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PubMed2004

Thermodynamics of folding, stabilization, and binding in an engineered protein--protein complex.

We analyzed the thermodynamics of a complex protein-protein binding interaction using the (engineered) Z(SPA)(-)(1) affibody and it's Z domain binding partner as a model. Free Z(SPA)(-)(1) exists in an equilibrium between a molten-globule-like (MG) state and a completely unfolded state, wheras a well-ordered structure is observed in the Z:Z(SPA)(-)(1) complex. The thermodynamics of the MG state unfolding equilibrium can be separated from the thermodynamics of binding and stabilization by combined analysis of isothermal titration calorimetry data and a separate van't Hoff analysis of thermal unfolding. We find that (i) the unfolding equilibrium of free Z(SPA)(-)(1) has only a small influence on effective binding affinity, that (ii) the Z:Z(SPA)(-)(1) interface is inconspicuous and structure-based energetics calculations suggest that it should be capable of supporting strong binding, but that (iii) the conformational stabilization of the MG state to a well-ordered structure in the Z:Z(SPA)(-)(1) complex is associated with a large change in conformational entropy that opposes binding.

Carrier Proteins↗
PubMed1999

Prediction of decoloration in paprika oleoresins. Application to studies of stability in thermodynamically compensated systems.

In six paprika oleoresins, the kinetic parameters for the decoloration reaction at three temperatures have been established. The thermodynamic study shows that the decoloration reaction in each oleoresin has its own activation entropy (DeltaS) and activation enthalpy (DeltaH). The six reactions studied show a constant ratio between DeltaH and DeltaS, which means that each reaction is an isokinetic form of only one reaction affected by thermodynamic compensation. Instead of one equation per oleoresin to predict pigment concentration as a mathematical function of time and temperature, one unique equation can be obtained in which DeltaH is a function of DeltaS. The validity of this equation has been tested by comparing the actual concentration remaining during a heat treatment and the calculated one. More than 90% of the calculated concentrations are within the range of variability of the actual mean. Due to the reduction in the number of variables in thermodynamic compensated systems, a general procedure to calculate the activation entropy in isokinetic reactions is proposed.

Capsicum↗
PubMed2002

Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics.

The periplasmic oligopeptide binding component (OppA) of the oligopeptide permease found in Gram-negative bacteria acts as a receptor for peptide transport across the cell membrane and is a potential target for antibacterial drug design. OppA exhibits broad specificity, binding to diverse peptides of 2-5 amino acid residues length. Crystallographic and calorimetric measurements have been carried out by Tame et al. of the binding of 28 peptides of sequence K-X-K to OppA, where X is a natural or nonnatural amino acid. Despite this extensive experimental characterization, a clear relationship between structural and thermodynamic parameters could not be readily identified, with a complicating factor being the observation of varying numbers of water molecules at the binding interface in the different complexes. Consequently, we have applied COMparative BINding Energy (COMBINE) analysis to derive quantitative structure-activity relationships (QSARs) for these 28 OppA-tripeptide complexes. This is the first application of COMBINE analysis to predict binding enthalpies and entropies, and predictive QSAR models were obtained for these quantities as well as for binding free energies. These QSAR models highlight several protein residues and bound water molecules in the binding site, as well as the electrostatic desolvation energies of the protein and the peptides, as responsible for most of the differences in binding thermodynamics between the peptides studied. The QSAR models aid rationalization of the determinants of binding affinity of the OppA:peptide complexes and provide guides for further ligand design. This study also points to the general applicability of COMBINE analysis to estimating thermodynamic parameters for protein-peptide complexes.

Bacterial Proteins↗
PubMed2005

Surface plasmon resonance thermodynamic and kinetic analysis as a strategic tool in drug design. Distinct ways for phosphopeptides to plug into Src- and Grb2 SH2 domains.

Thermodynamic and kinetic studies of biomolecular interactions give insight into specificity of molecular recognition processes and advance rational drug design. Binding of phosphotyrosine (pY)-containing peptides to Src- and Grb2-SH2 domains was investigated using a surface plasmon resonance (SPR)-based method. This SPR assay yielded thermodynamic binding constants in solution, and the kinetic information contained in the SPR signal allowed kinetic analysis, which demonstrated distinct ways for pY ligands to interact with the SH2 domains. The results for binding to Src SH2 were consistent with sequestration of water molecules in the interface of the pYEEI peptide/Src SH2 complex. The results for a pYVNV peptide binding to Grb2 SH2 suggested a conformational change for Grb2 SH2 upon binding, which is not observed for Src SH2. Binding of a cyclic construct, allowing the pYVNV sequence in the bound conformation, did not have the expected entropy advantage. The results suggest an alternative binding mode for this construct, with the hydrophobic ring-closing part interacting with the protein. In all cases, except for full-length Grb2 protein, the affinity for the immobilized peptide at the SPR sensor and in solution was identical. This study demonstrates that SPR thermodynamic and kinetic analysis is a useful strategic tool in drug design.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Full configuration interaction computer simulation study of the thermodynamic and kinetic stability of hydrated dielectrons.

