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PubMed1998

Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range.

The photocycle of bacteriorhodopsin and its thermodynamic parameters were studied in the pH range of 4.5-9. Measurements were performed at five different wavelengths (410, 500, 570, 610, and 650 nm), in the time interval 300 ns to 0.5 s, at six temperatures between 5 and 30 degreesC. Data were fitted to different photocycle models. The sequential model with reversible reactions gave a good fit, and the linear character of the Eyring plots was fulfilled. The parallel model with unidirectional reactions gave a poor fit, and the Eyring plot of the rate constants did not follow the expected linear behavior. When a parallel model with reversible reactions, which has twice as many free parameters as the sequential model, was considered, the quality of the fit did not improve and the Eyring plots were not linear. The sequential model was used to determine the thermodynamic activation parameters (activation enthalpy, entropy, and free energy) of the transitions and the free energy levels of the intermediates. pH dependence of the parameters revealed details of the transitions between the intermediates: the transitions M1 to M2 and N to O disclosed a large entropy increase, which could be interpreted as a loosening of the protein structure. The pH dependence of the energy levels explains the disappearance of intermediate O at high pH. A hypothesis is proposed to interpret the relation between the observed pKa of the photocycle energetics and the role of several amino acids in the protein.

Bacteriorhodopsins↗
PubMed1999

Thermodynamics of interactions between amino acid side chains: experimental differentiation of aromatic-aromatic, aromatic-aliphatic, and aliphatic-aliphatic side-chain interactions in water.

A stationary phase for high-pressure liquid chromatography has been prepared by derivatizing microparticulate silica gel with functionality mimicking the side chain of isoleucine. The chromatographic retentions of a series of hydrophobic and amphiphilic amino acid analytes on this stationary phase (Ile MSP) using an aqueous mobile phase were measured as a function of temperature from 273 K to 323 K. Observed temperature dependencies are consistent with a constant change in heat capacity, DeltaC degrees P, upon binding of the analyte to the stationary phase. The curvatures of plots of retention data versus temperature (related to the magnitude of DeltaC degrees P) are distinctly different for retention of aromatic and aliphatic analytes, with retention of aliphatic analytes Val, Ile, and Leu exhibiting the characteristic signature of the hydrophobic effect, i.e., a large negative DeltaC degrees P upon desolvation from water and a maximum of retention around room temperature. Retention of aromatic analytes (Trp, Phe, and Tyr) involves smaller heat capacity changes and pronounced negative enthalpies of interaction with the stationary phase. Estimates of DeltaC degrees P for the interactions of analyte side chains with the Ile side chain were obtained by fitting the temperature dependence of retention to an expression derived from thermodynamic considerations and chromatographic theory. Similar estimates were made for interactions with the Phe side chain, using previously published data for a phenylalanine mimic stationary phase (Phe MSP) (. Protein Sci. 1:786-795). As with the Ile MSP, the retentions of aliphatic analytes show temperature dependencies markedly different from those of aromatic analytes. Data from both phases indicate that a realistic differentiation can be made between the interactions of various types of amino acid side chains tested (i.e., aliphatic/aliphatic, aliphatic/aromatic, and aromatic/aromatic) by comparison of the corresponding thermodynamic functions for pairwise interactions. The retention of leucine on the Phe MSP and that of phenylalanine on the Ile MSP showed similar DeltaC degrees P values, suggesting that the aromatic-aliphatic interaction is reasonably independent of the residue attached to the stationary phase. This result is consistent with a one-to-one interaction and suggests a simple way to estimate the column-dependent phase factor, making it possible to compare entropies and free energies of interaction obtained using different MSPs. The possibilities for using MSP-derived interaction potentials in folding simulations are discussed.

Amino Acids↗
PubMed1999

Thermodynamics and kinetics of a folded-folded' transition at valine-9 of a GCN4-like leucine zipper.

