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PubMed1993

A thermodynamic and spectroscopic study on the binding of berenil to poly d(AT) and to poly (dA) x poly (dT).

The complete thermodynamic profile for the non-intercalative binding of berenil to the alternating copolymer poly d(AT) and to the homopolymer poly (dA) x poly (dT) was investigated. Differential Scanning Calorimetry (DSC) and UV absorbance spectroscopy have been used to characterize and to compare the binding of berenil to the different synthetic polymers. Both double stranded DNA's show two types of binding; one stronger binding mode at low berenil concentrations and a weaker, in the case of poly d(AT)-berenil complexes slightly cooperative binding mode at higher drug to base pair ratios. For the interaction of berenil with poly d(AT) the thermodynamic data delta G(bind)0 = -33 kJ/mol drug, delta H(bind)0 = -29 kJ/mol of drug and delta S(bind)0 = +13 J/Kmol of drug were calculated. For the minor groove binding of berenil to poly (dA) x poly (dT) the following values were obtained: delta G(bind)0 = -34 kJ/mol of drug, delta H(bind)0 = -25 kJ/mol of drug and delta S(bind)0 = +30 J/Kmol of drug. Temperature-dependent UV absorbance spectroscopy revealed for both duplexes a biphasic "melting" behavior. However, the saturated nucleic acids (drug to base pair ratio 0.33) "melted" monophasically and with a decreased length of the cooperative unit. The obtained apparent equilibrium constants K(app) for the complexation with the discharged drug molecule showed to be a sensitive function of the ionic environment. But in contradiction to the expected release of two counterions into the solvent only a value of 1.0 was observed for the alternating copolymer poly d(AT). The complexation of berenil with poly (dA) x poly (dT) is followed by a release of 1.4 ions indicating stronger electrostatic interactions. For both polynucleotides the predicted release of two ions is not achieved. This is due to the presence of a binding mode, which involves less electrostatic interactions. From the complete data set it is proposed that the mode of binding is closely related to that found for the analogue minor groove binders DAPI and netropsin.

Diminazene↗
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

A view of thermodynamics of hydration emerging from continuum studies.

Main physical-chemical features of hydration found in continuum studies and possible limitations of the method are analyzed. Particular attention is given to: the choice of thermodynamic observables to be compared to the calculations; representations of the solute polarizability; compensation between the loss of hydration enthalpy and gain in Coulomb interactions upon a complex formation; two minima in interaction potentials between polar groups in solution; similarities and dissimilarities between interaction potentials in solution from continuum and molecular theories; continuum calculations of entropies of hydration; and evaluation of a temperature dependence of thermodynamic characteristics of hydration with continuum methods.

Animals↗
PubMed1995

Partial molar heat capacities and volumes of Gly-X-Gly tripeptides in aqueous solution: model studies for the rationalization of thermodynamic parameters of proteins.

The thermodynamics of protein unfolding can be rationalized if the temperature dependence of the partial molar volumes and heat capacities of their constituent groups are known reliably. Despite many experimental and theoretical studies there are still several inconsistencies in the published thermodynamic data. We have investigated some of these inconsistencies by applying high sensitivity scanning densimetry and microcalorimetry to aqueous solutions of tripeptides of the structure Gly-X-Gly, where X is one of the amino acids Met, Asn, Gly and Ile. For these side-chains either no direct data have been determined or serious discrepancies exist between the values published by different laboratories. Partial molar heat capacities and volumes have been determined for the peptides in pure water, in water adjusted to pH = 4 and in 0.5 M sodium acetate buffer at pH = 4. The results obtained are critically compared with those in the literature.

Amino Acid Sequence↗
PubMed1985

Thermodynamics and kinetics of mouse prolactin-hepatic receptor interaction.

