Experimental evaluation of the effective dielectric constant of proteins

Equilibrium Studies on Pd(II)-Amine Complexes with Bio-Relevant Ligands in Reference to Their Antitumor Activity

This review article presents an overview of the equilibrium studies on Pd-amine complexes with bio-relevant ligands in reference to their antitumor activity. Pd(II) complexes with amines of different functional groups, were synthesized and characterized in many studies. The complex formation equilibria of Pd(amine)²⁺ complexes with amino acids, peptides, dicarboxylic acids and DNA constituents, were extensively investigated. Such systems may be considered as one of the models for the possible reactions occurring with antitumor drugs in biological systems. The stability of the formed complexes depends on the structural parameters of the amines and the bio-relevant ligands. The evaluated speciation curves can help to provide a pictorial presentation of the reactions in solutions of different pH values. The stability data of complexes with sulfur donor ligands compared with those of DNA constituents, can reveal information regarding the deactivation caused by sulfur donors. The formation equilibria of binuclear complexes of Pd(II) with DNA constituents was investigated to support the biological significance of this class of complexes. Most of the Pd(amine)²⁺ complexes investigated were studied in a low dielectric constant medium, resembling that of a biological medium. Investigations of the thermodynamic parameters reveal that the formation of the Pd(amine)²⁺ complex species is exothermic.

Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations

Considering that practically all reactions that involve nucleotides also involve metal ions, it is evident that the coordination chemistry of nucleotides and their derivatives is an essential corner stone of biological inorganic chemistry. Nucleotides are either directly or indirectly involved in all processes occurring in Nature. It is therefore no surprise that the constituents of nucleotides have been chemically altered-that is, at the nucleobase residue, the sugar moiety, and also at the phosphate group, often with the aim of discovering medically useful compounds. Among such derivatives are acyclic nucleoside phosphonates (ANPs), where the sugar moiety has been replaced by an aliphatic chain (often also containing an ether oxygen atom) and the phosphate group has been replaced by a phosphonate carrying a carbon-phosphorus bond to make the compounds less hydrolysis-sensitive. Several of these ANPs show antiviral activity, and some of them are nowadays used as drugs. The antiviral activity results from the incorporation of the ANPs into the growing nucleic acid chain-i.e., polymerases accept the ANPs as substrates, leading to chain termination because of the missing 3'-hydroxyl group. We have tried in this review to describe the coordination chemistry (mainly) of the adenine nucleotides AMP and ATP and whenever possible to compare it with that of the dianion of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2- = adenine(N9)-CH2-CH2-O-CH2-PO32) [or its diphosphate (PMEApp4-)] as a representative of the ANPs. Why is PMEApp4- a better substrate for polymerases than ATP4-? There are three reasons: (i) PMEA2- with its anti-like conformation (like AMP2-) fits well into the active site of the enzyme. (ii) The phosphonate group has an enhanced metal ion affinity because of its increased basicity. (iii) The ether oxygen forms a 5-membered chelate with the neighboring phosphonate and favors thus coordination at the Pα group. Research on ANPs containing a purine residue revealed that the kind and position of the substituent at C2 or C6 has a significant influence on the biological activity. For example, the shift of the (C6)NH2 group in PMEA to the C2 position leads to 9-[2-(phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer with only a moderate antiviral activity. Removal of (C6)NH2 favors N7 coordination, e.g., of Cu2+, whereas the ether O atom binding of Cu2+ in PMEA facilitates N3 coordination via adjacent 5- and 7-membered chelates, giving rise to a Cu(PMEA)cl/O/N3 isomer. If the metal ions (M2+) are M(α,β)-M(γ)-coordinated at a triphosphate chain, transphosphorylation occurs (kinases, etc.), whereas metal ion binding in a M(α)-M(β,γ)-type fashion is relevant for polymerases. It may be noted that with diphosphorylated PMEA, (PMEApp4-), the M(α)-M(β,γ) binding is favored because of the formation of the 5-membered chelate involving the ether O atom (see above). The self-association tendency of purines leads to the formation of dimeric [M2(ATP)]2(OH)- stacks, which occur in low concentration and where one half of the molecule undergoes the dephosphorylation reaction and the other half stabilizes the structure-i.e., acts as the "enzyme" by bridging the two ATPs. In accord herewith, one may enhance the reaction rate by adding AMP2- to the [Cu2(ATP)]2(OH)- solution, as this leads to the formation of mixed stacked Cu3(ATP)(AMP)(OH)- species, in which AMP2- takes over the structuring role, while the other "half" of the molecule undergoes dephosphorylation. It may be added that Cu3(ATP)(PMEA) or better Cu3(ATP)(PMEA)(OH)- is even a more reactive species than Cu3(ATP)(AMP)(OH)-. - The matrix-assisted self-association and its significance for cell organelles with high ATP concentrations is summarized and discussed, as is, e.g., the effect of tryptophanate (Trp-), which leads to the formation of intramolecular stacks in M(ATP)(Trp)3- complexes (formation degree about 75%). Furthermore, it is well-known that in the active-site cavities of enzymes the dielectric constant, compared with bulk water, is reduced; therefore, we have summarized and discussed the effect of a change in solvent polarity on the stability and structure of binary and ternary complexes: Opposite effects on charged O sites and neutral N sites are observed, and this leads to interesting insights.

