Binding Enthalpy Research Articles

Competitive binding of anticancer drugs 5-fluorouracil and cyclophosphamide with serum albumin: Calorimetric insights

BackgroundIsothermal titration calorimetry (ITC) has emerged as an excellent method to characterize drug–protein interactions. 5-Fluorouracil and cyclophosphamide have been used in combination for the treatment of breast carcinoma, though individually these drugs have also been useful in treating other types of cancer. A quantitative understanding of binding of these drugs with the transport protein under different conditions is essential for optimizing recognition by the protein and delivery at the target. MethodsThe values of binding constant, enthalpy, and entropy of binding have been determined by using ITC. Fluorescence and circular dichroism spectroscopies have been used to obtain further support to calorimetric observations, monitor conformational changes in the protein and establishing stoichiometry of association. ResultsThe thermodynamic parameters have enabled a quantitative understanding of the affinity of 5-fluorouracil and cyclophosphamide with bovine serum albumin. The nature of binding has been unraveled based on effect of ionic strength, tetrabutyl-ammonium bromide, and sucrose which interfere in ionic, hydrophobic, and hydrogen bonding interactions. The binding site has been identified by using site marker warfarin in combination with 5-fluorouracil and cyclophosphamide. Further, the experiments have been done to establish whether both the drugs share the same binding site, and the effect of antibiotic drug carbenecillin and anti-inflammatory drug naproxen on their association. General significanceTuning optimum association of drugs with the transport vehicles for effective drug delivery requires identification of the nature of interacting groups in terms of energetics of interactions. Such studies employing ITC have direct significance in rational drug design. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.

Intramolecular hydrogen bonding in 5-nitrosalicylaldehyde: IR spectrum and quantum chemical calculations

The structural parameters, and vibrational frequencies of 5-nitrosalicylaldehyde (5NSA) were studied by the FT-IR and Raman spectra and the quantum chemical calculations carried out at the B3LYP/6-311++G(d,p) level of theory in order to investigate the intramolecular hydrogen bonding (IHB) present in its structure. The strength and nature of IHB in the optimized structure of 5NSA were studied in detail by means of the atoms in molecules (AIM) and the natural bond orbital (NBO) approaches. The results obtained were then compared with the corresponding data for its parent molecule, salicylaldehyde (SA). Comparisons made between the geometrical structures for 5NSA and SA, their OH/OD stretching and out-of-plane bending modes, their enthalpies for the hydrogen bond, and their AIM parameters demonstrated a stronger H-bonding in 5NSA compared with that in SA.The calculated binding enthalpy (ΔHbind) for 5NSA was −10.92 kcal mol−1. The observed νOH and γOH appeared at about 3120 cm−1 and 786 cm−1 respectively. The stretching frequency shift of H-bond formation was 426 cm−1 which is consistent with ΔHbind and the strength of H-bond in 5NSA. The delocalization energies and electron delocalization indices derived by the NBO and AIM approaches indicate that the resonance effects were responsible for the stronger IHB in 5NSA than in SA.

Sequence Permutation of Positive Charges in a Model Peptide Antibiotic Produces Differing Enthalpic and Entropic Contributions to the Lipid-Peptide Binding Affinity

With rising disease rates and decreasing effectiveness of conventional antibiotics, there is an immediate need for new antibiotics. One promising solution is through cationic antimicrobial peptides, which act by perturbing bacterial membranes. The interaction of model peptides with membranes can provide valuable information about the role of helical structure and peptide charge distribution on peptide-membrane interactions. We are investigating model peptide antibiotics composed primarily of the hydrophobic dialkylated amino acid Aib (α-aminoisobutyric acid), which imparts a strong 310-helical bias due to steric hindrance at the α-carbon. Cationic lysine residues are placed in adjacent locations in the center of the helix (KK45) or one full turn apart (KK36). Large unilamellar vesicles (LUVs) composed of DMPC or DMPG were used as zwitterionic or anionic membrane models, respectively. NMR data indicates that in a membrane mimicing solvent (DMSO), KK45 adopts a kinked helical stucture, while KK36 adopts a canonical helical structure. We have previously seen that KK45 binding to anionic micells is more favorable than binding of KK36 to anionic micelles. However, unlike binding to micelles, NMR data suggests that binding of peptides to DMPG vesicles is more favorable for KK36 than for KK45. Here we present thermodynamic data characterizing the peptide-LUV interactions using isothermal titration calorimetry (ITC). Preliminary data suggests that binding to DMPG vesicles is exothermic, while binding to DMPC vesicles is endothermic. Complete characterization of the enthalpy of binding, entropy of binding, and thermodynamic binding constant will allow us to elucidate the relationship between peptide structure and the favorability of membrane binding.

