Net Protonation Research Articles

PKameasurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments.

Determining the net charge and protonation states populated by a small molecule in an environment of interest or the cost of altering those protonation states upon transfer to another environment is a prerequisite for predicting its physicochemical and pharmaceutical properties. The environment of interest can be aqueous, an organic solvent, a protein binding site, or a lipid bilayer. Predicting the protonation state of a small molecule is essential to predicting its interactions with biological macromolecules using computational models. Incorrectly modeling the dominant protonation state, shifts in dominant protonation state, or the population of significant mixtures of protonation states can lead to large modeling errors that degrade the accuracy of physical modeling. Low accuracy hinders the use of physical modeling approaches for molecular design. For small molecules, the acid dissociation constant (pKa) is the primary quantity needed to determine the ionic states populated by a molecule in an aqueous solution at a given pH. As a part of SAMPL6 community challenge, we organized a blind pKa prediction component to assess the accuracy with which contemporary pKa prediction methods can predict this quantity, with the ultimate aim of assessing the expected impact on modeling errors this would induce. While a multitude of approaches for predicting pKa values currently exist, predicting the pKas of drug-like molecules can be difficult due to challenging properties such as multiple titratable sites, heterocycles, and tautomerization. For this challenge, we focused on set of 24 small molecules selected to resemble selective kinase inhibitors-an important class of therapeutics replete with titratable moieties. Using a Sirius T3 instrument that performs automated acid-base titrations, we used UV absorbance-based pKa measurements to construct a high-quality experimental reference dataset of macroscopic pKas for the evaluation of computational pKa prediction methodologies that was utilized in the SAMPL6 pKa challenge. For several compounds in which the microscopic protonation states associated with macroscopic pKas were ambiguous, we performed follow-up NMR experiments to disambiguate the microstates involved in the transition. This dataset provides a useful standard benchmark dataset for the evaluation of pKa prediction methodologies on kinase inhibitor-like compounds.

Functionalization of the Aryl Moiety in the Pincer Complex (NCN)NiIIIBr2: Insights on NiIII-Promoted Carbon–Heteroatom Coupling

This report describes the C–O, C–N, and C–halogen functionalization of the NiIII–Ar moiety stabilized within a pincer framework that serves as a model system for studying C–heteroatom coupling reactions promoted by high-valent Ni compounds. Treating van Koten’s pincer complex (NCN)NiIIIBr2 under a nitrogen atmosphere with water, 1° or 2° alcohols, 1° amines, HCl, or HBr results in heterofunctionalization at the ipso-C of the pincer ligand’s aryl moiety. The yields of these heterofunctionalizations are generally <50%, which has been attributed to the occurrence of a comproportionation reaction between the trivalent precursor and a NiI species arising from the reductive elimination step in the functionalization process. Other side-reactions include a C–OH coupling with residual water and C–H coupling (net protonation) that is prevalent with mineral acids, some alcohols, and aqueous NH3. Kinetic measurements have established that the reaction with MeOH is first-order with respect to [(NCN)NiIIIBr2], and a ki...

Protonation of β-lactoglobulin in the presence of strong polyelectrolyte chains: a study using Monte Carlo simulation

In this work, the molecular interaction between the protein β-lactoglobulin and strong polyelectrolyte chains was studied using Monte Carlo simulations. Different coarse-grained models were used to represent the system components. Both net charge and protonation of the isolated dimeric protein were analyzed as a function of pH. The acid-base equilibrium of each titratable group was distinctively modified by the presence of polyanion or polycation chains. The complexation on the wrong side of pI was more evident with the polycation than with the polyanion. It was mainly due to a charge regulation mechanism, where the reversion in net charge of the protein was more pronounced at the left of isoelectric point of the protein. The glutamic and aspartic groups play a key role in this charge reversion. Both polyanion and polycation were spatially adsorbed in different region on the protein surface, suggesting the importance of the surface charge distribution of the protein.