Energy landscapes and dynamics of ion translocation through membrane transporters: a meeting ground for physics, chemistry, and biology

The dynamics of ion translocation through membrane transporters is visualized from a comprehensive point of view by a Gibbs energy landscape approach. The ΔG calculations have been performed with the Kirkwood-Tanford-Warshel (KTW) electrostatic theory that properly takes into account the self-energies of the ions. The Gibbs energy landscapes for translocation of a single charge and an ion pair are calculated, compared, and contrasted as a function of the order parameter, and the characteristics of the frustrated system with bistability for the ion pair are described and quantified in considerable detail. These calculations have been compared with experimental data on the ΔG of ion pairs in proteins. It is shown that, under suitable conditions, the adverse Gibbs energy barrier can be almost completely compensated by the sum of the electrostatic energy of the charge-charge interactions and the solvation energy of the ion pair. The maxima in ΔG_KTW with interionic distance in the bound H⁺ - A^- charge pair on the enzyme is interpreted in thermodynamic and molecular mechanistic terms, and biological implications for molecular mechanisms of ATP synthesis are discussed. The timescale at which the order parameter moves between two stable states has been estimated by solving the dynamical equations of motion, and a wealth of novel insights into energy transduction during ATP synthesis by the membrane-bound F_OF₁-ATP synthase transporter is offered. In summary, a unifying analytical framework that integrates physics, chemistry, and biology has been developed for ion translocation by membrane transporters for the first time by means of a Gibbs energy landscape approach.

Charge transfer across biomembranes: A solution to the conundrum of high desolvation free energy penalty in ion transport

Charge transfer across membranes is an important problem in a wide variety of fundamental physicochemical and biological processes. Since Mitchell's concept of the ion well advanced in 1968, several models of ion translocation across biomembranes, for instance through the membrane-bound FO portion of ATP synthase have been proposed. None of these models has considered the large desolvation free energy penalty of ~500 meV incurred in transferring a protonic charge from the aqueous phase into the membrane that hinders such charge transfer processes. The difficulty has been pointed out repeatedly. However, the problem of how the adverse ∆Gdesolvation barrier is overcome in order to enable rapid ion translocation in biomembranes has not been satisfactorily resolved. Hence the fact that the self-energy of the charges has been overlooked can be regarded as a main source of confusion in the field of bioenergetics. Further, in order to consider charges of a finite size (and not just point charges), the free energy of transferring the ions from water into a membrane phase of lower dielectric εm needs to be evaluated. Here a solution to the longstanding conundrum has been proposed by including the bound anion - the second ion in Nath's two-ion theory of energy coupling and ATP synthesis - in the free energy calculations. The mechanistic importance of the H+ - A- charge pair in causing rotation and ATP synthesis by ion-protein interactions is highlighted. The ∆G calculations have been performed by using the Kirkwood-Tanford-Warshel (KTW) theory that takes into account the self-energies of the ions. The results show that the adverse ∆Gdesolvation can be almost exactly compensated by the sum of the electrostatic free energy of the charge-charge interactions and the dipole solvation energy for long-range ion pairs. Results of free energy compensation using the KTW theory have been compared with experimental data on the ∆G of ion pairs and shown to be in reasonable agreement. A general thermodynamic cycle for coupled ion transfer has been constructed to further elucidate facilitated ion permeation between water and membrane phases. Molecular interpretations of the results and their implications for various mechanisms of energy transduction have been discussed. We firmly believe that use of electrostatic theories such as the KTW theory that properly include the desolvation free energy penalty arising from the self-energy of the relevant ions are crucial for quantifying charge transfer processes in bioenergetics. Finally, the clear-cut implication is that proton-only and single-ion theories of ATP synthesis, such as the chemiosmotic theory, are grossly inadequate to comprehend energy storage and transduction in biological processes.