Low Energy Barriers and a Dynamic Contact Network between Ribosomal Subunits Enable Rapid tRNA Translocation

During protein synthesis, tRNA molecules move from the ribosome's aminoacyl to peptidyl to exit sites, with the two ribosomal subunits remaining associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. Using molecular dynamics simulations, we here investigate conformational motions during spontaneous translocation, as well as the underlying energetics and kinetics. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by ‘sliding’ and ‘stepping’ mechanisms involving conserved L6, L5, and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement through maintaining constant binding affinity. Intersubunit rotations exhibit remarkably fast intrinsic submicrosecond dynamics, which requires a fine-tuned flat free energy landscape, as any larger barrier would slow down the conformational motions. Maintaining such subtle balance between the many interactions involved is remarkable, in particular considering the large shifts the many intersubunit bridges undergo. Based on the observed occupancies of intersubunit contacts during our simulations, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The total contribution of the tRNAs -- which contact both subunits -- to the intersubunit binding enthalpy is almost constant, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation.

The electric charge and climb of edge dislocations in perovskite oxides: The case of high-pressure MgSiO3 bridgmanite

Dislocation climb is expected to play a major role in high-temperature creep of complex ionic oxides, however the fundamental mechanisms for climb are poorly understood in this class of materials. In this work we investigate the interaction of vacancies with an edge dislocation by means of atomic-scale simulations in high-pressure MgSiO3 bridgmanite, a mineral whose natural conditions of deformation are favorable to climb. The evaluation of the interaction with oxygen vacancies reveals that the dislocation favors a non-stoichiometric, oxygen-poor configuration, associated with a positive electric charge of maximum value + 9.17 10−11 C m−1. This result is in qualitative agreement with experimental observations in related perovskite oxides. Subsequently, the interactions between dislocations and vacancies are dominated by electrostatics, with binding enthalpies of several eV in the vicinity of the dislocation core, superseding elastic effects. These results shed a new light on dislocation-vacancy interactions and dislocation climb in this class of materials.

Modeling the Detection of Organic and Inorganic Compounds Using Iodide-Based Chemical Ionization.

Iodide-based chemical ionization mass spectrometry (CIMS) has been used to detect and measure concentrations of several atmospherically relevant organic and inorganic compounds. The significant electronegativity of iodide and the strong acidity of hydroiodic acid makes electron transfer and proton abstraction essentially negligible, and the soft nature of the adduct formation ionization technique reduces the chances of sample fragmentation. In addition, iodide has a large negative mass defect, which, when combined with the high resolving power of a high resolution time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS), provides good selectivity. In this work, we use quantum chemical methods to calculate the binding energies, enthalpies and free energies for clusters of an iodide ion with a number of atmospherically relevant organic and inorganic compounds. Systematic configurational sampling of the free molecules and clusters was carried out at the B3LYP/6-31G* level, followed by subsequent calculations at the PBE/SDD and DLPNO-CCSD(T)/def2-QZVPP//PBE/aug-cc-pVTZ-PP levels. The binding energies, enthalpies, and free energies thus obtained were then compared to the iodide-based University of Washington HR-ToF-CIMS (UW-CIMS) instrument sensitivities for these molecules. We observed a reasonably linear relationship between the cluster binding enthalpies and logarithmic instrument sensitivities already at the PBE/SDD level, which indicates that relatively simple quantum chemical methods can predict the sensitivity of an iodide-based CIMS instrument toward most molecules. However, higher level calculations were needed to treat some outlier molecules, most notably oxalic acid and methylerythritol. Our calculations also corroborated the recent experimental findings that the molecules that the UW-CIMS detects at maximum sensitivity usually have binding enthalpies to iodide which are higher than about 26 kcal/mol, depending slightly on the level of theory.

Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases.

