The electrostatic contribution to DNA base-stacking interactions.

Base-stacking and phosphate-phosphate interactions in B-DNA are studied using the finite difference Poisson-Boltzmann equation. Interaction energies and dielectric constants are calculated and compared to the predictions of simple dielectric models. No extant simple dielectric model adequately describes phosphate-phosphate interactions. Electrostatic effects contribute negligibly to the sequence and conformational dependence of base-stacking interactions. Electrostatic base-stacking interactions can be adequately modeled using the Hingerty screening function. The repulsive and dispersive Lennard-Jones interactions dominate the dependence of the stacking interactions on roll, tilt, twist, and propellor. The Lennard-Jones stacking energy in ideal B-DNA is found to be essentially independent of sequence.     

Thermodynamics of drug-DNA interactions

Many anticancer, antibiotic, and antiviral drugs exert their primary biological effects by reversibly interacting with nucleic acids. Therefore, these biomolecules represent a major target in drug development strategies designed to produce next generation therapeutics for diseases such as cancer. In order to improve the clinical efficacy of existing drugs and also to design new ones it is necessary to understand the molecular basis of drug-DNA interactions in structural, thermodynamic, and kinetic detail. The past decade has witnessed an increase in the number of rigorous biophysical studies of drug-DNA systems and considerable knowledge has been gained in the energetics of these binding reactions. This is, in part, due to the increased availability of high-sensitivity calorimetric techniques, which have allowed the thermodynamics of drug-DNA interactions to be probed directly and accurately. The focus of this article is to review thermodynamic approaches to examining drug-DNA recognition. Specifically, an overview of a recently developed method of analysis that dissects the binding free energy of these reactions into five component terms is presented. The results of applying this analysis to the DNA binding interactions of both minor groove drugs and intercalators are discussed. The solvent water plays a key role in nucleic acid structure and consequently in the binding of ligands to these biomolecules. Any rational approach to DNA-targeted drug design requires an understanding of how water participates in recognition and binding events. Recent studies examining hydration changes that accompany DNA binding by intercalators will be reviewed. Finally some aspects of cooperativity in drug-DNA interactions are described and the importance of considering cooperative effects when examining these reactions is highlighted.     

Thermodynamics of lipid-peptide interactions

This review is focused on peptide molecules which exhibit a limited solubility in the aqueous phase and bind to the lipid membrane from the aqueous medium. Surface adsorption, membrane insertion, and specific binding are usually accompanied by changes in the heat content of the system and can be measured conveniently with isothermal titration calorimetry, avoiding the necessity of peptide labeling. The driving forces for peptide adsorption and binding are hydrophobicity, electrostatics, and hydrogen bonding. An exclusively hydrophobic interaction is exemplified by the immunosuppressant drug cyclosporine A. Its insertion into the membrane can be described by a simple partition equilibrium X(b)=K(0)C(eq). If peptide and membrane are both charged, electrostatic interactions are dominant leading to nonlinear binding curves. The concentration of the peptide near the membrane interface can then be much larger than its bulk concentration. Electrostatic effects must be accounted for by means of the Gouy-Chapman theory before conventional binding models can be applied. A small number of peptides and proteins bind with very high affinity to a specific lipid species only. This is illustrated for the lantibiotic cinnamycin (Ro 09-0198) which forms a 1:1 complex with phosphatidyethanolamine with a binding constant of 10(8) M(-1). Membrane adsorption and insertion can be accompanied by conformational transitions facilitated, in part, by hydrogen bonding mechanisms. The two membrane-induced conformational changes to be discussed are the random coil-to-alpha-helix transition of amphipathic peptides and the random coil-to-beta-structure transition of Alzheimer peptides.     

Thermodynamics and kinetics of phospholipid monomer-vesicle interaction

Resonance energy transfer between acyl chain labeled (7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylcholine (NBD-PC) and head group labeled (lissamine rhodamine B sulfonyl)phosphatidylethanolamine (N-Rh-PE) was used to monitor the rate of NBD-PC transfer between two populations of dioleoylphosphatidylcholine (DOPC) vesicles. Equilibration of NBD-PC between DOPC vesicles occurs by the diffusion of soluble monomers through the water phase, which is a first-order process. Conditions were used such that the apparent transfer rate constant is equal to the rate constant for monomer-vesicle dissociation into solution. The partition distribution of NBD-PC between DOPC vesicles and water was determined by measuring the loss of NBD-PC from vesicles into solution following the dilution of small amounts of vesicles in buffer. The acyl chain length and temperature dependence of both the rate and partition measurements were determined, and a free energy diagram for NBD-PC-soluble monomer-vesicle interactions was constructed. The conclusions of this analysis are the following: NBD-PC dissociation from and association with the bilayer require passage through a high-energy transition state resulting predominantly from enthalpic energy. The activation energy for NBD-PC-vesicle dissociation becomes more positive and the standard free energy of NBD-PC transfer from water to vesicles becomes more negative with increasing acyl chain length. The standard free energy of transfer for NBD-PC from water to vesicles results predominantly from differences in enthalpy between the membrane and water phases. The enthalpy of activation for association increases with acyl chain length and is larger than expected for an aqueous diffusion-limited process in bulk water.     