Effect of Bioconjugation on the Reduction Potential of Heme Proteins

The modification of protein surfaces employing cationic and anionic species enables the assembly of these biomaterials into highly sophisticated hierarchical structures. Such modifications can allow bioconjugates to retain or amplify their functionalities under conditions in which their native structure would be severely compromised. In this work, we assess the effect of this type of bioconjugation on the redox properties of two model heme proteins, that is, cytochrome c (CytC) and myoglobin (Mb). In particular, the work focuses on the sequential modification by 3-dimethylamino propylamine (DMAPA) and 4-nonylphenyl 3-sulfopropyl ether (S1) anionic surfactant. Bioconjugation with DMAPA and S1 are the initial steps in the generation of pure liquid proteins, which remain active in the absence of water and up to temperatures above 150 °C. Thin-layer spectroelectrochemistry reveals that DMAPA cationization leads to a distribution of bioconjugate structures featuring reduction potentials shifted up to 380 mV more negative than the native proteins. Analysis based on circular dichroism, MALDI-TOF mass spectrometry, and zeta potential measurements suggest that the shift in the reduction potentials are not linked to protein denaturation, but to changes in the spin state of the heme. These alterations of the spin states originate from subtle structural changes induced by DMAPA attachment. Interestingly, electrostatic coupling of anionic surfactant S1 shifts the reduction potential closer to that of the native protein, demonstrating that the modifications of the heme electronic configuration are linked to surface charges.

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model

The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.

Palladium(II) Complexes Containing Mixed Nitrogen-Sulphur Donor Ligands: Interaction of [Pd(Methionine Methyl Ester)(H2O)2](2+) with Biorelevant Ligands

Pd(MME)Cl₂ complex (MME = methionine methyl ester) was synthesised and characterized by physicochemical measurements. The reaction of [Pd(MME)(H₂O)₂]²⁺ with amino acids, peptides, or dicarboxylic acids was investigated at 25°C and 0.1 M ionic strength. Amino acids and dicarboxylic acids form 1 : 1 complexes. Peptides form both 1 : 1 complexes and the corresponding deprotonated amide species. The stability of the complexes formed was determined and the binding centres of the ligands were assigned. Effect of solvent on the stability constant of Pd(MME)-CBDCA complex, taken as a representative example, shows that the complex is more favoured in a medium of low dielectric constant. The concentration distribution diagrams of the complexes were evaluated.

Protonation equilibria of biologically active ligands in mixed aqueous organic solvents

The review is mainly concerned with the protonation equilibria of biologically active ligands like amino acids, peptides, DNA constituents, and amino acid esters in nonaqueous media. Equilibrium concentrations of proton-ligand formation as a function of pH were investigated. Also, thermodynamics associated with protonation equilibria were also discussed.

Study of pK values and effective dielectric constants of ionizable residues in pentapeptides and in staphylococcal nuclease (SNase) using a mean-field approach

The determination of pK values of amino acid residues as a function of temperature and ionic concentration is crucial to understanding the dynamics of various biological processes such as adsorption of peptides and their interactions with active sites of enzymes. In this study we developed a mean-field model to calculate the position-dependent dielectric constants of ionizable groups and the mean electrostatic potential on the surface. Such potential, which takes into account the contributions exerted by neighboring groups and ions in solution, is responsible for the fine-tuning of the pK value of each residue. The proposed model was applied to the amino acids Asp, Glu, Lys, His, Tyr, and Cys, and since the results were consistent with experimentally obtained values, the model was extended and applied to computation of pK values of Gly and Ala pentapeptides and of ionizable residues of the enzyme staphylococcal nuclease (SNase). In this latter case, we used an approach similar to a first-neighbors approximation, and the results turned out to be in good agreement with previously reported data when considering only the interactions of charged groups located at distances of maximally 20 Å. These considerations and the little computational cost involved turn the suggested approach into a promising tool for the modeling of force fields in computational simulations.