Members of the same protease family show different substrate specificity, even if they share identical folds, depending on the physiological processes they are part of. Here, we investigate the key factors for subpocket and global specificity of factor Xa, elastase, and granzyme B which despite all being serine proteases and sharing the chymotrypsin-fold show distinct substrate specificity profiles. We determined subpocket interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket interaction potentials determined for static X-ray structures turned out to be insufficient to explain serine protease specificity for all subpockets. Therefore, we generated conformational ensembles using molecular dynamics simulations. We identified representative binding site conformations using distance-based hierarchical agglomerative clustering and determined subpocket interaction potentials for each representative conformation of the binding site. Considering the differences in subpocket interaction potentials for these representative conformations as well as their abundance allowed us to quantitatively explain subpocket specificity for the nonprime side for all three example proteases on a molecular level. The methods to identify key regions determining subpocket specificity introduced in this study are directly applicable to other serine proteases, and the results provide starting points for new strategies in rational drug design.

Cyclometalated gold(III) trioxadiborrin complexes: studies of the bonding and excited states.

Trioxadiborrins are chelating ligands that assemble in dehydration reactions of boronic acids. They are structurally related to β-diketonate ligands, but have a 2-charge. Little is known of the bonding properties of trioxadiborrin ligands. Presented here are density-functional theory (DFT) studies of cyclometalated gold(III) trioxadiborrins. Substituent effects are evaluated, and comparison is made to the cyclometalating 2-(4-tolyl)pyridine (tpy) ligand on gold. The tpy ligand binds more strongly than any trioxadiborrin ligand considered here, and the two ligands bind competitively to gold. The 1,3-diphenyl trioxadiborrin ligand of 1 has a larger absolute binding enthalpy to gold than its β-diketonate analogue. Conjugation between boron and aryl substituents delocalizes charge and attenuates the trioxadiborrin's binding capacity. Steric effects that disrupt conjugation between boron and aryl substituents cause the trioxadiborrin to chelate more tightly. Fragment bond orders are divided into in-plane and out-of-plane contributions for square planar 1. In-plane bonding accounts for 88% of bond order between (tpy)Au2+ and the trioxadiborrin ligand. Cyclometalated gold(III) trioxadiborrin complexes were previously shown to be phosphorescent. Spin-unrestricted triplet-state geometry optimizations find that the ten largest excited-state distortions all occur on the tpy ligand. A plot of spin density in triplet 1 shows spin to reside predominantly on tpy. The 77 K luminescence spectrum of 1 is reported here. Time-dependent DFT and configuration interaction singles calculations (corrected for doubles excitations) overestimate the emission energy by ∼ 0.12 eV.

Layer-by-layer polysaccharide-coated liposomes for sustained delivery of epidermal growth factor

A three-dimensional layer-by-layer (LbL) structure composed by xanthan and galactomannan biopolymers over dioctadecyldimethylammonium bromide (DODAB) liposome template was proposed and characterized for protein drug delivery. The polymers and the surfactant interaction were sufficiently strong to create a LbL structure up to 8 layers, evaluated using quartz crystal microbalance (QCM) and zeta potential analysis. The polymer–liposome binding enthalpy was determined by isothermal titration calorimetry (ITC). The bilayer of biopolymer-coated liposomes with diameters of 165 (±15)nm, measured by dynamic light scattering (DLS), and ζ-potential of −4 (±13)mV. These bilayer-coated nanoparticles increased up to 5 times the sustained release of epidermal growth factor (EGF) at a first order rate of 0.005min−1. This system could be useful for improving the release profile of low-stability drugs like EGF.

Identifying the Interactions That Allow Separation of O2 from N2 on the Open Iron Sites of Fe2(dobdc)

The presence of open metal sites along with a high porosity makes the Fe2(dobdc) metal–organic framework, also called Fe-MOF-74, particularly well suited for separating gaseous mixtures. For instance, since Fe2(dobdc) adsorbs O2 more strongly than N2, it can, in principle, be used to separate O2 from air [Bloch et al. J. Am. Chem. Soc. 2011, 133, 14814]. In the present work, we investigate the reversible differential adsorption of N2 and O2 on Fe2(dobdc) with Kohn–Sham density functional theory applied to an 88-atom cluster model of the MOF. The cluster is chosen such that it is large enough to allow an accurate description of the most important contributions to the binding enthalpies and small enough to perform high-level quantum mechanical calculations. For the quantum mechanical calculations, we use well-validated exchange–correlation functionals to study the ground-state structures of the Fe–N2 and Fe–O2 interacting systems. The calculations agree with experiment in that O2 binds more strongly than N2...