Kinetic and thermodynamic parameters associated with the binding of secreted mouse prolactin (smPRL) to mouse hepatic receptors were investigated. When the reaction temperature was increased from 8 degrees C to 37 degrees C, the association rate constant k+1, increased approximately 5-fold, from 2.3 X 10(4) M-1 . S-1 to 12.6 X 10(4) M-1 . S-1. An Arrhenius plot indicated that there was a linear relationship between ln (k+1) and 1/T. When the reaction temperature was increased from 8 degrees C to 37 degrees C, the equilibrium binding constant, Ka, decreased approximately 1.5-fold, from 2.8 X 10(8) M-1 to 1.9 X 10(8) M-1. When the pH of the binding reaction was lowered from 9.0 to 6.2, Ka decreased approximately 3-fold, from 2.6 X 10(8) M-1 to 0.9 X 10(8) M-1. Transition state thermodynamic parameters for the formation of the smPRL-receptor complex, represented by delta G+', delta H+' and delta S+', were +45.7 kJ/mol, +41.2 kJ/mol and -15.1 J/(mol . K), respectively. Parameters for the equilibrium reaction, described by delta G0', delta H0' and delta S0', were -47.6 kJ/mol, -10.6 kJ/mol and +124 J/(mol . K), respectively. Over the temperature range studied, a Van't Hoff plot of the binding constants demonstrated a linear relationship between ln (ka) and 1/T, indicating that changes in enthalpy for the binding reaction were temperature independent. The binding reaction was largely entropically driven (delta S0' greater than 0), suggesting that hydrophobic interactions are involved in forming the smPRL-receptor complex.

Animals↗
PubMed1990

Fever: thermodynamics applied to the leucocyte.

A fever, by raising the temperature of leucocytes, accelerates and so enhances their antimicrobial action against infections. This is in keeping with thermodynamic principles which apply to chemical and biochemical reactions. In keeping with the same thermodynamic principles, when the temperature of matter is raised, at certain critical temperatures its form and behaviour change dramatically and radically. Visible water, for example, boils at 100 degrees C into invisible steam. By analogy to such dramatic changes of behaviour it has been proposed as a hypothesis, that when the temperature of the leucocyte is raised in vitro to the extreme limit just before it dies, its behaviour will also change in a radical and dramatic manner to produce a totally new class of antimicrobial substances or antibiotics, called leucocyte derived antibiotics, LDA. The new LDA should have a wide spectrum of action against infecting micro-organisms including viruses that provoke a fever in the body. They should also have some anti-tumour effects in patients providing such leucocytes. Preliminary observations suggest that when the temperature of leucocytes is raised in vitro to the point of near cell death they can indeed produce new antimicrobial and antitumoral substances.

Fever↗
PubMed1994

Thermodynamics of the binding of BTCP (GK 13) and related derivatives on the dopamine neuronal carrier.

We have studied the thermodynamic properties of the binding of a coherent series of uptake inhibitors derived from BTCP (GK 13 = N-[1-(2-benzo(b)thiophenyl)cyclohexyl]piperidine) to the dopamine neuronal carrier labelled with [3H]GBR 12783 (1-[2-(diphenylmethoxy)ethyl]4-(3-phenyl-2-propenyl)-piperazine). GK 13 (30 nM) and its 2-naphthyl derivative GK 189 (15 nM) competitively inhibited the specific binding of [3H]GBR 12783 to sites present in rat striatal membranes. Hill numbers calculated for the inhibition of the specific binding of [3H]GBR 12783 by BTCP derivatives were close to 1 (range 0.79-1.18). Increasing the temperature from 0 degrees to 30 degrees C induced a decrease in the affinity of [3H]GBR 12783 and GK derivatives which was generally less pronounced than that obtained when temperature was raised from 30 degrees C to 37 degrees C. Increasing the incubation temperature led to a decrease in both enthalpy (delta H degrees) and entropy (delta S degrees). We observed at 37 degrees C a large negative enthalpy change (range -48, -79 kJ/mol) and a negative, binding unfavorable, change in entropy. This indicates that the GK derivatives binding is enthalpy-driven. Furthermore, data obtained in the present study show that changes in thermodynamic parameters are not a function of the inhibitor's affinity for the dopamine neuronal carrier and this suggests that bonds involved in the inhibitor-carrier interaction are more likely related to the carrier configuration than to the chemical structure of the inhibitor.

Animals↗
PubMed2005

Thermodynamic properties of damaged DNA and its recognition by xeroderma pigmentosum group A protein and replication protein A.

The effects of the lesions induced by single, site-specific 1,2-GG or 1,3-GTG intrastrand adducts of cis-diamminedichloroplatinum(II) formed in oligodeoxyribonucleotide duplexes on energetics of DNA were examined by means of differential scanning calorimetry. These effects were correlated with affinity of these duplexes for damaged-DNA binding-proteins XPA and RPA; this affinity was examined by gel electrophoresis. The results confirm that rigid DNA bending is the specific determinant responsible for high-affinity interactions of XPA with damaged DNA, but that an additional important factor, which affects affinity of XPA to damaged DNA, is a change of thermodynamic stability of DNA induced by the damage. In addition, the results also confirm that RPA preferentially binds to DNA distorted so that hydrogen bonds between complementary bases are interrupted. RPA also binds to non-denaturational distortions in double-helical DNA, but affinity of RPA to these distortions is insensitive to alterations of thermodynamic stability of damaged DNA.