Thermodynamic investigation of the binary and ternary complexes involving 1-aminocyclopropane carboxylic acid with reference to plant hormone

Complex formation equilibria of 1-aminocyclopropane carboxylic acid (ACC) and 3,3-bis(1-methylimidazol-2-yl) propionic acid (BIMP) with metal ions Cu2+, Ni2+, Co2+, Zn2+, Mn2+ and Fe2+ were investigated. ACC forms 1:1 and 1:2 complexes in addition to the hydrolysed form of the 1:1 complex, except in the case of Mn2+ and Fe2+, where the hydrolysed complex is not formed. BIMP forms 1:1 and 1:2 complexes in addition to the hydrolsed form of the 1:1 complex in the case of Mn2+ and Cu2+, however the hydrolysed complex is not detected for Ni2+, Co2+, Zn2+ and Fe2+. The concentration distribution diagrams of the complexes were determined. The Fe2+-complex with BIMP is exothermic and the thermodynamic parameters were calculated. The effect of organic solvent on the acid dissociation constants of 1-aminocyclopropane carboxylic acid (ACC) and 3,3-bis(1-methylimidazol-2-yl) propionic acid (BIMP) and the formation constants of Fe2+ complexes were investigated. Fe2+ forms a mixed-ligand complex with ACC and BIMP with stoichiometric coefficients 1:1:1. The formation constant was determined. The ternary complex is enhanced by back donation from the negatively charged 1-aminocyclopropane carboxylate to the π-system of BIMP. From the concentration distribution diagram, the ternary complex prevails in the physiological pH range.

Equilibrium Studies of Dibutyltin(IV)-Zwitterionic Buffer Complexation

Equilibrium studies in aqueous solution are reported for dibutyltin(IV) (DBT) complexes of the zwitterionic buffers “Good’s buffers” Mes and Mops. Stoichiometric and formation constants of the complexes formed were determined at different temperatures and ionic strength 0.1 mol·L⁻¹ NaNO₃. The results show that the best fit of the titration curves were obtained when the complexes ML, MLH₋₁, MLH₋₂ and MLH₋₃ were considered beside the hydrolysis product of the dibutyltin(IV) cation. The thermodynamic parameters ΔH^o, ΔS^o and ΔG^o calculated from the temperature dependence of the formation constant of the dibutyltin(IV) complexes with 2-(N-morpholino)ethanesulfonic acid (Mes) and 3-(N-mor-pholino)-propanesulfonic acid (Mops) were investigated. The effect of dioxane as a solvent on the formation constants of DBT–Mes and DBT–Mops complexes decrease linearly with the increase of dioxane proportion in the medium. The concentration distribution of the various complexes species was evaluated as a function of pH.

Characterization of metal ion-nucleic acid interactions in solution

Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

Elucidation of isoform-dependent pH sensitivity of troponin i by NMR spectroscopy

Myocardial ischemia is characterized by reduced blood flow to cardiomyocytes, which can lead to acidosis. Acidosis decreases the calcium sensitivity and contractile efficiency of cardiac muscle. By contrast, skeletal and neonatal muscles are much less sensitive to changes in pH. The pH sensitivity of cardiac muscle can be reduced by replacing cardiac troponin I with its skeletal or neonatal counterparts. The isoform-specific response of troponin I is dictated by a single histidine, which is replaced by an alanine in cardiac troponin I. The decreased pH sensitivity may stem from the protonation of this histidine at low pH, which would promote the formation of electrostatic interactions with negatively charged residues on troponin C. In this study, we measured acid dissociation constants of glutamate residues on troponin C and of histidine on skeletal troponin I (His-130). The results indicate that Glu-19 comes in close contact with an ionizable group that has a pK(a) of ∼6.7 when it is in complex with skeletal troponin I but not when it is bound to cardiac troponin I. The pK(a) of Glu-19 is decreased when troponin C is bound to skeletal troponin I and the pK(a) of His-130 is shifted upward. These results strongly suggest that these residues form an electrostatic interaction. Furthermore, we found that skeletal troponin I bound to troponin C tighter at pH 6.1 than at pH 7.5. The data presented here provide insights into the molecular mechanism for the pH sensitivity of different muscle types.