Spin inversion transfer (SIT) NMR experiments are reported probing the thermodynamics and kinetics of interconversion of two folded forms of a GCN4-like leucine zipper near room temperature. The peptide is 13Calpha-labeled at position V9(a) and results are compared with prior findings for position L13(e). The SIT data are interpreted via a Bayesian analysis, yielding local values of T1a, T1b, kab, kba, and Keq as functions of temperature for the transition FaV9 right arrow over left arrow FbV9 between locally folded dimeric forms. Equilibrium constants, determined from relative spin counts at spin equilibrium, agree well with the ratios kab/kba from the dynamic SIT experiments. Thermodynamic and kinetic parameters are similar for V9(a) and L13(e), but not the same, confirming that the molecular conformational population is not two-state. The energetic parameters determined for both sites are examined, yielding conclusions that apply to both and are robust to uncertainties in the preexponential factor (kT/h) of the Eyring equation. These conclusions are 1) the activation free energy is substantial, requiring a sparsely populated transition state; 2) the transition state's enthalpy far exceeds that of either Fa or Fb; 3) the transition state's entropy far exceeds that of Fa, but is comparable to that of Fb; 4) "Arrhenius kinetics" characterize the temperature dependence of both kab and kba, indicating that the temperatures of slow interconversion are not below that of the glass transition. Any postulated free energy surface for these coiled coils must satisfy these constraints.

Amino Acid Sequence↗
PubMed2002

Effect of molecular structure on thermodynamic properties of carbohydrates. A calorimetric study of aqueous di- and oligosaccharides at subzero temperatures.

For aqueous solutions of di- and oligosaccharides thermodynamic properties have been investigated at subzero temperatures using differential scanning calorimetry. The amount of unfrozen water observed is found to increase linearly with the glass transition temperatures of anhydrous carbohydrates. Furthermore, the amount of unfrozen water shows a linear relationship with known solution properties of aqueous carbohydrates, such as partial molar compressibility and heat of solution. The different effectiveness among various di- and oligosaccharides to avoid ice formation is associated with the combination of constitutive monosaccharides and attendant molecular structure features including the position and type of the glycosidic linkage between the constituent units. More unfrozen water is induced in the presence of a carbohydrate having a poorer compatibility with the three-dimensional hydrogen-bond network of water. A series of these results obtained imply that there is a common key of carbohydrate stereochemistry governing several different thermodynamic amounts of a given system involving carbohydrates. In this context, a modified stereospecific-hydration model can be used to interpret the present results in terms of stereochemical effects of carbohydrates.

Calorimetry, Differential Scanning↗
PubMed2002

Temperature dependence of the affinity enhancement of selective adenosine A1 receptor agonism: a thermodynamic analysis.

The 2-amino-benzoylthiophene derivatives LUF 5468 [(2-amino-4-ethyl-5-methyl-3-thienyl)[3-(trifluoromethyl)phenyl]methanone] and LUF 5484 [(2-amino-4,5,6,7-tetrahydrobenzo[b]thiophen-3-yl)(3,4-dichlorophenyl)methanone] have been shown to allosterically enhance the adenosine A(1) receptor agonist binding. We report a thermodynamic analysis of the agonist affinity obtained at human adenosine A(1) receptors, in the presence and absence of LUF 5468 and LUF 5484. Moreover, an analysis of the temperature dependence for association and dissociation rates of N(6)-cyclohexyladenosine (CHA) binding was performed in the absence and presence of LUF 5484. Thermodynamic data were obtained by affinity measurements performed at different temperatures followed by van't Hoff analysis. The results indicate that the agonist binding is always totally entropy-driven, and that the modulators contribute to decrease the deltaG(o), deltaH(o) and deltaS(o) values. It is concluded that the enhancers are able to increase the non-bonded interactions of the binding site with agonists as CHA, N(6)-cyclopentlyladenosine (CPA), 2'-methyl-N(6)-cyclopentyladenosine (MeCPA) and 2-chloro-2'methyl-N(6)-cyclopentyladenosine (MeCCPA).

Animals↗
PubMed2001

Thermodynamic analysis of the binding of galactose and poly-N-acetyllactosamine derivatives to human galectin-3.

Galectin-3, with a wide tissue distribution and marked developmental regulation, provides significant insights into the progression of various disease and developmental stages. Recognized by its specificity for galactose, a detailed characterization of its sugar binding ability has been investigated by isothermal titration calorimetry. The results presented here complement well with the earlier studies utilizing hapten inhibition assays. Among the various lactose derivatives studied, A-tetrasaccharide emerged with the highest affinity for binding to galectin-3 combining site. This blood group saccharide exhibited a binding affinity 37-fold higher and a 102 kJ/mol more favorable change in enthalpy over lactose at 280 K indicating the existence of additional subsites for both the alpha1-3-linked N-acetylgalactosamine at the non-reducing end and the alpha1-2-linked L-fucosyl residue. The thermodynamic parameters evaluated for other ligands substantiate further the carbohydrate recognition domain to be part of an extended binding site. Binding thermodynamics of galectin-3 with the galactose derivatives are essentially enthalpically driven and exhibit compensatory changes in DeltaH degrees and TDeltaS owing to solvent reorganization.