Base Sequence↗
PubMed2005

Effect of deuterium oxide on the thermodynamic quantities associated with phase transitions of phosphatidylcholine bilayer membranes.

The bilayer phase transitions of three kinds of phospholipids, dipalmitoylphosphatidylcholine (DPPC), distearoylphosphatidylcholine (DSPC) and dihexadecylphosphatidylcholine (DHPC), in deuterium oxide (D(2)O) and hydrogen oxide (H(2)O) were observed by differential scanning calorimetry (DSC) under ambient pressure and light-transmittance measurements under high pressure. The DSC measurements showed that the substitution of H(2)O by D(2)O affected the pretransition temperatures and the main-transition enthalpies of all PC bilayers. The temperature-pressure phase diagrams for these PC bilayer membranes in both solvents were constructed by use of the data of light-transmittance measurements. Regarding the main transition of all PC bilayer membranes, there was no appreciable difference between the transition temperatures in D(2)O and H(2)O under high pressure. On the other hand, the phase transitions among the gel phases including the pretransition were significantly affected by the solvent substitution. The thermodynamic quantities of phase transitions for the PC bilayer membranes were evaluated and the differences in thermodynamic properties by the water substitution were considered from the difference of interfacial-free energy per molecule in the bilayer in both solvents. It was proved that the substitution of H(2)O by D(2)O causes shrinkage of the molecular area of phospholipid at bilayer interface due to the difference in bond strength between deuterium and hydrogen bonds and produces the great influence on the bilayer phase with the smaller area. Further, the induction of bilayer interdigitation in D(2)O turned out to need higher pressures than in H(2)O.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2005

G148-GA3: a streptococcal virulence module with atypical thermodynamics of folding optimally binds human serum albumin at physiological temperatures.

The third albumin binding domain of streptococcal protein G strain 148 (G148-GA3) belongs to a novel class of prokaryotic albumin binding modules that is thought to support virulence in several bacterial species. Here, we characterize G148-GA3 folding and albumin binding by using differential scanning calorimetry and isothermal titration calorimetry to obtain the most complete set of thermodynamic state functions for any member of this medically significant module. When buffered at pH 7.0 the 46-amino acid alpha-helical domain melts at 72 degrees C and exhibits marginal stability (15 kJ/mol) at 37 degrees C. G148-GA3 unfolding is characterized by small contributions to entropy from non-hydrophobic forces and a low DeltaCp (1.1 kJ/(deg mol)). Isothermal titration calorimetry reveals that the domain has evolved to optimally bind human serum albumin near 37 degrees C with a binding constant of 1.4 x 10 7 M(-1). Analysis of G148-GA3 thermodynamics suggests that the domain experiences atypically small per residue changes in structural dynamics and heat capacity while transiting between folded and unfolded states.

Bacterial Proteins↗
PubMed2004

Thermodynamics of i-tetraplex formation in the nuclease hypersensitive element of human c-myc promoter.

More than 85% of c-myc transcription is controlled by the nuclease hypersensitive element III(1) upstream of the P1 promoter of this oncogene. The purine-rich sequence in the anti-sense strand forms a G-quadruplex, which has been recently implicated in colorectal cancer, and is proposed as a silencer element [Proc. Natl. Acad. Sci. USA 101 (2004) 6140]. This prompted us to characterize the thermodynamics and proton/counterion effect of the complementary pyrimidine-rich sequence, which forms a C-tetraplex. We report the thermodynamic parameters for folding of the pyrimidine-rich DNA fragment from this region into a C-tetraplex. At 20 degrees C, we observed a DeltaG of -10.36+/-0.13kcalmol(-1) with favorable enthalpy (DeltaH=75.99+/-0.99kcalmol(-1)) and unfavorable entropy (TDeltaS=65.63+/-0.88 kcalmol(-1)) at pH 5.3 in 20mM NaCl for tetraplex folding. Similar characteristic stabilizing enthalpy and destabilizing entropy were observed at other pH and ionic strengths. Folding was induced by uptake of about two to three protons per mole of tetraplex while a marginal (0.5-1mol/mol) counterion uptake was observed. In the context of current understanding of c-myc transcription we envisage a role of the i-motif in remodeling the G-quadruplex silencer.