Calcium, Ammonia, Redox-Active Tyrosine YZ, and Proton-Coupled Electron Transfer in the Photosynthetic Oxygen-Evolving Complex.

A redox-active tyrosine, YZ (Y161 in the D1 polypeptide), is essential in photosystem II (PSII), which conducts photosynthetic oxygen evolution. On each step of the light-driven oxygen evolving reaction, YZ radical is formed by a chlorophyll cation radical. YZ radical is then reduced by a Mn4CaO5 cluster in a proton coupled electron transfer (PCET) reaction. YZ is hydrogen bonded to His190-D1 and to water molecules in a hydrogen-bonding network, involving calcium. This network is sensitive to disruption with ammonia and to removal and replacement of calcium. Only strontium supports activity. Here, we use electron paramagnetic resonance (EPR) spectroscopy to define the influence of ammonia treatment, calcium removal, and strontium/barium substitution on YZ radical PCET at two pH values. A defined oxidation state of the metal cluster (S2) was trapped by illumination at 190 K. The net reduction and protonation of YZ radical via PCET were monitored by EPR transients collected after a 532 nm laser flash. At 190 K, YZ radical cannot oxidize the Mn4CaO5 cluster and decays on the seconds time scale by recombination with QA-. The overall decay half-time and biexponential fits were used to analyze the results. The reaction rate was independent of pH in control, calcium-reconstituted PSII (Ca-PSII). At pH 7.5, the YZ radical decay rate decreased in calcium-depleted (CD-PSII) and barium/strontium-reconstituted PSII (Ba-PSII, Sr-PSII), relative to Ca-PSII. At pH 6.0, the YZ radical decay rate was not significantly altered in CD-PSII and Sr-PSII but decreased in Ba-PSII. A two-pathway model, involving two competing proton donors with different pKa values, is proposed to explain these results. Ammonia treatment decreased the YZ decay rate in Ca-PSII, Sr-PSII, and CD-PSII, consistent with a reaction that is mediated by the hydrogen-bonding network. However, ammonia treatment did not alter the rate in Ba-PSII. This result is interpreted in terms of the large ionic radius of barium and the elevated pKa of barium-bound water, which are expected to disrupt hydrogen bonding. In addition, evidence for a functional interaction between the S2 protonated water cluster (Wn+) and the YZ proton donation pathway is presented. This interaction is proposed to increase the rate of the YZ PCET reaction.

2-Pyridyl-phosphine and -diphosphine complexes of nickel(0), their reactivity (including aqueous solution chemistry), and some related, incidental methylphosphonium iodides

The chemistry of Ni0-dicarbonyl(pyridylphosphine) complexes of the type Ni(CO)2L2, where L is either P-bonded PPh3−npyn (n=1–3, py=2-pyridyl; abbreviated PNx, x=1–3, species 1a–c), or L2 is (P–P)-chelated py2P(CH2)2Ppy2 or ▪, is further developed from earlier studies by our group [the P–P ligands are abbreviated, respectively, as d(py)pe and d(py)pcp]. The complexes are synthesized from C6H6 solutions of Ni(CO)2(PPh3)2, and the Ni(CO)2(PPh3)(PNx) intermediates (1a∗–c∗) are detected; Ni(CO)2[d(py)pcp] (2b) is shown by X-ray analysis to have a distorted tetrahedral structure; and the NiII species [Ni2(CO)4(μ-PN2)2]Cl4 is isolated from a light-induced reaction in CDCl3 solution. Complex 2b dissolves in water at ambient conditions via a net double protonation of pyridyl N-atoms, the {Ni(CO)2[2H-d(py)pcp]}2+ being isolated as the bis(triflate) salt; the dication decomposes in minutes with formation of [Ni(H2O)6]2+, CO, the phosphine dioxide, and deprotonated d(py)pcp. Some twenty-two Ni0 complexes, exemplified by Ni(P–P)2, Ni(PNx)2(P–P), Ni(PNx)4, and related PPh3- and Ph2P(CH2)2PPh2 (dppe)-containing species, are synthesized from Ni(1,5-COD)2 and their reactivity studied; for example, oxidative addition of MeI generates trans-Ni(Me)(I)(PN3)2 and trans-Ni(Me)(I)(P–P)2 but, with non-pyridyl containing reactants such as Ni(PPh3)4 and Ni(dppe)2, only (monomethyl)phosphonium iodides are formed. Such iodides, and the bis(methyl) analogues [(CH3)2(diphosphine)]I2, are then studied for clarification of some observed Ni chemistry. The NMR trends (a)–(d) are noted within the series of Ni0 complexes, and are rationalized: (a) the 2JPP values in 1a∗–c∗, and the separation between the two doublets, parallel the number of N-atoms present; (b) the 31P{1H} signals in the Ni(PNx)4 and Ni(PNx)2(P–P) complexes shift downfield in the order PN1<PN2<PN3 within linear dependences; (c) the 2JPP values for the Ni(PR3)2(P–P) complexes (R=Ph and PNx) decrease in the order R=Ph>PN1>PN2>PN3; (d) and the separation between the two 31P{1H} triplets of the Ni(PNx)2(P–P) complexes generally depends on the relative numbers of phenyl and pyridyl groups.