The hydrated electron is a unique solvent-supported state comprised of an excess electron that is confined to a cavity by the surrounding water. Theoretical studies have suggested that two-electron solvent-supported states also can be formed; in particular, simulations indicate that two excess electrons could pair up and occupy a single cavity, forming a so-called hydrated dielectron. Although hydrated dielectrons have not been observed directly by experiment, their existence has been posited to explain the lack of an ionic strength effect in hydrated electron bimolecular annihilation [Schmidt, K. H.; Bartels, D. M. Chem. Phys. 1995, 190, 145]. To determine whether dielectrons may be created in the laboratory, we use thermodynamic integration (TI), combined with mixed quantum/classical molecular dynamics simulation, to examine the thermodynamic stability of hydrated electrons and dielectrons. For the dielectron calculations, we solve the two-electron quantum problem using full configuration interaction. Our results suggest that hydrated dielectrons are thermodynamically unstable relative to separated (single) hydrated electrons, although we also show that increasing the pressure could drive the equilibrium toward the formation of dielectrons. Because the simulations suggest that hydrated dielectrons are kinetically stable, we also examine a scenario for creating metstable, nonequilibrium populations of dielectrons, which involves the capture of a newly injected electron by a preexisting, equilibrated hydrated electron. These calculations, which allow for the full nonadiabatic relaxation of the injected electron, show that hydrated electrons may indeed act as trapping sites for unequilibrated electrons, so that capture may be a viable mechanism for creating dielectrons. We suggest possible experimental procedures to create such nonequilibrium hydrated dielectrons using either pulse radiolysis or ultrafast spectroscopic techniques.

Computer Simulation↗
PubMed2004

In situ determination of the thermodynamic surface properties of chemically modified surfaces on a local scale: an attempt with the atomic force microscope.

We have monitored deflection-distance curves with an atomic force microscope (AFM) in contact mode, with a silicon nitride tip, on chemically modified silicon wafers, in the air. The wafers were modified on their surface by grafting self-assembled monolayers (SAMs) of different functional groups such as methyl, ester, amine, or methyl fluoride. A chemically modified surface with a functionalized hydroxyl group was also considered. Qualitative analysis allowed us to compare adhesive forces versus chemical features and surface energy. The systematic calibration procedure of the AFM measurements was performed to produce quantitative data. Our results show that the experimentally determined adhesive force or thermodynamic work of adhesion increases linearly with the total surface energy determined with contact angles measured with different liquids. The influence of capillary condensation of atmospheric water vapor at the tip-sample interface on the measured forces is discussed. Quantitative assessment values were used to determine in situ the SAM-tip thermodynamic work of adhesion on a local scale, which have been found to be in good agreement with quoted values. Finally, the determination of the surface energy of the silicon wafer deduced from the thermodynamic work of adhesion is also proposed and compared with the theoretical value.

Microscopy, Atomic Force↗
PubMed1996

Synthesis, miscoding specificity, and thermodynamic stability of oligodeoxynucleotide containing 8-methyl-2'-deoxyguanosine.

8-Methyl-2'-deoxyguanosine (8-MedG) was synthesized by reacting dG under the methyl radical generating system and incorporated into oligodeoxynucleotides using phosphoramidite techniques. The site-specifically modified oligodeoxynucleotide containing a single 8-MedG was then used as a template for primer extension reactions catalyzed by the 3' --> 5' exonuclease-free (exo-) Klenow fragment of Escherichia Coli DNA polymerase I and mammalian DNA polymerase alpha. Primer extension catalyzed by the exo- Klenow fragment readily passed the 8-MedG lesion in the template while that catalyzed by pol alpha was retarded opposite the lesion. The fully extended products formed during DNA synthesis were analyzed to quantify the miscoding specificities of 8-MedG. Both DNA polymerases incorporated primarily dCMP, the correct base opposite the lesion, along with small amounts of incorporation of dGMP and dAMP. In addition, two-base deletion was observed only when the exo- Klenow fragment was used. The thermodynamic stability of 8-MedG in the duplex was also studied. The duplex containing 8-MedG:dG was more thermally and thermodynamically stable than that of dG:dG. The duplex containing 8-MedG:dA was more thermodynamically stable than that of dG:dA. We conclude that 8-MedG is a miscoding lesion and capable of generating G --> C and G --> T transversions and deletion in cells.