Antigens, Differentiation↗
PubMed1997

Thermodynamic characterizations of an intramolecularly hydrogen bonded C5-structure across proteinogenic residue.

Thermodynamic investigations of a smallest possible intramolecularly hydrogen bonded C5-structure, across a Thr residue, in model peptides Boc-Xxx-Thr-NH2 (Xxx = Ile, 1 or Leu, 2), indicated unusual thermal stability of the structure in non-polar medium. An analysis of van't Hoff plots, constructed from variable temperature 1H NMR data, yielded the thermodynamic parameters of a hydrogen bonded five-membered ring. The non-significance of the spatial organizations of the preceding CdeltaH3 bearing hydrophobic proteinogenic residue on the thermal stability of the C5-structure has been observed. The results revealed that the contribution of this element of secondary structure is quantifiable and the stability appeared to be roughly comparable to other intramolecularly hydrogen bonded reverse turn structures frequently observed in polypeptides and proteins.

Amides↗
PubMed1999

The thermodynamics and kinetics of electron transfer in the cytochrome P450cam enzyme system.

In anaerobic environments the first electron transfer in substrate-free P450cam is known to be thermodynamically unfavourable, but in the presence of dioxygen the reduction potential for the reaction shifts positively to make electron transfer thermodynamically favourable. Nevertheless a slower rate of electron transfer is observed in the substrate-free P450cam compared to substrate-bound P450cam. The ferric haem centre in substrate-free P450cam changes from six co-ordinate to five co-ordinate when reduced whereas in substrate-bound P450cam the iron centre remains five co-ordinate in both oxidation states. The slower rate of electron transfer in the substrate-free P450cam is therefore attributed to a larger reorganisation energy as predicted by Marcus theory.

Animals↗
PubMed1999

Thermodynamics of nucleotide binding to NBS-I of the Bacillus subtilis preprotein translocase subunit SecA.

SecA is the dissociatable nucleotide and preprotein binding subunit of the bacterial translocase. The thermodynamics of nucleotide binding to soluble SecA at nucleotide binding site I were determined by isothermal titration calorimetry. Binding of ADP and non-hydrolyzable ATPgammaS is enthalpy-driven (DeltaH(0) of -14.44 and -5.56 kcal/mol, respectively), but is accompanied by opposite entropic contributions (DeltaS(0) of -18.25 and 9.55 cal/mol/K, respectively). ADP binding results in a large change in the heat capacity of SecA (DeltaC(p)=-780 cal/mol/K). It is suggested that ADP binding promotes the interaction between the two thermodynamically discernible domains of SecA which is accompanied by a shielding of hydrophobic surface from solvent.

Adenosine Diphosphate↗
PubMed1998

Imposing thermodynamic restrictions on the elastic constant-fabric tensor relationship.

Zysset and Curnier (1995) rederive the general representation for the fourth rank elasticity tensor in terms of the fabric tensor given originally by Cowin (1985). Zysset and Curnier (1995) then obtain a form of the representation that is sufficiently restricted to satisfy the thermodynamic constraint that the compliance tensor be positive definite. Zysset and Curnier (1995, 1996) argue that their representation has an advantage over that of Cowin (1985) because it has, a priori, been sufficiently restricted to satisfy the thermodynamic constraint that the compliance tensor be positive definite. The purpose of this note is to point out that the limitations of the Zysset and Curnier (1995, 1996) sufficiency representation are quite severe, restricting the flexibility of the model by allowing only five of the nine normally independent orthotropic elastic coefficients to be independent. Potential users should consider employing the Cowin (1985) representation and subsequently imposing the condition that the elasticity tensor be positive definite.

Algorithms↗
PubMed2002

Characterisation of reversed-phase stationary phases for the liquid chromatographic analysis of basic pharmaceuticals by thermodynamic data.

This paper describes the characterisation of reversed-phase liquid chromatography (RPLC) columns using thermodynamic measurements. Retention versus 1/T data were used to construct Van't Hoff plots. The slope of these plots indicates the standard enthalpy of transfer of the analyte from the mobile to the stationary phase. The standard entropy can be calculated from the intercept. Van't Hoff plots were linear for the investigated RPLC columns, meaning that for basic analytes over the temperature range studied no changes in the retention mechanism occurred. Enthalpies and entropies of transfer of basic analytes from the mobile to the stationary phase revealed information about the types of interaction of protonated and neutral compounds with the stationary phases. However, a clear view using the present set of basic compounds on how these thermodynamic data may explain the observed substantial differences in peak symmetry cannot be given. It is considered that addition of N,N-dimethyloctylamine (DMOA) to the eluent will results in a dynamically coating of the stationary phase. Addition of DMOA to the eluent resulted for protonated basic compounds in a reduction of both enthalpy and entropy. In practice, with DMOA in the eluent symmetrical peaks were obtained. It is assumed that this is due to blocking residual silanols and/or ion exclusion effects.

