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PubMed1988

Characteristic thermodynamic properties of hydrated water for 20 amino acid residues in globular proteins.

Thermodynamic properties associated with hydrated water of proteins of known three-dimensional structure were computed and average values of hydration free energy, enthalpy, and heat capacity of unfolding for every amino acid residue were obtained. Each amino acid residue had characteristic values; in particular, the quantities for a side chain reflected the character of the amino acid, while those for the main chain were more or less the same except for glycine, alanine, and proline. The major contribution to the quantities was from the end group(s) of a side chain. The following interesting features were found. 1) The hydration quantity of unfolding derived from the native and extended conformations for a protein was approximately equal to the sum of the corresponding average quantities of component amino acid residues in the protein. 2) The profile of a quantity such as hydration free energy of unfolding along the sequence computed from the accessible surface areas of the native and extended conformations showed a strong correlation with the profile obtained by allocating the average value for the amino acid residue at every position on the sequence. The correlation coefficients between two profiles for unfolding quantities of hydration, i.e., free energy, enthalpy, heat capacity, and free energy of side chain are 0.72, 0.62, 0.80, and 0.75, respectively. Thus, every amino acid residue in the native conformation of a globular protein seems to be located in such a position that a thermodynamic quantity for each residue is approximately equal to its average value.

Amino Acids↗

PubMed1976

Studies on luciferase from Photobacterium phosphoreum. VIII. FMN-H2O2 initiated bioluminescence and the thermodynamics of the elementary steps of the luciferase reaction.

Bacterial luciferase from Photobacterium phosohoreum was found to produce bioluminescence on reaction with FMN and H2O2 in the presence of aldehyde. This luminescence is presumably produced by the same X1 intermediate as that found in FMNH2-O2 initiated luminescence. From the ratio of the light intensities of the FMN-H2O2 initiated reactions, we calculated the association constant of the reaction, luciferase+FMN+H2O2in equilibriumX1, and estimated its temperature dependence. From these results we calculated the thermodynamic parameters of the reaction, luciferase+FMNH2+O2in equilibriumX1. We found that the free energy level of X1 is only 3.2 kcal below that of fr-e FMN and H2O2. We also estimated the thermodynamic parameters of other steps of the luminescent reaction. The values obtained showed that the formation of X1 from luciferase, FMNH2 and O2 involves a positive entropy change, but the intermediate is in a state stabilized against decomposition. Results also suggest a considerable degree of electronic rearrangement on formation of the excited-state molecule from the X1-aldehyde complex.

Aldehydes↗

PubMed2002

Thermodynamic characterization of variants of mesophilic cytochrome c and its thermophilic counterpart.

Thermal stability was measured for variants of cytochrome c-551 (PA c-551) from a mesophile, Pseudomonas aeruginosa, and a thermophilic counterpart, Hydrogenobacter thermophilus cytochrome c-552 (HT c-552), by differential scanning calorimetry (DSC) at pH 3.6. The mutated residues in PA c-551, selected with reference to the corresponding residues in HT c-552, were located in three spatially separated regions: region I, Phe7 to Ala/Val13 to Met; region II, Glu34 to Tyr/Phe43 to Tyr; and region III, Val78 to Ile. The thermodynamic parameters determined indicated that the mutations in regions I and III caused enhanced stability through not only enthalpic but also entropic contributions, which reflected improved packing of the side chains. Meanwhile, the mutated region II made enthalpic contributions to the stability through electrostatic interactions. The obtained differences in the Gibbs free energy changes of unfolding [Delta(DeltaG)] showed that the three regions contributed to the overall stability in an additive manner. HT c-552 had the smallest heat capacity change (DeltaC(P)), resulting in higher DeltaG values over a wide temperature range (0-100 degrees C), compared to the PA c-551 variants; this contributed to the highest stability of HT c-552. Our DSC measurement results, in conjunction with mutagenesis and structural studies on the homologous mesophilic and thermophilic cytochromes c, provided an extended thermodynamic view of protein stabilization.

Bacteria↗

PubMed1993

Breakdown in the relationship between thermal and thermodynamic stability in an interleukin-1 beta point mutant modified in a surface loop.

Sequence variants of the beta-barrel protein interleukin-1 beta have been analyzed for their stabilities toward irreversible thermal inactivation by monitoring the generation of light scattering aggregates on heating. The derived temperatures for the onset of aggregation (T(agg) values) correlate well with the free energies of unfolding of these proteins with the exception of one variant, Lys97-->Val (K97V), which undergoes aggregation at a temperature 7 degrees C lower than expected based on its thermodynamic stability. This lower than expected thermal stability may be due to generation of an aggregation-prone unfolding intermediate at a temperature lower than the Tm of the global transition. This hypothesis is supported by the location of residue 97 in the long 86-99 loop which has structural features suggesting it may comprise a small, independent folding unit or microdomain. The excellent correlation of thermal and thermodynamic stabilities of seven of the eight variants tested is consistent with accepted models for thermal inactivation of proteins. At the same time the poor fit of the K97V variant underscores the risk in using thermal stability data in quantitative analysis of mutational studies of the folding stability of proteins.