Base Sequence↗
PubMed2006

Use of thermodynamic parameters for design of double-walled microsphere fabrication methods.

Double-walled microspheres (DWMS), with drug localized to the particle core, present a promising route for control of drug release rates, for example, by varying the degradation rate or erosion mechanism of the polymer used to form the shell or the thickness of the shell. DWMS are often difficult to fabricate, however. Thermodynamic descriptions for polymer-polymer immiscibility, drug distribution between phases and polymer-solution spreading coefficient provide predictions of appropriate solvents and polymer concentrations for efficiently producing well-formed DWMS. As an example, thermodynamic parameters for a polyphosphoester/poly(D,L-lactide-co-glycolide) (PLG) DWMS system, encapsulating piroxicam, have been calculated and the predictions tested experimentally. Appropriate choices of solvents and initial polymer concentrations resulted in DWMS with the desired polyphosphoester shells and piroxicam located selectively in PLG cores.

Chromatography, Gel↗
PubMed2005

Potential of Agave lechuguilla biomass for Cr(III) removal from aqueous solutions: thermodynamic studies.

Thermodynamic studies on the bioadsorption of Cr(III) onto Agave lechuguilla biomass were conduced. The experimental results at different temperatures were modeled using the Langmuir and Freundlich isotherms to obtain the characteristic parameters of each model. Both the Freundlich and Langmuir models were found to represent the bioadsorption process. The average adsorption capacities calculated from Freundlich (4.7 mg/g) and Langmuir (14.2 mg/g) isotherms showed A. lechuguilla to be an effective biomass in the removal of Cr(III) from an aqueous solution. Thermodynamic parameters (deltaG0, deltaH0 and deltaS0) determined in the temperature range from 10 to 40 degrees C along with the parameters of the Dubinin-Radushkevick equation support the idea that the binding of Cr(III) may be caused by interactions with functional groups such as carboxyl groups located on the outer surface of the cell tissue of the bioadsorbent.

Adsorption↗
PubMed2005

Berberine, a strong polyriboadenylic acid binding plant alkaloid: spectroscopic, viscometric, and thermodynamic study.

The interaction of berberine with single stranded poly(rA) structure was investigated using a combination of spectrophotometric, spectrofluorimetric, circular dichroic, viscometric, and thermodynamic studies. The interaction process was characterized by typical hypochromic and bathochromic effects in the absorption spectrum of berberine, enhancement of fluorescence intensity of berberine, increase of viscosity, and perturbation of circular dichroic spectrum of single stranded poly(rA). Scatchard plot obtained from spectrophotometric analysis showed that berberine bound strongly to single stranded poly(rA) in a non-cooperative manner. In contrast, berberine does not show any significant effect (i) in its absorbance and fluorescence spectra on binding to double stranded poly(rA), (ii) alter the circular dichroic spectrum of double stranded poly(rA), or (iii) increase of viscosity of double stranded poly(rA) indicating that it does not bind at all to double stranded poly(rA) structure. Thermodynamic parameters indicated that the binding of the alkaloid to single stranded poly(rA) is an endothermic process and entropy driven. All these findings, taken together clearly support that berberine binds strongly to single stranded poly(rA) structure by a mechanism of partial intercalation leading to its use in gene regulation in eukaryotic cells.

Berberine↗
PubMed2005

Unified Markov thermodynamics based on stochastic forms to classify drugs considering molecular structure, partition system, and biological species: distribution of the antimicrobial G1 on rat tissues.

To date, molecular descriptors do not commonly account for important information beyond chemical structure. The present work, attempts to extend, in this sense, the stochastic molecular descriptors, incorporating information about the specific biphasic partition system, the biological species, and chemical structure inside the molecular descriptors. Consequently, MARCH-INSIDE molecular descriptors may be identified with time-dependent thermodynamic parameters (entropy and mean free energy) of partition process. A classification function was developed to classify data of 423 drugs and up to 14 different partition systems at the same time. The model has shown a high overall accuracy of 92.1% (293 out of 318 cases) in training series and 90% (36 out of 40 cases) in predicting ones. Finally, we illustrate the use of the model by predicting a high probability (%) for G1 (a novel antibacterial drug) to undergo partition on different biotic systems (rat organs): liver (97.7), spleen (97.5), lung (97.4), and adipose tissue (97.6). These theoretical results coincide with herein reported steady state plasma concentrations (c) and partition coefficients (P) in liver (c=42.25+/-7.86/P=4.75), spleen (11.47+/-4.43/P=1.29), lung (17.04+/-3.58/P=1.91), and adipose tissue (28.19+/-11.82/P=3.17). All values were relative to (14)C-labeled-radioactive-G1 in plasma (c=8.9+/-3.05) after 3h of oral administration. In closing, the present stochastic forms derive average thermodynamic parameters fitting on a more clearly physicochemical framework with respect to classic vector-matrix-vector forms, which include, as particular cases, quadratic forms such as Wiener index, Randic invariants, Zagreb descriptors, Harary index, Balaban index, and Marrero-Ponce quadratic molecular indices.