Chromatography, Liquid↗
PubMed2003

Complex formation of a calcium-dependent antibody: a thermodynamical consideration.

The elution of FLAG-fusions (an octapeptide with the sequence DYKDDDDK) from immobilized anti-FLAG antibody M1 cannot be explained by a switch of the equilibrium binding constant to a lower value. To get a further insight into thermodynamics, the binding of anti-FLAG antibody M1 to the FLAG peptide was studied by real-time biosensor technology at seven different temperatures in the range from 5 to 35 degrees C. Binding studies were performed in the presence and absence of calcium. Thermodynamic parameters such as change in Gibbs free energy (deltaG), enthalpy (deltaH) and entropy (deltaS) were evaluated from the corresponding equilibrium data applying the integrated Van't Hoff equation. In contrast to similar kinetic data obtained, the contribution of deltaH and deltaS to deltaG in the presence or absence of calcium results in a different conformation of the antibody-antigen complex under binding and non-binding conditions. Therefore, complex dissociation with EDTA must be effected during a transition state of complex formation and dissociation.

Antibodies, Monoclonal↗
PubMed1999

Synthesis and properties of two new liquid crystals: an analytical and thermodynamic study.

Synthesis, analytical performances, thermodynamic and surface properties of two new liquid crystals substituted with poly(ethylene oxide) chains are described. The first of them is N,N'-diphenyl-[4-[2,3,4-tri[2-(2-metoxyethoxy)ethoxy]benzylidene]i mine]piperidine (LC1) and the second is 2-hydroxy-3-methyl-4-[4-[2-(2-butoxyethoxy)ethoxy]] 4'-[4-[2-(2-butoxyethoxy)ethoxy]styryl]azobenzene (LC2). The nematic ranges of the two liquid crystals, determined by differential scanning calorimetry do not interfere. The analytical and thermodynamic studies of LC1 and LC2 in the solid, nematic and liquid state were done using a series of appropriate solutes. Comparison of the analytical performances shows a better efficiency in the nematic state.

Azo Compounds↗
PubMed2002

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.

We perform a detailed analysis of the thermodynamics and folding kinetics of the SH3 domain fold with discrete molecular dynamic simulations. We propose a protein model that reproduces some of the experimentally observed thermodynamic and folding kinetic properties of proteins. Specifically, we use our model to study the transition state ensemble of the SH3 fold family of proteins, a set of unstable conformations that fold to the protein native state with probability 1/2. We analyze the participation of each secondary structure element formed at the transition state ensemble. We also identify the folding nucleus of the SH3 fold and test extensively its importance for folding kinetics. We predict that a set of amino acid contacts between the RT-loop and the distal hairpin are the critical folding nucleus of the SH3 fold and propose a hypothesis that explains this result.

Amino Acid Sequence↗
PubMed2002

Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior.

Effects of amino acid substitutions at four fully buried sites of the ubiquitin molecule on the thermodynamic parameters (enthalpy, Gibbs energy) of unfolding were evaluated experimentally using differential scanning calorimetry. The same set of substitutions has been incorporated at each of four sites. These substitutions have been designed to perturb packing (van der Waals) interactions, hydration, and/or hydrogen bonding. From the analysis of the thermodynamic parameters for these ubiquitin variants we conclude that: (i) packing of non-polar groups in the protein interior is favorable and is largely defined by a favorable enthalpy of van der Waals interactions. The removal of one methylene group from the protein interior will destabilize a protein by approximately 5 kJ/mol, and will decrease the enthalpy of a protein by 12 kJ/mol. (ii) Burial of polar groups in the non-polar interior of a protein is highly destabilizing, and the degree of destabilization depends on the relative polarity of this group. For example, burial of Thr side-chain in the non-polar interior will be less destabilizing than burial of Asn side-chain. This decrease in stability is defined by a large enthalpy of dehydration of polar groups upon burial. (iii) The destabilizing effect of dehydration of polar groups upon burial can be compensated if these buried polar groups form hydrogen bonding. The enthalpy of this hydrogen bonding will compensate for the unfavorable dehydration energy and as a result the effect will be energetically neutral or even slightly stabilizing.