Thermodynamics and kinetics of the glyoxylate cycle

Because the standard Gibbs energies of formation of all the species of reactants in the glyoxylate cycle are known at 298.15 K, it is possible to calculate the apparent equilibrium constants of the five reactions in the cycle in the pH range 5-9 and ionic strengths from 0 to approximately 0.35 M. In making calculations on such a system, it is convenient to specify concentrations of coenzymes like NADox and NADred because they are involved in many reactions and may be in steady states. Calculations are given for [NADox] = 1000[NADred] and [NADox] = 10[NADred]. Equilibrium compositions are calculated using computer programs when all the reactants are present initially and when only glyoxylate and CoA are present initially. The kinetics of the reactions in the glyoxylate cycle at specified concentrations of NADox and NADred are calculated by numerical solution of the steady-state rate equations for the case where the reactant concentrations are below their Michaelis constants and only glyoxylate and CoA are present initially.     

Thermodynamics of sequence-specific protein-DNA interactions

The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.     

Thermodynamics of carbohydrate-lipid interactions.

Thermodynamic analyses of carbohydrate-lipid interactions were performed by investigating the effects of a series of carbohydrates, including monosaccharides, disaccharides, and trisaccharides, on the phase-transition properties of aqueous dispersions of 1,2-dipalmitoyl phosphatidylcholine (DPPC). The temperature of the lipid's main phase transition from the gel to liquid-crystalline phase is essentially unchanged in the presence of carbohydrate. The change in the free energy (delta G) of the transition is zero when a carbohydrate is added to aqueous dispersions of DPPC, while the enthalpy (delta H) and the entropy of the melting of DPPC are decreased. The thermodynamic information was used to examine carbohydrate-lipid interactions. Such interactions were elucidated according to our knowledge of the specific properties of carbohydrates in aqueous solutions and the previously proposed hydrophobic interaction involving hydrocarbon tails of the lipid in aqueous dispersions.     

Thermodynamics of phospholipid-sucrose interactions.

The effect of 0-1.0 M sucrose on the phase-transition properties of 1,2-dipalmitoyl-3-sn-phosphatidylcholine (1,2-DPPC) was examined by high-sensitivity differential scanning calorimetry at a scan rate of 0.1 K min-1. Increasing the concentration of sucrose caused a small, but experimentally significant, increase in the temperature (Tm) of maximal excess apparent specific heat (Cmax) and in delta T 1/2 (the transition width at 1/2 Cmax), a reduction in Cmax, and a small decrease (approximately 8-10% at 1.0 M sucrose compared with 0 M sucrose) in the calorimetric enthalpy (delta Hcal) of the gel-to-liquid crystalline transition. The calorimetric parameters of the pretransition of 1,2-DPPC were not significantly affected by sucrose in the concentration range examined, except there was a 1.0 degree C increase in the temperature (Tp) of maximal excess apparent specific heat in the presence of 1.0 M sucrose. The results are discussed in terms of the possible molecular mechanisms that could have caused the observed changes and are contrasted with the results obtained by C. -H. Chen et al. (1981, Biophys. J., 36:359-367).     

Thermodynamics of fusion peptide-membrane interactions

The fusion peptides of viral membrane fusion proteins play a key role in the mechanism of viral spike glycoprotein mediated membrane fusion. These peptides insert into the lipid bilayers of cellular target membranes where they adopt mostly helical secondary structures. To better understand how membranes may be converted to high-energy intermediates during fusion, it is of interest to know how much energy, enthalpy and entropy, is provided by the insertion of fusion peptides into lipid bilayers. Here, we describe a detailed thermodynamic analysis of the binding of analogues of the influenza hemagglutinin fusion peptide of different lengths and amino acid compositions. In small unilamellar vesicles, the interaction of these peptides with lipid bilayers is driven by enthalpy (-16.5 kcal/mol) and opposed by entropy (-30 cal mol(-1) K(-1)). Most of the driving force (deltaG = -7.6 kcal/mol) comes from the enthalpy of peptide insertion deep into the lipid bilayer. Enthalpic gains and entropic losses of peptide folding in the lipid bilayer cancel to a large extent and account for only about 40% of the total binding free energy. The major folding event occurs in the N-terminal segment of the fusion peptide. The C-terminal segment mainly serves to drive the N-terminus deep into the membrane. The fusion-defective mutations G1S, which causes hemifusion, and particularly G1V, which blocks fusion, have major structural and thermodynamic consequences on the insertion of fusion peptides into lipid bilayers. The magnitudes of the enthalpies and entropies of binding of these mutant peptides are reduced, their helix contents are reduced, but their energies of self-association at the membrane surface are increased compared to the wild-type fusion peptide.     

