Change In pK Research Articles

Effect of Protonation State on the Stability of Amyloid Oligomers Assembled from TTR(105-115).

Amyloid fibrils are self-assembled aggregates of polypeptides that are implicated in the development of several human diseases. A peptide derived from amino acids 105-115 of the human plasma protein transthyretin forms homogeneous and well-defined fibrils and, as a model system, has been the focus of a number of studies investigating the formation and structure of this class of aggregates. Self-assembly of TTR(105-115) occurs at low pH, and this work explores the effect of protonation on the growth and stability of small cross-β aggregates. Using molecular dynamics simulations of structures up to the decamer in both protonated and deprotonated states, we find that, whereas hexamers are more stable for protonated peptides, higher order oligomers are more stable when the peptides are deprotonated. Our findings imply a change in the acid pK of the protonated C-terminal group during the formation of fibrils, which leads to stabilization of higher-order oligomers through electrostatic interactions.

Combined Density Functional Theory (DFT) and Continuum Calculations of pKain Carbonic Anhydrase

Deprotonation of zinc-bound water in carbonic anhydrase II is the rate-limiting step in the catalysis of carbon dioxide between gas- and water-soluble forms. To understand the factors determining the extent of dissociation, or pK(a), of the zinc-bound water, we apply quantum chemistry calculations to the active site coupled with a continuum model of the surrounding environment. Experimentally determined changes in pK(a) associated with mutations of the active site are well reproduced by this approach. Analysis of the active site structure and charge/dipole values provides evidence that mutations cause changes in both conformation of the active site structure and local polarization, which accounts for the shifts in pK(a). More specifically, the shifts in pK(a) correlate with the dipole moments of the zinc-bound water upon deprotonation. The data further support the conclusion that the distinct pK(a) values found in mutations of the same type, but applied to different sites, result from asymmetric ligation and different electronic environments around the zinc ion.

The Membrane Modulates Internal Proton Transfer in Cytochrome c Oxidase

The functionality of membrane proteins is often modulated by the surrounding membrane. Here, we investigated the effect of membrane reconstitution of purified cytochrome c oxidase (CytcO) on the kinetics and thermodynamics of internal electron and proton-transfer reactions during O(2) reduction. Reconstitution of the detergent-solubilized enzyme in small unilamellar soybean phosphatidylcholine vesicles resulted in a lowering of the pK(a) in the pH dependence profile of the proton-uptake rate. This pK(a) change resulted in decreased proton-uptake rates in the pH range of ~6.5-9.5, which is explained in terms of lowering of the pK(a) of an internal proton donor within CytcO. At pH 7.5, the rate decreased to the same extent when vesicles were prepared from the pure zwitterionic lipid 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or the anionic lipid 1,2-dioleoyl-sn-glycero-3-phospho(1-rac-glycerol) (DOPG). In addition, a small change in the internal Cu(A)-heme a electron equilibrium constant was observed. This effect was lipid-dependent and explained in terms of a lower electrostatic potential within the membrane-spanning part of the protein with the anionic DOPG lipids than with the zwitterionic DOPC lipids. In conclusion, the data show that the membrane significantly modulates internal charge-transfer reactions and thereby the function of the membrane-bound enzyme.

Photodynamic ion sensor systems with spiropyran: photoactivated acidity changes in plasticized poly(vinyl chloride)

We aim to introduce photoactivated optical ion sensors based on a triggered ion exchange process as novel dynamic tools. The quantification of the acidity change upon photoactivation of spiropyran within an organic membrane phase during photoexcitation is described here for the first time, suggesting a large pK(a) change of more than 6 orders of magnitude.

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease

The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment.

Exploring conformational changes coupled to ionization states using a hybrid Rosetta‐MCCE protocol

A hybrid protocol combining Rosetta fullatom refinement and Multi-Conformation Continuum Electrostatics (MCCE) to estimate pK(a) is applied to the blind prediction of 94 mutated residues in Staphylococcal nuclease (SNase), as part of the pK(a)-cooperative benchmark test. The standard MCCE method is limited to sidechain conformational changes. The Rosetta refinement protocol is used to add the backbone conformational changes in pK(a) calculations. The non-electrostatic energy component from Rosetta and the electrostatic energy from MCCE are combined to weight the calculated ionization states. Of 63 measured pK(a)s, the root mean squared deviation (RMSD) between the calculated pK(a)s and the measured values is 4.3, showing an improvement compared to the RMSD of 6.6 in the standard MCCE calculations, using a low protein dielectric constant of 4. The breakdown of pK(a) shift from the solution values (ΔpK(a)) shows that the desolvation energy contributes the most in the standard MCCE calculations. Lowering desolvation penalties and optimizing electrostatic interactions with the Rosetta/MCCE protocol reduces the ΔpK(a) to favor the charged states. Analysis also showed that the Rosetta/MCCE protocol samples conformations with pK(a)s close to the solution values. The question remains whether the correct conformational changes coupled to the ionization changes are found here. Nevertheless, a challenge emerges to accurately estimate the reorganization energy, which is not directly measured from the electrostatic environment of the site of interest. Possible improvements to the protocol are also discussed.