Tautomeric populations of the charged species of 1,12-diamino-3,6,9-triazadodecane (SpmTrien) studied with computer simulations and cluster expansions

Correct net charge and protonation pattern in the polyamine backbone is one of the major factors that define the interactions of this class of compounds. 1,12-diamino-3,6,9-triazadodecane (SpmTrien) is a isosteric charge deficient analogue of naturally occurring spermine (Spm) with different biological features. The tautomeric populations of each SpmTrien charge state were estimated with computer simulations, molecular dynamics (MD) and quantum mechanical calculations, and cluster expansions separately. In the computer simulations, tautomeric populations of each charge state were obtained by constrained least-squares fitting the theoretically calculated (GIAO B3LYP/6-311 + G**) 15 N NMR chemical shieldings of SpmTrien tautomers to the experimentally measured chemical shifts. Theoretical chemical shieldings were calculated for water complexes of SpmTrien obtained from MD simulations in explicit water. Both methods gave highly similar realistic results. SpmTrien has many major populations of tautomers at biologically relevant charge states of three (+3) and four (+4) thus enabling a large variety of structures for specific ionic interactions. Copyright © 2013 John Wiley & Sons, Ltd.

Thermodynamics of the GTP-GDP-operated Conformational Switch of Selenocysteine-specific Translation Factor SelB

SelB is a specialized translation factor that binds GTP and GDP and delivers selenocysteyl-tRNA (Sec-tRNA(Sec)) to the ribosome. By analogy to elongation factor Tu (EF-Tu), SelB is expected to control the delivery and release of Sec-tRNA(Sec) to the ribosome by the structural switch between GTP- and GDP-bound conformations. However, crystal structures of SelB suggested a similar domain arrangement in the apo form and GDP- and GTP-bound forms of the factor, raising the question of how SelB can fulfill its delivery function. Here, we studied the thermodynamics of guanine nucleotide binding to SelB by isothermal titration calorimetry in the temperature range between 10 and 25 °C using GTP, GDP, and two nonhydrolyzable GTP analogs, guanosine 5'-O-(γ-thio)triphosphate (GTPγS) and guanosine 5'-(β,γ-imido)-triphosphate (GDPNP). The binding of SelB to either guanine nucleotide is characterized by a large heat capacity change (-621, -467, -235, and -275 cal × mol(-1) × K(-1), with GTP, GTPγS, GDPNP, and GDP, respectively), associated with compensatory changes in binding entropy and enthalpy. Changes in heat capacity indicate a large decrease of the solvent-accessible surface area in SelB, amounting to 43 or 32 amino acids buried upon binding of GTP or GTPγS, respectively, and 15-19 amino acids upon binding GDP or GDPNP. The similarity of the GTP and GDP forms in the crystal structures can be attributed to the use of GDPNP, which appears to induce a structure of SelB that is more similar to the GDP than to the GTP-bound form.