Thermodynamics and kinetics of a molecular motor ensemble

If, contrary to conventional models of muscle, it is assumed that molecular forces equilibrate among rather than within molecular motors, an equation of state and an expression for energy output can be obtained for a near-equilibrium, coworking ensemble of molecular motors. These equations predict clear, testable relationships between motor structure, motor biochemistry, and ensemble motor function, and we discuss these relationships in the context of various experimental studies. In this model, net work by molecular motors is performed with the relaxation of a near-equilibrium intermediate step in a motor-catalyzed reaction. The free energy available for work is localized to this step, and the rate at which this free energy is transferred to work is accelerated by the free energy of a motor-catalyzed reaction. This thermodynamic model implicitly deals with a motile cell system as a dynamic network (not a rigid lattice) of molecular motors within which the mechanochemistry of one motor influences and is influenced by the mechanochemistry of other motors in the ensemble.     

Thermodynamics and kinetics of incorporation into a membrane

Some very recent work on the equilibrium and rate of incorporation of the pore forming peptide alamethicin into phospholipid bilayers is briefly reviewed. The experimental methods and the proceedings to evaluate and interpret the data are generally applicable analogously to other cases of substrates which somehow associate with a membrane. For the special system under consideration, a very high degree of incorporation is observed, reflecting internal aggregation and thermodynamically non-ideal repulsive interactions. These points are included in a basic model which is shown to provide a quantitative fit of the measured results. Stopped-flow experiments have shown that the overall incorporation occurs as a practically one-step process. Its rate is remarkably fast, only slightly slower than the diffusion controlled upper limit. All the kinetic data can be quite satisfactorily interpreted in terms of a reaction scheme with steady-state intermediates comprising the obvious diffusional translocations as well as the accompanying conformational change. In particular, the special findings for the alamethicin system suggest a most simple working hypothesis of the molecular mechanism underlying the voltage-dependent gating effect.     

Thermodynamics and kinetics of actin filament nucleation.

We have performed computer simulations and free energy calculations to determine the thermodynamics and kinetics of actin nucleation and thus identify a probable nucleation pathway and critical nucleus size. The binding free energies of structures along the nucleation pathway are found through a combination of electrostatic calculations and estimates of the entropic and surface area contributions. The association kinetics for the formation of each structure are determined through a series of Brownian dynamics simulations. The combination of the binding free energies and the association rate constants determines the dissociation rate constants, allowing for a complete characterization of the nucleation and polymerization kinetics. The results indicate that the trimer is the size of the critical nucleus, and the rate constants produce polymerization plots that agree very well with experimental results over a range of actin monomer concentrations.     

Thermodynamics and kinetics of the thermal unfolding of plastocyanin

The thermal denaturation of plastocyanin in aqueous solution was investigated by means of DSC, ESR and absorbance techniques, with the aim of determining the thermodynamic stability of the protein and of characterizing the thermally induced conformational changes of its active site. The DSC and absorbance experiments indicated an irreversible and kinetically controlled denaturation path. The extrapolation of the heat capacity and optical data at infinite scan rate made it possible to calculate the kinetic and thermodynamic parameters associated with the denaturation steps. The denaturation pathway proposed, and the parameters found from the calorimetric data, were checked by computer simulation using an equation containing the information necessary to describe the denaturation process in detail. ESR and absorbance measurements have shown that structural changes of the copper environment occur during the protein denaturation. In particular, the geometry of the copper-ligand atoms changes from being tetrahedral to square planar and the disruption of the active site precedes the global protein denaturation. The thermodynamic enthalpic change, the half-width transition temperature, and the value of ΔCp, were used to calculate the thermodynamic stability, ΔG, of the reversible process over the entire temperature range of denaturation. The low thermal stability found for plastocyanin, is discussed in connection with structural factors stabilizing the native state of a protein. Received: 17 July 1997 / Revised version: 22 November 1997 / Accepted: 15 January 1998     