Water-exclusion and liquid-structure forces in implicit solvation

A continuum model of solvation is proposed to describe (i) long-range electrostatic effects of water exclusion resulting from incomplete and anisotropic hydration in crowded environments and (ii) short-range effects of liquid-structure forces on the hydrogen-bond interactions at solute/water interfaces. The model is an extension of the phenomenological screened coulomb potential-based implicit model of solvation. The developments reported here allow a more realistic representation of highly crowded and spatially heterogeneous environments, such as those in the interior of a living cell. Only the solvent is treated as a continuum medium. It is shown that the electrostatic effects of long-range water-exclusion can strongly affect protein-protein binding energies and are then related to the thermodynamics of complex formation. Hydrogen-bond interactions modulated by the liquid structure at interfaces are calibrated based on systematic calculations of potentials of mean force in explicit water. The electrostatic component of the model is parametrized for monovalent, divalent and trivalent ions. The conceptual and practical aspects of the model are discussed based on simulations of protein complexation and peptide folding. The current implementation is ~1.5 times slower than the gas-phase force field and exhibits good parallel performance.

Complex formation reactions of palladium(II)-1,3-diaminopropane with various biologically relevant ligands. Kinetics of hydrolysis of glycine methyl ester through complex formation

The interaction of [Pd(DAP)(H2O)2]2+ (DAP = 1,3-diaminopropane) with some selected bio-relevant ligands, containing different functional groups, were investigated. The ligands used are dicarboxylic acids, amino acids, peptides and DNA constituents. Stoichiometry and stability constants of the complexes formed are reported at 25°C and 0.1 M ionic strength. The results show the formation of 1:1 complexes with amino acids and dicarboxylic acids. The effect of chelate ring size of the dicarboxylic acid complexes on their stability constants is examined. Peptides form both 1:1 complexes and the corresponding deprotonated amide species. DNA constituents form 1:1 and 1:2 complexes. The effect of dioxane on the acid dissociation constants of CBDCA and the formation constant of its complex with Pd(DAP)2+ was reported. The kinetics of hydrolysis of glycine methyl ester bound to [Pd(DAP)(H2O)2]2+ was studied at 25°C and 0.1M ionic strength.

Kinetics of base hydrolysis of α-amino acid esters catalyzed by palladium(II) piperazine complex

The kinetics of base hydrolysis of glycine, histidine, and methionine methyl esters in the presence of [Pd(pip)(H2O)2]2+ complex, where pip is piperazine, is studied in aqueous solutions, at T = 25°C, and I = 0.1 mol dm−3. The rate of ester hydrolysis for glycine methyl ester is studied at different temperature and dioxane/water solutions of different compositions. The kinetic data are fit under the assumption that the hydrolysis proceeds in one step. The activation parameters for the base hydrolysis of the complexes are evaluated

Xanthosine 5'-monophosphate (XMP). Acid-base and metal ion-binding properties of a chameleon-like nucleotide

The four acidity constants of threefold protonated xanthosine 5'-monophosphate, H(3)(XMP)(+), reveal that in the physiological pH range around 7.5 (X - H x MP)(3-) strongly dominates and not XMP(2-) as commonly given in textbooks and often applied in research papers. Therefore, this nucleotide, which participates in many metabolic processes, should be addressed as xanthosinate 5'-monophosphate as is stated in this critical review. Micro acidity constant schemes allow quantification of intrinsic site basicities. In 9-methylxanthine nucleobase deprotonation occurs to more than 99% at (N3)H, whereas for xanthosine it is estimated that about 30% are (N1)H deprotonated and for (X - H x MP)(3-) it is suggested that (N1)H deprotonation is further favored, especially in macrochelates where the phosphate-coordinated M(2+) interacts with N7. The formation degree of these macrochelates in the (X - H x MP x M)(-) species of Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) amounts to 90% or more. In the monoprotonated (M x X - H x MP x H)(+/-) complexes, M(2+) is located at the N7/[(C6)O] unit as the primary binding site and it forms macrochelates with the P(O)(2)(OH)(-) group to about 65% for nearly all metal ions considered (i.e., including Ba(2+), Sr(2+), Ca(2+), Mg(2+)); this indicates outer-sphere binding to P(O)(2)(OH)(-). Finally, a new method quantifying the chelate effect is applied to the M(X - H x MP)(-) species, stabilities and structures of mixed-ligand complexes are considered, and the stability constants for several M(X - H x DP)(2-) and M(X - H x TP)(3-) complexes are estimated (112 references).

Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model

Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.