A combinatorial histidine scanning library approach to engineer highly pH‐dependent protein switches

There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK(a) change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine "hot-spots," which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications.

A novel potentiometric hydrogen peroxide sensor based on pK a changes of vinylphenylboronic acid membranes

A potentiometric hydrogen peroxide (H 2O 2) sensing scheme was developed using arylboronic acid as the electrode modifier. It is well-known that both aliphatic and aryl boronic acid undergo electrophilic displacement reaction with H 2O 2. This reaction involves replacement of boronic acid by the hydroxyl group of peroxide resulting in a change in pK a value that can be exploited for sensing of H 2O 2. Vinylphenylboronic acid (VPBA) ink was prepared using Nafion as the binder and it was drop cast on an electrode surface. Morphology of the modified electrode was analysed using scanning electron microscopy (SEM). The present modifier exhibited a linear relationship between the difference in electrode potential (∆Ep) vs. [H 2O 2] with a Nernstian slope of 26 ± 2 mV in the concentration range of 10 − 1 –10 − 5 M. Application of the VPBA modified electrode for hydrogen peroxide sensing was studied in an industrial dye-bleach effluent.

Phase I, dose-finding study of monotherapy with AZD8931, an inhibitor of ErbB1, 2, and 3 signaling, in patients (pts) with advanced solid tumors.

3097 Background: AZD8931 is an oral, equipotent inhibitor of ErbB1, ErbB2 and ErbB3 receptor signaling. Methods: This open-label, multiple ascending (standard 3+3 design) dose cohort study (NCT00637039) determined the safety, tolerability, and PK of AZD8931. Pts received a single oral dose of AZD8931 followed by a 4-day observation and then AZD8931 bid for 21 consecutive days (continuation post day 21 was optional). Results: 28 pts (mean age 56 years) received AZD8931 (n=5, 40 mg bid; n=8, 80 mg bid; n=6, 160 mg bid; n=6, 240 mg bid; n=3, 300 mg bid); 21 had metastatic disease and 27 had received prior cancer therapy. The most common primary tumors were ovary (n=8) and breast (n=5). The 21-day repeat-dosing period was completed by 22 pts and 9 remained on treatment after this period. Median duration of exposure to AZD8931 was 22 days (range 7–140). DLTs were identified in 1/6 pts in the 240 mg bid cohort (Grade [Gr] 3 rash) and in 2/2 evaluable pts in the 300 mg bid cohort (Gr 3 and Gr 4 diarrhea). Skin and subcutaneous tissue disorders and GI disorders were the most common system organ class AEs. In the 40 mg bid group cohort all skin-type AEs (n=5) were mild (Gr 1). AZD8931 demonstrated rapid absorption (median tmax was 1–3 h), was well distributed, had moderate to high clearance and terminal t½ of 11 h. Following continuous bid dosing, steady state was achieved by day 2, accumulation was ~1.5-fold and no time-dependent changes in PK were observed. Exposure increased proportionally with dose up to 160 mg; for single doses >160 mg, exposure increased slightly greater than proportionally with dose. Of 21 pts evaluable for response at day 21, 12 had stable disease and 9 had disease progression. Conclusions: The MTD of AZD8931 determined from tolerability data during the DLT period was 240 mg bid. However, more long-term data are needed to define a dose of AZD8931 suitable for chronic treatment. AZD8931 dose (n) 40 mg bid (5) 80 mg bid (8) 160 mg bid (6) 240 mg bid (6) 300 mg bid (3) Total (28) Patients with an AE considered related to study treatment, n Any grade 5 8 6 6 3 28 Grade ≥3 1 3 3 4 3 14 SAE 0 0 0 0 1 1 Most frequent grade ≥3 skin-related and GI AEs, n Diarrhea 1 0 2 2 2 7 Acne-type rash 0 3 0 1 0 4 Skin exfoliation 0 1 0 1 0 2 Ascites 0 1 1 0 0 2

Combined X-ray, NMR, and Kinetic Analyses Reveal Uncommon Binding Characteristics of the Hepatitis C Virus NS3-NS4A Protease Inhibitor BI 201335

Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.