Partition coefficient-Lewis basicity correlation in four dioxycyclobutenedion-bridged novel ball-type phthalocyanines

The novel ball-type bis-metallo [Zn(II), Co(II) and Cu(II)] phthalocyanines were synthesized from 4,4′-(3,4-dioxocyclobut-1-ene-1,2-diyl)-bis(oxy)] diphthalonitrile, which can be obtained by the reaction of 4-nitrophthalonitrile with 3,4-dihydroxy-3cyclobuten-1,2-dione. The novel ball-type phthalocyanines with cyclobutene unit were characterized by elemental analysis, UV–vis, FT-IR, 1H NMR, and MALDI-TOF mass spectroscopy. The response and recovery behaviours of the films to different analytes, which span a broad range of Lewis base, were investigated by utilizing an AT-cut quartz crystal resonator. Frequency changes during transient exposures to these vapours were rapid and reversible. The sensing behaviour of the films for a broad range of Lewis bases and the correlation between the partition coefficients and Lewis base enthalpies were investigated. Partition coefficients obtained from the linear response regimes of the calibration curves were in the 800–22,000 range. Results show that partition coefficients may be correlated exponentially with binding enthalpy.

Comparative investigation of the binding characteristics of poly-l-lysine and chitosan on alginate hydrogel

The binding properties of poly-l-lysine and chitosan to alginate have been evaluated quantitatively and compared. Poly-l-lysine bound to alginate hydrogel more rapidly than chitosan as poly-l-lysine has a smaller molar hydrodynamic volume. In addition, poly-l-lysine showed a much higher binding capacity (6.14:1) for alginate hydrogel beads than chitosan (2.71:1), and a little higher binding stoichiometry (0.58) to sodium alginate molecules in solution than chitosan (0.49). An exothermic heat of alginate-poly-l-lysine complexes formation of 2.02kJ/mol was detected. For alginate–chitosan complexes, the binding enthalpy has been seen to be −3.49kJ/mol. The stability of the polyelectrolyte complexes was related to their binding enthalpy. The alginate-poly-l-lysine complexes could be disintegrated and rebuilt. By contrast, chitosan was bound with alginate in a steady state. These results provide fundamental insights regarding the structure and property relationships of macromolecules, and will be helpful in designing and selecting appropriate polymers.

Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry.

We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 - both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably.

Long-Range Allosteric Linkage Between Exosites Reciprocally Regulates the Zymogenicity of Prothrombin Derivatives