Animals↗
PubMed2004

Heat capacity effects in protein folding and ligand binding: a re-evaluation of the role of water in biomolecular thermodynamics.

Large "anomalous" heat capacity (DeltaC(p)) effects are a common feature of the thermodynamics of biomolecular interactions in aqueous solution and, as a result of the improved facility for direct calorimetric measurements, there is a growing body of experimental data for such effects in protein folding, protein-protein and protein-ligand interactions. Conventionally such heat capacity effects have been ascribed to hydrophobic interactions, and there are some remarkably convincing demonstrations of the usefulness of this concept. Nonetheless, there is also increasing evidence that hydrophobic interactions are not the only possible source of such effects. Here we re-evaluate the possible contributions of other interactions to the heat capacity changes to be expected for cooperative biomolecular folding and binding processes, with particular reference to the role of hydrogen bonding and solvent water interactions. Simple models based on the hydrogen-bonding propensity of water as a function of temperature give quantitative estimates of DeltaC(p) that compare well with experimental observations for both protein folding and ligand binding. The thermodynamic contribution of bound waters in protein complexes is also estimated. The prediction from simple lattice models is that trapping of water in a complex should give more exothermic binding (DeltaDeltaH-6 to -12 kJ mol(-1)) with lower entropy (DeltaDeltaS(0) approximately -11 J mol(-1) K(-1)) and more negative DeltaC(p) (by about -75 J mol(-1) K(-1)) per water molecule. More generally, it is clear that significant DeltaC(p) effects are to be expected for any macromolecular process involving a multiplicity of cooperative weak interactions of whatever kind.

Calorimetry, Differential Scanning↗
PubMed2006

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences.

Single amino acid substitutions rarely produce substantial changes in protein structure. Here we show that substitution of the C-cap residue in the alpha-helix of ubiquitin with proline (34P variant) leads to dramatic structural changes. The resulting conformational perturbation extends over the last two turns of the alpha-helix and leads to enhanced flexibility for residues 27-37. Thermodynamic analysis of this ubiquitin variant using differential scanning calorimetry reveals that the thermal unfolding transition remains highly cooperative, exhibiting two-state behavior. Similarities with the wild type in the thermodynamic parameters (heat capacity change upon unfolding and m-value) of unfolding monitored by DSC and chemical denaturation suggests that the 34P variant has comparable buried surface area. The hydrophobic core of 34P variant is not packed as well as that of the wild type protein as manifested by a lower enthalpy of unfolding. The increased mobility of the polypeptide chain of this ubiquitin variant allows the transient opening of the hydrophobic core as evidenced by ANS binding. Taken together, these results suggest exceptional robustness of cooperativity in protein structures.

Amino Acid Sequence↗
PubMed2006

Thermodynamics of proteins in unusual environments.

Some aspects of protein thermodynamics in unconventional environments are addressed and discussed. Aqueous medium, especially dilute solution is the 'usual' ambient, which mediates all the interactions between protein and nearby molecules. When the water content is low, the surroundings may be considered 'unusual', exerting new stresses on the protein molecule and demanding different responses and property changes. The unusual systems considered in this article are low-water protein environments, including nearly dry state powders, organic solvent dispersions and reverse micelles' inclusions. The changes of hydration experienced by the protein after immobilization on solid supports are emphasized with respect to the free bulk solution state. Finally, the aqueous medium altered by water connectivity perturbing agents (polysaccharides) or in macromolecular crowding conditions (in the presence of polyols) is also considered as highly not ideal protein environments. The different responses elicited by the protein under the stress induced by drastic surrounding alterations may give insights for the controlled exploitation of the protein's biological and thermodynamic properties.

Calorimetry, Differential Scanning↗