Chemical Phenomena↗
PubMed1997

Thermodynamics of peroxynitrite and its CO2 adduct.

The equilibrium constant, K3, of aqueous homolysis of peroxynitrous acid into hydroxyl and nitrogen dioxide free radicals was estimated to be 5 x 10(-10) M. This value was derived from a thermodynamic cycle by use of the experimentally known delta fH degree(ONOO-,aq) = -10.8 kcal/mol and the enthalpy of ionic dissociation of ONOOH(aq), delta H degree 1 = 0 kcal/mol, as well as of the entropy of gaseous ONOOH, S degree(ONOOH,g) = 72 eu. Furthermore we assumed the entropy of hydration of ONOOH, delta S degree 2, to be -25 eu, a value closely bracketed by the hydration entropies of analogous substances. The rate constant of radical recombination of OH. with NO2. to yield ONOOH, k-3, was resimulated from experimental data and found to be ca. 5 x 10(9) M-1 s-1. Together with the estimated K3, this yields the homolysis rate constant k3 = 2.5 s-1. This value is close to 0.5 s-1, the rate constant of formation of a reactive intermediate during the isomerization of peroxynitrous acid to nitrate. Our thermodynamic estimate is therefore consistent with substantial amounts of OH. and NO2. free radicals being formed in this process. The thermodynamic implications for the carbon dioxide/peroxynitrite system are also discussed.

Carbon Dioxide↗
PubMed2001

Thermodynamic aspects of hydrophobicity and biological QSAR.

A protein contains a large amount of water molecules, and the nature of the interactions of the water molecules with a protein play an important role in the thermodynamics of the ligand binding process. In this paper, thermodynamic aspects of drug-receptor interactions, enthalpy-entropy compensation or reinforcement, hydrophobicity, and biological 2D- and 3D-QSAR are discussed. Comparisons of the thermodynamic QSAR of phenyl esters of N-benzoyl L-alanine in phosphate buffer and pentanol provide useful insight for the ligand-enzyme interactions.

Alanine↗
PubMed1990

Implications of thermodynamics of protein folding for evolution of primary sequences.

Natural proteins exhibit essentially two-state thermodynamics, with one stable fold that dominates thermodynamically over a vast number of possible folds, a number that increases exponentially with the size of the protein. Here we address the question of whether this feature of proteins is a rare property selected by evolution or whether it is in fact true of a significant proportion of all possible protein sequences. Using statistical procedures developed to study spin glasses, we show that, given certain assumptions, the probability that a randomly synthesized protein chain will have a dominant fold (which is the global minimum of free energy) is a function of temperature, and that below a critical temperature the probability rapidly increases as the temperature decreases. Our results suggest that a significant proportion of all possible protein sequences could have a thermodynamically dominant fold.

Amino Acid Sequence↗
PubMed1993

Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide.

The three-dimensional structures of proteins reveal that the distribution of amino acids within the major classes of secondary structure is not random but that each amino acid has its own preferred secondary structural arrangements. Propensity scales for residues in alpha-helices have been generated through the use of various host-guest systems. Here we measure the thermodynamic beta-sheet propensities of each of the twenty commonly occurring amino acids. A previously studied zinc-finger peptide was used as the host system in which amino acids were substituted into a guest site, a solvent-exposed position in an antiparallel beta-sheet. As these peptides are unfolded in the absence of bound metal but are folded in their presence, it is assumed that the thermodynamics of metal binding fully reflect peptide-folding energy. A competitive cobalt(II)-binding assay was used to determine these energies with high precision. The relative free energies correlate well with previously derived potential values based on statistical analysis of protein structures. We are therefore able to present a thermodynamic beta-sheet propensity scale for all the commonly occurring amino acids in aqueous solution.

Amino Acid Sequence↗
PubMed2002

Anaerobic microbial metabolism can proceed close to thermodynamic limits.