The binding of ligands to anion binding exosite I (ABEI) and exosite II (ABEII) on prothrombin (II) derivatives plays an integral role in regulating their function. These exosites are located on opposite faces of the proteinase domain and exhibit unique binding specificities. Fragment 1.2 (F12) binds to ABEII and acts as a zymogen-promoting allosteric ligand. Conversely, Na+ and active site ligands stabilize the proteinase state. Here, we investigated the allosteric linkage between ABEI and the Na+ binding site, active site or ABEII using multiple ABEI ligands and prothrombin derivatives differentially poised along the zymogen to proteinase continuum. Prethrombin 2 (P2) represents the most zymogen-like state that differs from thrombin (IIa) because it is not cleaved at the R320 site. To mimic the zymogen-like character of P2 in a cleaved IIa molecule, residues responsible for N-terminal insertion and proteinase formation (IVE) were swapped with TAT to produce IIaTAT, a mutant with vastly diminished proteolytic activity. Alanine was substituted with the catalytic serine residue in IIa (IIaS195A) to represent the proteinase without a ligand at its active site. The thermodynamics of interactions between the thrombin inhibitor and ABEI ligand hirugen (Hir) and the various reference states was assessed using isothermal titration calorimetry (ITC). Titration of Hir into P2, IIaTAT or IIaS195A revealed thermodynamically more favorable binding to proteinase-like IIaS195A in comparison to zymogen-like P2 or IIaTAT. Binding of Hir to IIaS195A was affected by the concentration of Na+ at constant ionic strength. Global analysis done in the presence of increasing concentrations of Na+ revealed a 5-fold increase in Hir binding affinity when IIaS195A is ligated with Na+; demonstrating positive allosteric linkage between ABEI and Na+ binding. Using a truncated Staphylocoagulase variant that binds ABEI without N-terminus insertion (SC13-325), we found that SC13-325 binding alone promoted active site opening and fluorescent inhibitor incorporation in zymogen-like P2. These data reinforce the observation that ABEI ligands promote a proteinase-like state in prothrombin derivatives through positive allosteric linkage with the Na+ binding and active sites. Interestingly, inhibitor incorporation and ITC studies both showed that SC13-325 interacts poorly with II, but strongly with P2 despite both species being zymogens. These findings imply that the ABEII ligand F12, which is produced upon cleavage of II at R271 to form P2, may display negative allosteric linkage with ABEI. Titration of SC13-325 into pre-formed complexes of P2/F12 revealed a drastic reduction in affinity of SC13-325 for P2 when F12 is bound to ABEII. Thus, F12 binding at ABEII negatively affects ABEI binding. Further studies used soluble thrombomodulin (sTM) as the most physiologically pertinent ligand for ABEI. ITC and global analysis of the binding of F12 to P2 in the presence of different concentrations of sTM revealed a ~1200-fold decrease in binding affinity and enthalpy for either the binding of F12 to P2 bound to sTM or the binding of sTM to P2 bound to F12. These data illustrate the strong negative linkage associated with the binding of protein ligands to ABEI and ABEII which yields the appearance of competitive and mutually exclusive binding at the two sites despite the fact that they are on opposite sides of the proteinase domain. Allosteric linkage between ligand binding at the two exosites is centered on the ability of F12 binding to ABEII and favor zymogen-like forms and ligand binding to ABEI to favor proteinase-like forms. Thus, allosteric linkage among exosites is vital to the interconversion of prothrombin species along the zymogen to proteinase spectrum. These ligand-dependent conformational shifts and associated changes in function are likely to greatly contribute to the dynamic roles that IIa plays during coagulation. DisclosuresNo relevant conflicts of interest to declare.

CARBON, NITROGEN AND HYDROGEN IN STEELS: PLASTICITY AND BRITTLENESS

Interstitial elements in steel, carbon, nitrogen and hydrogen, are analyzed in terms of their effect on the electron structure, properties of dislocations, strengthening, plasticity and fracture. It is shown that similarities and differences in the mechanical properties of corresponding solid solutions are controlled by the effect of the above mentioned elements on the density of electron states at the iron Fermi level and, as a result, on the concentration of free electrons. The latter is decreased by the carbon and increased due to nitrogen and hydrogen in the iron, which changes the character of interatomic bonds: carbon enhances their covalent component, whereas nitrogen and hydrogen strengthen the metallic one. The velocity of dislocations in the course of plastic deformation is discussed using the approach of mobile and immobile interstitial atoms. In the fi rst case, they are obstacles for dislocation slip, and mobility of dislocations is determined by the enthalpy of binding between interstitial atoms and dislocations. If interstitial atoms are suffi ciently mobile to accompany dislocations, the character of interatomic bonds within the interstitial clouds around the dislocations is locally changed. As a result, the specifi c energy of dislocations (line tension) and the distance between them in the pile-ups are changed in accordance with the local change of the shear modulus around the dislocations. Based on the performed studies, the effect of interstitial elements on the mechanical properties of steels is discussed. Particularly, the essential similarity between the hydrogen-caused brittleness and the nitrogen-induced ductile-to-brittle transition in the austenitic steels is interpreted.

Electronic Structure Insights into the Solvation of Magnesium Ions with Cyclic and Acyclic Carbonates.

A computational framework to rank the solvation behavior of Mg(2+) in carbonates by using molecular dynamics simulations and density functional theory is reported. Based on the binding energies and enthalpies of solvation calculated at the M06-2X/6-311++G(d,p) level of theory and the free energies of solvation from ABF-MD simulations, we find that ethylene carbonate (EC) and the ethylene carbonate:propylene carbonate (EC:PC) binary mixture are the best carbonate solvents for interacting with Mg(2+) . Natural bond orbital and quantum theory of atoms in molecules analyses support the thermochemistry calculations with the highest values of charge transfer, perturbative stabilization energies, electron densities, and Wiberg bond indices being observed in the Mg(2+) (EC) and Mg(2+) (EC:PC) complexes. The plots of the noncovalent interactions indicate that those responsible for the formation of Mg(2+) carbonate complexes are strong-to-weak attractive interactions, depending on the regions that are interacting. Finally, density of state calculations indicate that the interactions between Mg(2+) and the carbonate solvents affects the HOMO and LUMO states of all carbonate solvents and moves them to more negative energy values.