Thermodynamics of lipid interactions in complex bilayers

The mutual interactions between lipids in bilayers are reviewed, including mixtures of phospholipids, and mixtures of phospholipids and cholesterol (Chol). Binary mixtures and ternary mixtures are considered, with special emphasis on membranes containing Chol, an ordered phospholipid, and a disordered phospholipid. Typically the ordered phospholipid is a sphingomyelin (SM) or a long-chain saturated phosphatidylcholine (PC), both of which have high phase transitions temperatures; the disordered phospholipid is 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) or dioleoylphosphatidylcholine (DOPC). The unlike nearest-neighbor interaction free energies (ω_AB) between lipids (including Chol), obtained by an variety of unrelated methods, are typically in the range of 0-400 cal/mol in absolute value. Most are positive, meaning that the interaction is unfavorable, but some are negative, meaning it is favorable. It is of special interest that favorable interactions occur mainly between ordered phospholipids and Chol. The interpretation of domain formation in complex mixtures of Chol and phospholipids in terms of phase separation or condensed complexes is discussed in the light of the values of lipid mutual interactions.     

Thermodynamics of alpha-lactalbumin-DL-alpha-dipalmitoylphosphatidylcholine interactions and effect of the antioxidant nicotinamide on these interactions

Differential scanning calorimetry has been used to understand the thermodynamics of the interactions of dl-alpha-dipalmitoylphosphatidylcholine (DPPC) with alpha-lactalbumin and the effect of the antioxidant nicotinamide on these interactions. Nicotinamide decreases the thermal transition temperature of both the lipid and the protein at high concentrations. The thermal unfolding transitions of the protein were two state and calorimetrically reversible. There was no significant change in the shape and thermodynamic parameters accompanying the lipid endotherms, suggesting that nicotinamide did not penetrate the lipid bilayer. The thermal unfoldings of alpha-lactalbumin in the presence of DPPC as cosolute also adhered to two-state reversible mechanism. The changes in the thermodynamic parameters accompanying the thermal transitions were small, indicating no significant interaction of alpha-lactalbumin with DPPC. The changes in the thermodynamic parameters indicate that the lipid bilayer organization, as well as the partitioning of the extrinsic protein alpha-lactalbumin into the bilayer, is not affected in the entire studied concentration range of the lipid. It is observed that the presence of increasing concentration of nicotinamide (as high as 1.0 mol dm(-3)) in the lipid-protein mixture does not affect its partitioning into the lipid bilayer, although nicotinamide preferentially interacts with alpha-lactalbumin. The change in the effect of nicotinamide on lipid transition temperature in the mixture and literature report suggests that nicotinamide may be forming a hydrogen-bonded complex with the protein through its amide functionality. The surface tension data of aqueous nicotinamide in combination with the thermal denaturation results of protein in presence of nicotinamide confirmed that surface tension effect does not have any significant contribution to the effect of nicotinamide on protein.     

Thermodynamics aspects of interactions between small ligands and DNA

DNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measures changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other techniques measure changing in drug environment. With the increasing availability of sensitive microcalorimeters, particular interest has arisen in the thermodynamics of drug-DNA interaction. Using such methods permit direct determination of enthalpy changes associated with reactions. One experiment permits to obtain also binding constant, hence an almost complete thermodynamic profile can be established. This profile offers key insights into the molecular forces that drive complex formation and permit to estimate which kind of interaction are responsible of forming these complexes.     

Thermodynamics and kinetics of protein folding: an evolutionary perspective

This article appeals to an evolutionary model which postulates that primordial proteins were described by small polypeptide chains which (i) lack disulfide bridges, and (ii) display slow folding rates with multi-state kinetics, to determine relations between structural properties of proteins and their folding kinetics. We parameterize the energy landscape of proteins in terms of thermodynamic activation variables. The model studies evolutionary changes in these thermodynamic parameters, and we invoke relations between these activation variables and structural properties of the protein to predict the following correspondence between protein structure and folding kinetics. 1. Proteins with inter- and intra-chain disulfide bridges: large variability in both folding rates and stability of intermediates, multi-state kinetics. 2. Proteins which lack inter and intra-chain disulfide bridges. 2.1 Single-domain chains: fast folding rates; unstable intermediates; two-state kinetics. 2.2 Multi-domain monomers: intermediate rates; metastable intermediates; multi-state kinetics. 2.3 Multi-domain oligomers: slow rates; metastable intermediates; multi-state kinetics. The evolutionary model thus provides a kinetic characterization of one important subfamily of proteins which we describe by the following properties: Folding dynamics of single-domain proteins which lack disulfide bridges are described by two-state kinetics. Folding rate of this class of proteins is positively correlated with the thermodynamic stability of the folded state.