Many fermentative bacteria obtain energy for growth by reactions in which the change in free energy (DeltaG') is less than that needed to synthesize ATP. These bacteria couple substrate metabolism directly to ATP synthesis, however, by classical phosphoryl transfer reactions. An explanation for the energy economy of these organisms is that biological systems conserve energy in discrete amounts, with a minimum, biochemically convertible energy value of about -20 kJ mol-1 (refs 1, 2, 3). This concept predicts that anaerobic substrate decay ceases before the minimum free energy value is reached, and several studies support this prediction. Here we show that metabolism by syntrophic associations, in which the degradation of a substrate by one species is thermodynamically possible only through removal of the end product by another species, can occur at values close to thermodynamic equilibrium (DeltaG' approximately 0 kJ mol-1). The free energy remaining when substrate metabolism halts is not constant; it depends on the terminal electron-accepting reaction and the amount of energy required for substrate activation. Syntrophic associations metabolize near thermodynamic equilibrium, indicating that bacteria operate extremely efficient catabolic systems.

Archaea↗
PubMed1996

In vitro evolution of thermodynamically stable turns.

To determine the role of primary structure in specifying turns, random sequences (guests) were substituted for the native turn sequences in a series of proteins (hosts) of differing thermodynamic stabilities.The fraction of inserts that result in active proteins is measured as a function of the stability of the host and temperature. With a highly stable host, more than half of the inserts give functional proteins. However, a smaller fraction of sequences supports folding as the stability of the host decreases, and the temperature increases. The sequences of many of the selected inserts resemble the wild-type turn, and those that diverge match other established turn preferences. Thermodynamic measurements show that turn sequences selected under stringent conditions result in the most stable proteins. Thus, beta-turns appear to be under evolutionary pressure favouring thermodynamically stable structures.

Amino Acid Sequence↗
PubMed2000

Thermodynamically distinct high and low affinity states of the A(1) adenosine receptor induced by G protein coupling and guanine nucleotide ligation states of G proteins.

The influence of the receptor-G protein coupling state and the guanine nucleotide ligation state of the G protein on the binding mechanism of A(1) adenosine receptor ligands has been investigated in [(3)H]-1,3-dipropyl-8-cyclopentylxanthine ([(3)H]-DPCPX) binding studies in rat brain membranes. Thermodynamic parameters of binding of A(1) adenosine receptor ligands of different intrinsic activities were determined in the absence or presence of GDP and compared to the binding mechanism after receptor-G protein uncoupling. In agreement with previous studies, it was found that xanthine and non-xanthine antagonists showed an enthalpy- or enthalpy- and entropy-driven binding mechanism under all conditions. In contrast to antagonists, the binding mechanism of agonists was strongly affected by the G protein coupling state or the absence or presence of guanine nucleotides. Binding of full and partial agonists to the high-affinity state of the A(1) receptor was entropy-driven in the absence of GDP, and a good correlation between intrinsic activities and the contribution of entropy was observed. In the absence of GDP, binding of full and partial agonists and antagonists to the high affinity state of the receptor was thermodynamically discriminated. In contrast, no such discrimination was found in the presence of GDP. The binding mechanism of agonists to the low-affinity state of the receptor was identical to that of antagonists only after uncoupling of the receptor from G proteins by pretreatment with N-ethylmaleimide or guanosine-5'-(gamma-thio)-triphosphate (GTPgammaS). These results indicate the existence of two thermodynamically distinct high- and low-affinity states of the A(1) adenosine receptor.

Animals↗
PubMed2005

Critical appraisal of available thermodynamic data for the complexation of antimony(III) and antimony(V) by low molecular mass organic ligands.

Antimony is an element of increasing environmental significance but one whose chemical speciation has received little attention and, until recently, one which had not been modelled in any comprehensive way. This paper reports thermodynamic data for computer speciation models of antimony in aqueous, multicomponent solutions of environmental and biological interest involving low molecular mass organic ligands. The available data have been critically evaluated and entered into a thermodynamic database. The JESS suite of computer programs has been used to develop the thermodynamically-consistent mass balance equations used for modelling purposes. No data could be found for Sb(V) complexes and only a few of the existing data for Sb(III) complexes can be considered as being reliably described.

Antimony↗
PubMed2003

Thermodynamic characterization of a tetrahaem cytochrome isolated from a facultative aerobic bacterium, Shewanella frigidimarina: a putative redox model for flavocytochrome c3.