Protein–protein binding is often associated with changes in protonation state

pK(a) values of ionizable residues have been calculated using the PROPKA method and structures of 75 protein-protein complexes and their corresponding free forms. These pK(a) values were used to compute changes in protonation state of individual residues, net changes in protonation state of the complex relative to the uncomplexed proteins, and the correction to a binding energy calculated assuming standard protonation states at pH 7. For each complex, two different structures for the uncomplexed form of the proteins were used: the X-ray structures determined for the proteins in the absence of the other protein and the individual protein structures taken from the structure of the complex (referred to as unbound and bound structures, respectively). In 28 and 77% of the cases considered here, protein-protein binding is accompanied by a complete (>95%) or significant (>50%) change in protonation state of at least one residue using unbound structures. Furthermore, in 36 and 61% of the cases, protein-protein binding is accompanied by a complete or significant net change in protonation state of the complex relative to the separated monomers. Using bound structures, the corresponding values are 12, 51, 20, and 48%. Comparison to experimental data suggest that using unbound and bound structures lead to over- and underestimation of binding-induced protonation state changes, respectively. Thus, we conclude that protein-protein binding is often associated with changes in protonation state of amino acid residues and with changes in the net protonation state of the proteins. The pH-dependent correction to the binding energy contributes at least one order of magnitude to the binding constant in 45 and 23%, using unbound and bound structures, respectively.

Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding toEscherichia coli SSB protein

Many macromolecular interactions, including protein-nucleic acid interactions, are accompanied by a substantial negative heat capacity change, the molecular origins of which have generated substantial interest. We have shown previously that temperature-dependent unstacking of the bases within oligo(dA) upon binding to the Escherichia coli SSB tetramer dominates the binding enthalpy, DeltaH(obs), and accounts for as much as a half of the observed heat capacity change, DeltaC(p). However, there is still a substantial DeltaC(p) associated with SSB binding to ssDNA, such as oligo(dT), that does not undergo substantial base stacking. In an attempt to determine the origins of this heat capacity change, we have examined by isothermal titration calorimetry (ITC) the equilibrium binding of dT(pT)(34) to SSB over a broad pH range (pH 5. 0-10.0) at 0.02 M, 0.2 M NaCl and 1 M NaCl (25 degrees C), and as a function of temperature at pH 8.1. A net protonation of the SSB protein occurs upon dT(pT)(34) binding over this entire pH range, with contributions from at least three sets of protonation sites (pK(a1) = 5.9-6.6, pK(a2) = 8.2-8.4, and pK(a3) = 10.2-10.3) and these protonation equilibria contribute substantially to the observed DeltaH and DeltaC(p) for the SSB-dT(pT)(34) interaction. The contribution of this coupled protonation ( approximately -260 to -320 cal mol(-1) K(-1)) accounts for as much as half of the total DeltaC(p). The values of the "intrinsic" DeltaC(p,0) range from -210 +/- 33 cal mol(-1) degrees K(-1) to -237 +/- 36 cal mol(-1)K(-1), independent of [NaCl]. These results indicate that the coupling of a temperature-dependent protonation equilibria to a macromolecular interaction can result in a large negative DeltaC(p), and this finding needs to be considered in interpretations of the molecular origins of heat capacity changes associated with ligand-macromolecular interactions, as well as protein folding.

The role of electrostatic interactions for cytochrome c oxidase function.