Amino Acids↗
PubMed2002

A buried polar residue in the hydrophobic interface of the coiled-coil peptide, GCN4-p1, plays a thermodynamic, not a kinetic role in folding.

The hydrophobic interfaces of coiled-coil proteins and peptides are typically interspersed with buried polar residues. These polar residues are known to be important for defining oligomeric specificity and chain orientation in coiled-coil formation; however, their effects on the folding/assembly reaction have not been investigated. The commonly studied 33-residue dimeric leucine zipper peptide, GCN4-p1, contains a single polar Asn in the center of the hydrophobic interface at position 16. Peptides containing either a valine or an alanine replacement at this position, N16V and N16A, respectively, were studied in order to investigate both the thermodynamic and kinetic roles of the buried polar side-chain on the folding of GCN4-p1. Equilibrium sedimentation confirmed that both the N16V and N16A mutations reduce the dimeric specificity of GCN4-p1, leading to the population of both dimers and trimers in the absence of denaturant. Guanidine hydrochloride-induced equilibrium unfolding of the mutant peptides demonstrated that N16V is more stable than the wild-type sequence, while the N16A peptide is moderately destabilized. Comparison of the refolding reactions indicate that Asn16 is not involved in the rate-limiting association step leading to the native dimer; only the unfolding reaction is sensitive to the mutations. More complex unfolding kinetics for both peptides at high peptide concentrations can be attributed to the presence of trimers in the absence of denaturant. These results show that the role of buried polar residues in leucine zipper peptides can be primarily thermodynamic; subunit exchange reactions can be controlled by the stability of the native coiled coil and its influence on the unfolding/dissociation process.

Alanine↗
PubMed2002

A structure-based interpretation of E.coli GrpE thermodynamic properties.

GrpE is the nucleotide exchange factor for the Escherichia coli molecular chaperone DnaK, the prokaryotic homologue of Hsp70. Thermodynamic properties of GrpE structural domains were characterized by examining a number of structural and point mutants using circular dichroism, differential scanning calorimetry and analytical ultracentrifugation. These structural domains are the long paired N-terminal helices, the central four-helix bundle, and the C-terminal compact beta-domains. We show that the central four-helix bundle (t(m) approximately 75 degrees C) provides a stable platform for the association of the long paired N-terminal helices (t(m) approximately 50 degrees C), which can then function as a temperature sensor. The stability of the N-terminal helices is linked to the presence of the C-terminal compact beta-domains of GrpE, providing a potential mechanism for coupling of DnaK-binding activity of GrpE with temperature. On the basis of our thermodynamic analysis of E.coli GrpE, we present a structure-based model for the melting properties of the nucleotide exchange factor, wherein the long paired helices function as a molecular thermocouple.

Bacterial Proteins↗
PubMed2002

Thermodynamics of peptide binding to the transporter associated with antigen processing (TAP).

The ATP-binding cassette (ABC) transporter TAP plays an essential role in antigen processing and immune response to infected or malignant cells. TAP translocates proteasomal degradation products from the cytosol into the endoplasmic reticulum, where MHC class I molecules are loaded with these peptides. Kinetically stable peptide-MHC complexes are transported to the cell surface for inspection by cytotoxic T lymphocytes. The transport cycle of TAP is initiated by peptide binding, which is responsible for peptide selection and for stimulation of ATP-hydrolysis and subsequent translocation. Here we have analysed the driving forces for the formation of the peptide-TAP complex by kinetic and thermodynamic methods. First, the apparent peptide association and dissociation rates were determined at various temperatures. Strikingly, very high activation energies for apparent association (E(a)(ass)=106 kJmol(-1)) and dissociation (E(a)(diss)=80 kJmol(-1)) of the peptide-TAP complex were found. Next, the temperature-dependence of the peptide affinity constants was investigated by equilibrium-binding assays. Along with calculations of free enthalpy deltaG, enthalpy deltaH and entropy deltaS, a large positive change in heat capacity was resolved (deltaC degrees =23 kJmol(-1)K(-1)), indicating a fundamental structural reorganization of the TAP complex upon peptide binding. The inspection of the conformational entropy reveals that approximately one-fourth of all TAP residues is rearranged. These thermodynamic studies indicate that at physiological temperature, peptide binding is endothermic and driven by entropy.

ATP-Binding Cassette Transporters↗