The facultative aerobic bacterium Shewanella frigidimarina produces a small c-type tetrahaem cytochrome (86 residues) under anaerobic growth conditions. This protein is involved in the respiration of iron and shares 42% sequence identity with the N-terminal domain of a soluble flavocytochrome, isolated from the periplasm of the same bacterium, which also contains four c -type haem groups. The thermodynamic properties of the redox centres and of an ionizable centre in the tetrahaem cytochrome were determined using NMR and visible spectroscopy techniques. This is the first detailed thermodynamic study performed on a tetrahaem cytochrome isolated from a facultative aerobic bacterium and reveals that this protein presents unique features. The redox centres have negative and different redox potentials, which are modulated by redox interactions between the four haems (covering a range of 8-56 mV) and by redox-Bohr interactions between the haems and an ionizable centre (-4 to -36 mV) located in close proximity to haem III. All of the interactions between the five centres are clearly dominated by electrostatic effects and the microscopic reduction potential of haem III is the one most affected by the oxidation of the other haems and by the protonation state of the molecule. Altogether, this study indicates that the tetrahaem cytochrome isolated from S. frigidimarina (Sfc) has the thermodynamic properties to work as an electron wire between its redox partners. Considering the high degree of sequence identity between Sfc and the cytochrome domain of flavocytochrome c(3), the structural similarities of the haem core, and that the macroscopic potentials are also identical, the results obtained in this work are rationalized in order to put forward a putative redox model for flavocytochrome c(3).

Cytochrome c Group↗
PubMed1984

Thermodynamics of steroid binding to the human glucocorticoid receptor.

The thermodynamics of the interaction of glucocorticoids with their receptor were studied in cytosol from human lymphoblastoid cells. The rate and affinity constants of dexamethasone and cortisol between 0 degree and 25 degrees C were calculated by curve-fitting from time-course and equilibrium kinetics. The data were consistent with a simple reversible bimolecular interaction. Arrhenius and Van't Hoff plots were curvilinear for both steroids. At equilibrium, the solution for the equation delta G = delta H - T X delta S (eqn. 1) was (in kJ X mol-1) -47 = 36 - 83 (dexamethasone) and -42 = -9 - 33 (cortisol) at 0 degree C. Enthalpy and entropy changes decreased quasi-linearly with temperature such that, at 25 degrees C, the respective values were -50 = -75 + 25 and -43 = -48 + 5. Thus, for both steroids, the interaction was entropy-driven at low temperature and became entirely enthalpy-driven at 20 degrees C. Thermodynamic values for the transition state were calculated from the rate constants. For the forward reaction, eqn. (1) gave 45 = 84 - 39 (dexamethasone) and 46 = 60 - 14 (cortisol) at 0 degree C, and 44 = 24 + 20 (dexamethasone) and 46 = 28 + 18 (cortisol) at 25 degrees C. These data fit quite well with a two-step model [Ross & Subramanian (1981) Biochemistry 20, 3096-3102] proposed for ligand-protein interactions, which involves a partial immobilization of the reacting species governed by hydrophobic forces, followed by stabilization of the complex by short-range interactions. On the basis of this model, an analysis of the transition-state thermodynamics led to the conclusion that no more than half of the steroid molecular area is engaged in the binding process.

Cell Line↗
PubMed1988

A study of the hydration and thermodynamics of warm-water and cold-water fish collagens.

The hydrated volumes, Vh, of collagens extracted from various fish species were calculated by using the Simha-Einstein equation, and it was found that the hydration of warm-water fish collagen is greater than that of cold-water fish collagen (halibut). Although the intrinsic viscosities of warm-water fish (bigeye-tuna, carp and catfish) collagens are almost the same, the hydrated volume of bigeye-tuna collagen is approx. 1.5 and 3 times those of carp and catfish collagens respectively. The extent of hydration at 20 degrees C is in the following order: bigeye tuna greater than carp greater than catfish greater than halibut. The various thermodynamic activation parameters (delta G*, delta H* and delta S*) were calculated and it was found that they are useful for determining the exact denaturation temperature. It was calculated that the denaturation temperatures of halibut, bigeye-tuna, carp and catfish collagens are 17, 31, 32 and 26-30 degrees C respectively. The variations of hydration, intrinsic viscosity, denaturation temperature and the thermodynamic parameters with the variation of concentration of catfish collagen were also thoroughly examined. The change of thermodynamic parameters from coiled-coil to random-coil conformation upon denaturation of collagen were calculated from the amount of proline and hydroxyproline residues and compared with viscometric results.

Animals↗