In recent years, the enormous increase in high-resolution three-dimensional structures of proteins together with the development of powerful theoretical techniques have provided the basis for a more detailed examination of the role of electrostatics in determining the midpoint potentials of redox-active metal centers and in influencing the protonation behavior of titratable groups in proteins. Based on the coordinates of the Paracoccus denitrificans cytochrome c oxidase, we have determined the electrostatic potential in and around the protein, calculated the titration curves for all ionizable residues in the protein, and analyzed the response of the protein environment to redox changes at the metal centers. The results of this study provide insight into how charged groups can be stabilized within a low-dielectric environment and how the range of their electrostatic effects can be modulated by the protein. A cluster of 18 titratable groups around the heme a3-CuB binuclear center, including a hydroxide ion bound to the copper, was identified that accounts for most of the proton uptake associated with redox changes at the binuclear site. Predicted changes in net protonation were in reasonable agreement with experimentally determined values. The relevance of these findings in the light of possible mechanisms of redox-coupled proton movement is discussed.

Relationship of proton uptake on the cytoplasmic surface and reisomerization of the retinal in the bacteriorhodopsin photocycle: An attempt to understand the complex kinetics of the pH changes and the N and O intermediates

In the bacteriorhodopsin photocycle the recovery of the initial BR state from the M intermediate occurs via the N and O intermediates. The molecular events in this process include reprotonation of the Schiff base and the subsequent uptake of a proton from the cytoplasmic side, as well as reisomerization of the retinal from 13-cis to all-trans. We have studied the kinetics of the intermediates and the proton uptake. At moderately low pH little of the N state accumulates, and the O state dominates in the reactions that lead from M to BR. The proton uptake lags behind the formation of O, suggesting the sequence N(0)<==>O(0) + H+ (from the bulk)-->O(+1)-->BR+H+ (to the bulk), where the superscripts indicate the net protonation state of the protein relative to BR. Together with a parallel study of ours at moderately high pH, these results suggest that the sequence of proton uptake and retinal reisomerization depends on pH: at low pH the isomerization occurs first and O accumulates, but at high pH the isomerization is delayed and therefore N accumulates. Although this model contains too many rate constants for rigorous testing, we find that it will generate most of the characteristic pH-dependent kinetic features of the photocycle with few assumptions other than pH dependency for protonation at the proton release and uptake steps.

FTIR difference spectroscopy of the bacteriorhodopsin mutant Tyr-185 .fwdarw. Phe: Detection of a stable O-like species and characterization of its photocycle at low temperature

Fourier transform infrared difference spectroscopy has been used to study the photocycle of the mutant Tyr-185-->Phe expressed in native Halobacterium halobium and isolated as intact purple membrane fragments. We find several changes in the low-temperature bR-->K, bR-->L, and bR-->M FTIR difference spectra of Y185F relative to wild-type bR which are not directly related to the absorption bands associated with Tyr-185. We show that these features arise from the photoreaction of a stable red-shifted species (OY185F) with a vibrational spectrum similar to the O intermediate. By using photoselection and FTIR spectroscopy, we have been able to characterize the photoproducts of this OY185F species. A K-like photoproduct is formed at 80 K which has a 13-cis structure. However, it differs from K630, exhibiting an intense band at 990 cm-1 most likely due to a hydrogen-out-of-plane vibrational mode of the chromophore. At 170 and 250 K, photoexcitation of OY185F produces an intermediate with vibrational features similar to the N intermediate in the wild-type bR photocycle. However, no evidence for an M-like intermediate is found. Although Asp-96 undergoes a change in its environment/protonation state during the OY185F photocycle, no protonation changes involving Asp-85 and Asp-212 were detected. These results provide strong evidence that light adaptation of Y185F produces two species similar to bR570 and the O intermediate. Differences in their respective photocycles can be explained on the basis of differences in the protonation states of the residues Asp-85 and Asp-212 which are ionized in bR570 and undergo net protonation upon OY185F formation.

Microcalorimetric study of wheat germ agglutinin binding to N-acetylglucosamine and its oligomers.

