to generate families of conformational structures in which specific residues have been mutated. The most probable conformations of the mutated peptides are identified by systematically rotating around the side-chain and backbone torsional angles and calculating the Gibbs potential function of each conformation according to the structural parametrization. The accuracy of this approach has been tested by chemically synthesizing two different mutants of pepstatin A. In one mutant, the alanine at position five has been replaced by a phenylalanine, and in the second one a glutamate has been added at the carboxy terminus of pepstatin A. The thermodynamics of association of pepstatin A and the two mutants have been measured experimentally and the results compared with the predictions. The difference between experimental and predicted Gibbs energies for pepstatin A and the two mutants is 0.23 +/- 0.06 kcal/mol. The excellent agreement between experimental and predicted values demonstrates that this approach can be used in the optimization of peptide ligands.
Aspartic Acid Endopeptidases↗
The structural stability of the co-chaperonin GroES.
The structural stability of the co-chaperonin GroES has been studied by high sensitivity differential scanning calorimetry and circular dichroism under different solvent conditions. The thermal folding/unfolding of GroES is a spontaneous reversible process involving a highly cooperative transition between folded heptamers and unfolded monomers. During the denaturation process folded monomers are energetically unfavourable and consequently never become populated to an appreciable degree. Analysis of the high resolution structure indicates that isolated folded monomers of GroES bury a significantly smaller fraction of their total surface than typical globular proteins of similar molecular mass. For this reason the intramolecular interactions within each GroES monomer appear not to be sufficient for thermodynamic stabilization. The stabilization of the heptameric structure is due primarily to intersubunit interactions rather than intrasubunit interactions. These interactions favor oligomerization both enthalpically and entropically. Despite the high density of charged residues, the stability of GroES shows no measurable dependence on salt concentration at pH 7. On the other hand, millimolar concentrations of magnesium stabilize GroES, presumably by specific binding. The stabilization elicited by Mg2+ is consistent with a dissociation constant of the order of 0.5 mM and approximately three binding sites per heptamer. These results emphasize the role of quaternary structure in the stabilization of small oligomeric proteins.
Calorimetry, Differential Scanning↗