Crystallography, X-Ray↗

PubMed2004

An improved non-linear thermodynamic model of voltage-dependent ionic currents.

Thermodynamic models of ionic currents are used to deduce exact functional form of rate constant. It is first assumed that free energy depends linearly on voltage. A major criticism of this approach is that time constant can reach arbitrarily small values resulting in an aberrant behavior. Recently, non-linear effects of electric field on the free energy were considered to solve this problem based on T-type calcium channel. In this study, we show that the current model approximately captures the voltage-dependence of the time constant only in a specific range of voltage and does not provide saturation of the time constant outside this range. Then, we propose an improved non-linear thermodynamic model and illustrate its applicability based on T-type calcium channel.

Animals↗

PubMed1979

Thermodynamic studies of cellular adhesion.

Cellular adhesion of granulocytes and of platelets to solid substrates of different surface tensions has been studied from a thermodynamic aspect. A simple thermodynamic model predicts that cellular adhesion should increase as the surface tension of the solid substrate increases provided that the surface tension of the liquid medium in which the cells are suspended is lower than the surface tension of the cells themselves. If, however, the surface tension of the liquid medium is higher than the surface tension of the cells, then a decrease in cell adhesion with increasing substrate surface tension can be predicted. These predictions are completely substantiated by granulocyte adhesion tests in which the surface tension of the suspending liquid medium is varied through the addition of different volumes of dimethyl sulfoxide (DMSO). Platelet adhesion experiments also confirmed these predictions, the only difference being that it is not possible to obtain a suspending liquid medium with a surface tension higher than that of platelets themselves, as a consequence of the exudation of surface active substances by the platelets.

Blood Platelets↗

PubMed1986

Thermodynamic properties of erythrocyte Li efflux may facilitate detection of essential hypertension in pregnant women.

Thermodynamic properties of red cell lithium efflux were examined in pregnant women in relation to hypertension. Twenty-two normotensive women, 15 women with essential hypertension, and 27 with pregnancy-induced hypertension were studied. The rates of Li efflux at 37 degrees C in the three groups of pregnant women were similar and nondiscriminatory. The temperature dependence of the Li efflux, known to be uniquely modified in essential hypertension, allowed the differentiation of most (73%) of the pregnant women with essential hypertension as well. Among the women with pregnancy-induced hypertension, 63% showed a temperature-dependence pattern typical for normotensives, and they may be classified as patients with toxemia of pregnancy. The others (37%) showed a thermodynamic pattern of essential hypertension, but a follow-up study is required to ascertain whether they will indeed develop essential hypertension in the future.

Adult↗

PubMed1991

Non-equilibrium thermodynamic sensitivity of oxidative phosphorylation.

A new method was developed to analyse the dynamic properties of oxidative phosphorylation, in particular the sensitivity of the phosphate potential with respect to fluctuating cellular ATP utilization. This treatment is based on the eigenvalue sensitivity analysis of an experimentally supported non-equilibrium thermodynamic model of oxidative phosphorylation. Such an analysis allows direct access to the kinetic information, while circumventing the awkward conventional numerical integration of a set of nonlinear differential equations. This procedure revealed, for the parameters characteristic for liver of starved rats in vivo, that the sensitivity of oxidative phosphorylation to a fluctuating ATP utilization is minimal at a degree of coupling q = 0.95. This means that the phosphate potential is highly buffered with respect to fluctuating energy demands at the degree of coupling. This value of q agrees well with the degree of coupling qeef, at which net ATP production of oxidative phosphorylation--at optimal efficiency--occurs in the most economic way. This simultaneous maximization of kinetic stability and economic thermodynamic efficiency at the same degree of coupling appears to be a coincidence.

Adenosine Triphosphate↗

PubMed2006

Summarizing lecture: factors influencing enzymatic H-transfers, analysis of nuclear tunnelling isotope effects and thermodynamic versus specific effects.

In the articles in this Discussion, a wide variety of topics are treated, including reorganization energy, initially introduced for electron transfers ('environmentally assisted tunnelling'), nuclear tunnelling, H/D and 12C/13C kinetic isotope effects (KIEs), the effect of changes of distal and nearby amino acid residues using site-directed mutagenesis, and dynamics versus statistical effects. A coordinate-free form of semi-classical theory is used to examine topics on data such as tunnelling versus 'over-the-barrier' paths and temperature and pressure effects on KIEs. The multidimensional semi-classical theory includes classically allowed and classically forbidden transitions. More generally, we address the question of relating kinetic to thermodynamic factors, as in the electron transfer field, so learning about specific versus thermodynamic effects in enzyme catalysis and KIEs.

Amino Acids↗

PubMed2003

Thermodynamic molecular switch in sequence-specific hydrophobic interaction: two computational models compared.