The energetics of association of wheat germ agglutinin (WGA) with N-acetylglucosamine (GlcNAc) and its beta(1,4) oligomers have been measured using isothermal titration calorimetry. Association constants of 0.4, 5.3, 11.1, 12.3, and 19.1 mM-1 and enthalpies of binding of -6.1, -15.6, -19.4, -19.3, and -18.2 kcal mol-1 were obtained at 26 degrees C for the titration of WGA with GlcNAc, (GlcNAc)2, (GlcNAc)3, (GlcNAc)4, and (GlcNAc)5, respectively. The term T delta S was always of negative value, indicating that the binding process is enthalpically driven. Titrations of WGA performed at pH 4.5 did not differ significantly from those performed at pH 7.0, suggesting that no groups with a pKa in this range are directly involved in the binding event. Also, performing the titration in a buffer system with a higher enthalpy of protonation did not change the enthalpy of binding confirming that there is no net protonation or deprotonation when WGA binds GlcNAc residues at pH 7. A model of four independent binding sites was found to adequately describe the binding curves, except in the case of (GlcNAc)4 which exhibited positive cooperativity. The energetic values are discussed within the context of the structure of the WGA-(GlcNAc)2 complex.

Phosphorus-31, nitrogen-15, and carbon-13 and NMR of glyphosate: comparison of pH titrations to the herbicidal dead-end complex with 5-enolpyruvoylshikimate-3-phosphate synthase

The herbicidal dead-end ternary complex (E{sup S3P}{sub Glyph}) of glyphosate (N-(phosphonomethyl)glycine) with 5-enolpyruvoylshikimate-3-phosphate synthase (EPSPS) and the substrate shikimate 3-phosphate (S3P) has been characterized by {sup 31}P, {sup 15}N, and {sup 13}C NMR. The NMR spectra of EPSPS-bound glyphosate show unique chemical shifts ({delta}) for each of the three nuclei. By {sup 31}P NMR, glyphosate in the dead-end complex is a distinct species 3.5 ppm downfield from free glyphosate. The {sup 13}C signal of glyphosate in the dead-end complex is shifted 4 ppm downfield from that of free glyphosate. The {sup 15}N signal for glyphosate (99%) in the dead-end complex is 5 ppm further downfield than that of any free zwitterionic species and 10 ppm downfield from that of the average free species at pH 10.1. The structures of each ionic state of glyphosate are modeled with force field calculations by using MacroModel. A correlation is made for the {sup 31}P {delta} and the C-P-O bond angle, and the {sup 13}C and {sup 15}N {delta} values are postulated to be related to C-C-O and C-N-C bond angles, respectively. The downfield {sup 31}P chemical shift perturbation for S3P in the EPSPS binary complex is consistent with ionization of the 3-phosphate ofmore » S3P upon binding. Comparison with the S3P {sup 31}P {delta} vs pH titration curve specifies predominantly the dianion of the 3-phosphate in the E{sup S3P} binary complex, while the E{sup S3P}{sub Glyph} complex indicates net protonation at the 3-phosphate. Chemical shift perturbations of this latter type may be explained by changes in the O-P-O bond angle.« less

Proton release during the reductive half-reaction of D-amino acid oxidase.

Changes in the net protonation of D-amino acid oxidase during binding of competitive inhibitors and during reduction by amino acids have been monitored using phenol red as a pH indicator. At pH 8.0, no uptake or release of protons from solution occurs upon binding the inhibitors benzoate, anthranilate, picolinate, or L-leucine. The Kd values for both picolinate and anthranilate were determined from pH 5.4 to 9.0. The results are consistent with a single group on the enzyme having a pK of 6.3 which must be unprotonated for tight binding, as is the case with benzoate binding (Quay, S., and Massey, V. (1977) Biochemistry 16, 3348-3354) and with tight binding of the inhibitor form with an unprotonated amino group. Upon reduction of the enzyme by amino acid substrates, two protons are released to solution. The first is released concomitantly with reduction to the reduced enzyme-imino acid charge transfer complex. The second is released only upon dissociation of the charge transfer complex to free reduced enzyme and imino acid. The first proton is assigned as arising from the amino acid group and the second from the amino acid alpha-hydrogen. These results are consistent with the flavin in reduced D-amino acid oxidase being anionic.