Characterization of the interaction between bovine serum albumin and doxycycline by chemiluminescence and molecular docking

ABSTRACTThe interaction of bovine serum albumin with doxycycline was investigated using chemiluminescence and molecular docking. Doxycycline at concentrations from 1.0 to 2.5 × 103 pmol · L−1 quenched the chemiluminescence from the luminol–bovine serum albumin system. The data were analyzed using a chemiluminescence mathematic model for protein–ligand interaction, log[(I0 – I)/I] = logK + nlog[D]. The binding constant of bovine serum albumin with doxycycline was 3.36 × 105 L · mol−1 at 298 K with one binding site. The binding constant, enthalpy change, entropy change, and binding free energy change showed that the bonding of doxycycline to bovine serum albumin was spontaneous and enthalpy driven via hydrogen bonding and van der Waals forces. Further molecular docking analysis substantiated that doxycycline was well positioned in the pocket at the subdomain IIA (site I) of bovine serum albumin with a binding constant of 3.31 × 105 L · mol−1. Doxycycline served as both a hydrogen acceptor and donor and mainly interacted with the Arg217 residue through four hydrogen bonds with an average length of 2.55 Å. The chemiluminescence mechanism of doxycycline on luminol–bovine serum albumin system was evaluated, showing that a ternary complex of luminol–bovine serum albumin–doxycycline was formed with luminol and doxycycline at sites III and I of bovine serum albumin.

On the link between conformational changes, ligand binding and heat capacity

BackgroundConformational changes coupled to ligand binding constitute the structural and energetics basis underlying cooperativity, allostery and, in general, protein regulation. These conformational rearrangements are associated with heat capacity changes. ITC is a unique technique for studying binding interactions because of the simultaneous determination of the binding affinity and enthalpy, and for providing the best estimates of binding heat capacity changes. Scope of reviewStill controversial issues in ligand binding are the discrimination between the “conformational selection model” and the “induced fit model”, and whether or not conformational changes lead to temperature dependent apparent binding heat capacities. The assessment of conformational changes associated with ligand binding by ITC is discussed. In addition, the “conformational selection” and “induced fit” models are reconciled, and discussed within the context of intrinsically (partially) unstructured proteins. Major conclusionsConformational equilibrium is a major contribution to binding heat capacity changes. A simple model may explain both conformational selection and induced fit scenarios. A temperature-independent binding heat capacity does not necessarily indicate absence of conformational changes upon ligand binding. ITC provides information on the energetics of conformational changes associated with ligand binding (and other possible additional coupled equilibria). General significancePreferential ligand binding to certain protein states leads to an equilibrium shift that is reflected in the coupling between ligand binding and additional equilibria. This represents the structural/energetic basis of the widespread dependence of ligand binding parameters on temperature, as well as pH, ionic strength and the concentration of other chemical species. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.

Influence of interstitial carbon, nitrogen, and hydrogen on the plasticity and brittleness of steel

The introduction of carbon, nitrogen, and hydrogen in steel is analyzed in terms of the electron structure, dislocation properties, hardening, and failure of the steel. The similarity and differences in the mechanical properties of the corresponding solution solutions are discussed in relation to the influence of these elements on the density of electron states at the Fermi level of iron and correspondingly on the concentration of free electrons. Carbon reduces the concentration of free electrons, while nitrogen and hydrogen have the opposite effect. Hence, the atomic interaction is changed: specifically, its covalent or metallic component will be intensified. The dislocation rate in deformation is analyzed in the approximation of mobile and immobile interstitial atoms. In the first case, the interstitial atoms obstruct dislocational slip; the mobility of the dislocations is determined by the binding enthalpy of the dislocations with impurity atoms. If the interstitial atoms may accompany dislocations, the atomic bond is locally changed in dislocational atmospheres. That affects the unit energy of the dislocations and the distance between them in the slip planes. On the basis of the research results, the significant similarity between the hydrogen brittleness of austenitic steel and the ductile–brittle transition in alloying with nitrogen is explained.

Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.