We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in DeltaCp(o)(T)reaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related K(eq). We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273-333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed. The change in inherent chemical bond energy at 0 K, DeltaH(o)(T0) is 7.53 kcal mol(-1) compared with 2.4 kcal mol(-1), while is 365 K as compared with 355 K, for the Nemethy-Scheraga and Planck-Benzinger model, respectively. At , the thermal agitation energy is about five times greater than DeltaH(o)(T0) in the Planck-Benzinger model, that is 465 K compared to 497 K in the Nemethy-Scheraga model. The results imply that the negative Gibbs free energy minimum at a well-defined , where TDeltaS(o) = 0 at about 355 K, has its origin in the sequence-specific hydrophobic interactions, which are highly dependent on details of molecular structure. The Nemethy-Scheraga model shows no evidence of the thermodynamic molecular switch that we have found to be a universal feature of biological interactions. The Planck-Benzinger method is the best known for evaluating the innate temperature-invariant enthalpy, DeltaH(o)(T0), and provides for better understanding of the heat of reaction for biological molecules.

Chemical Phenomena↗

PubMed2001

Thermodynamically important contacts in folding of model proteins.

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.

Amino Acids↗

PubMed2006

Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each beadlike amino acid interacts with the others through a contact potential controlled by a random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical ensembles, namely, a coil-like ensemble, an unfolded globule, and a folded ensemble (plus two other states, frozen and random coils, populated only at extreme temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed.

Amino Acid Sequence↗

PubMed2006

Modeling protein thermodynamics and fluctuations at the mesoscale.

We use an extended Go model, in unfrustrated and frustrated variants, to study the energy landscape and the fluctuations of a model protein. The model exhibits two transitions, folding and dynamical transitions, when changing the temperature. The inherent structures corresponding to the minima of the landscape are analyzed and we show how their energy density can be obtained from simulations around the folding temperature. The scaling of this energy density is found to reflect the folding transition. Moreover, this approach allows us to build a reduced thermodynamics in the inherent structure landscape. Equilibrium studies, from full molecular dynamics (MD) simulations and from the reduced thermodynamics, detect the features of a dynamical transition at low temperature and we analyze the location and time scale of the fluctuations of the protein, showing the need of some frustration in the model to get realistic results. The frustrated model also shows the presence of a kinetic trap which strongly affects the dynamics of folding.

Computer Simulation↗

PubMed2000

Cell proliferation in normal and malignant transformed cells: thermodynamic model of signal transduction.

We present a new thermodynamic model for the mechanism of activation and regulation of cell proliferation in the G1 stage. In this model, the interactions between growth factors and transmembrane proteins play a crucial role in cell growth control for a normal tissue-culture system. We calculate a phase diagram of normal and malignant transformed states of a cell signal transduction system. We propose thermodynamic reasons why cancer cells can continually grow without activation by the growth factors.

Biophysical Phenomena↗

PubMed2003

Line thermodynamics: adsorption at a membrane edge.

We report a novel experimental study of line thermodynamics. Our system consists of detergent molecules adsorbing at the edges of freestanding lipid bilayers. Adsorption reduces the line tension T of the membrane edges. Measuring T as a function of the bulk detergent concentration C, we obtain a line adsorption isotherm. Using an extension of Gibbs's surface thermodynamics to lines, we estimate the "line excess density" of adsorbants and the energy of adsorption per site.

Adsorption↗

PubMed2005

Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch.

We develop a rigorous nonequilibrium thermodynamics for an open system of nonlinear biochemical reactions responsible for cell signal processing. We show that the quality of the biological switch consisting of a phosphorylation-dephosphorylation cycle, such as those in protein kinase cascade, is controlled by the available intracellular free energy from the adenosine triphosphate (ATP) hydrolysis in vivo: DeltaG=k(B)Tln(([ATP]/K(eq)[ADP]), where K(eq) is the equilibrium constant. The model reveals the correlation between the performance of the switch and the level of DeltaG. The result demonstrates the importance of nonequilibrium thermodynamics in analyzing biological information processing, provides its energetic cost, establishes an interplay between signal transduction and energy metabolism in cells, and suggests a biological function for phosphoenergetics in the ubiquitous phosphorylation signaling.

Adenosine Diphosphate↗

PubMed2002

Thermodynamic relationships between protein-solvent and protein-protein interactions.

How the solvent modulates the weak inter-particle interactions in solution and affects macromolecule solubility is not yet understood. Well-established thermodynamic relationships link second virial coefficient and preferential solute binding parameter. We present the meaning of these thermodynamic parameters and the way to measure them. When a solvation shell has a composition different from the bulk solvent, a negative contribution is found in the second virial coefficient corresponding to an effective attraction between the macromolecules in solution. A quantitative evaluation using simple models of solvated particles in solution suggests that solvation could induce, at high or low concentration of a small molecule solute, attractive inter-particle interactions corresponding to favorable crystallization conditions.

Binding Sites↗

PubMed2005

A pivoting algorithm for metabolic networks in the presence of thermodynamic constraints.

A linear programming algorithm is presented to constructively compute thermodynamically feasible fluxes and change in chemical potentials of reactions for a metabolic network. It is based on physical laws of mass conservation and the second law of thermodynamics that all chemical reactions should satisfy. As a demonstration, the algorithm has been applied to the core metabolic pathway of E. coli.

Algorithms↗