Lyme Disease Enolpyruvyl-UDP-GlcNAc Synthase: Fosfomycin-Resistant MurA from Borrelia burgdorferi, a Fosfomycin-Sensitive Mutant, and the Catalytic Role of the Active Site Asp

MurAs (enolpyruvyl-UDP-GlcNAc synthases) from pathogenic bacteria such as Borrelia burgdorferi (Lyme disease) and tuberculosis are fosfomycin resistant because an Asp-for-Cys substitution prevents them from being alkylated by this epoxide antibiotic. Previous attempts to characterize naturally Asp-containing MurAs have resulted in no protein or no activity. We have expressed and characterized His-tagged Lyme disease MurA (Bb_MurA(H6)). The protein was most soluble at high salt concentrations but maximally active around physiological ionic strength. The steady-state kinetic parameters at pH 7 were k(cat) = 1.07 ± 0.03 s(-1), K(M,PEP) = 89 ± 12 μM, and K(M,UDP-GlcNAc) = 45 ± 7 μM. Mutating the active site Asp to Cys, D116C, caused a 21-fold decrease in k(cat) and rendered the enzyme fosfomycin sensitive. The pH profile of k(cat) was bell-shaped and centered around pH 5.3 for Bb_MurA(H6), with pK(a1) = 3.8 ± 0.2 and pK(a2) = 7.4 ± 0.2. There was little change in pK(a1) with the D116C mutant, 3.5 ± 0.3, but pK(a2) shifted to >11. This demonstrated that the pK(a2) of 7.4 was due to D116, almost 3 pH units above an unperturbed carboxylate, and that it must be protonated for activity. This supports D116's proposed role as a general acid/base catalyst. As fosfomycin does not react with simple thiols, nor most protein thiols, the reactivity of D116C with fosfomycin, combined with the strongly perturbed pK(a2) for D116, strongly implies an unusual active site environment and a chemical role in catalysis for Asp/Cys. There is also good evidence for C115 having a role in product release. Both roles may be operative for both Asp- and Cys-containing MurAs.

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding. These changes are explored as a function of the ligand type (small molecule, protein, and nucleic acid), and distance from the binding region. Standard continuum solvent methodology is used to compute, on an equal footing, pK changes upon ligand binding for a total of 5899 ionizable residues in 20 protein-protein, 20 protein-small molecule, and 20 protein-nucleic acid high-resolution complexes. The size of the data set combined with an extensive error and sensitivity analysis allows us to make statistically justified and conservative conclusions: in 60% of all protein-small molecule, 90% of all protein-protein, and 85% of all protein-nucleic acid complexes there exists at least one ionizable residue that changes its charge state upon ligand binding at physiological conditions (pH = 6.5). Considering the most biologically relevant pH range of 4–8, the number of ionizable residues that experience substantial pK changes (ΔpK > 1.0) due to ligand binding is appreciable: on average, 6% of all ionizable residues in protein-small molecule complexes, 9% in protein-protein, and 12% in protein-nucleic acid complexes experience a substantial pK change upon ligand binding. These changes are safely above the statistical false-positive noise level. Most of the changes occur in the immediate binding interface region, where approximately one out of five ionizable residues experiences substantial pK change regardless of the ligand type. However, the physical origins of the change differ between the types: in protein-nucleic acid complexes, the pK values of interface residues are predominantly affected by electrostatic effects, whereas in protein-protein and protein-small molecule complexes, structural changes due to the induced-fit effect play an equally important role. In protein-protein and protein-nucleic acid complexes, there is a statistically significant number of substantial pK perturbations, mostly due to the induced-fit structural changes, in regions far from the binding interface.

Statistics and Physical Origins of pK and Ionization State Changes Upon Protein-Ligand Binding

Statistics and Physical Origins of pK and Ionization State Changes Upon Protein-Ligand Binding

The effects of sub-chronic clozapine and haloperidol administration on isolation rearing induced changes in frontal cortical N-methyl- d-aspartate and D 1 receptor binding in rats

Glutamate and dopamine disturbances are implicated in frontal cortical dysfunction in schizophrenia. Little, however, is known about the nature of dopamine D 1 and N-methyl- d-aspartate (NMDA) receptor interactions in the illness, nor of the extent of their co-involvement in antipsychotic drug response. It is well known that early life adversity may pre-date the development of schizophrenia. Using a neurodevelopmental model of schizophrenia, namely post weaning social isolation rearing (SIR), we studied the effect of SIR (post natal day 21–61) on frontal cortical NMDA and D 1 receptor binding characteristics with/without chronic haloperidol (0.1 mg/kg/day i.p.) or clozapine (5 mg/kg/day i.p.) treatment, undertaken from post-natal day 50–60. SIR increased frontal cortical NMDA-density, with decreased affinity (decreased pK D), but reduced D 1 receptor density (without effects on pK D). In socially reared animals, clozapine but not haloperidol increased NMDA receptor density without effects on pK D. Neither drug markedly affected D 1 receptor density, although clozapine increased D 1 affinity. Increased NMDA density in SIR animals was unaffected by haloperidol, but further increased by clozapine. However, SIR-associated decrease in NMDA affinity remained unaltered despite drug treatment. Reduced D 1 receptor density in SIR animals was exacerbated by haloperidol, but unaltered by clozapine, without changes in pK D. SIR thus induces opposing effects on frontal cortical NMDA and D 1 radio-receptor binding characteristics, which has direct bearing on the mutual interplay of these receptors in schizophrenia. The ability of SIR to affect NMDA receptor affinity warrants deeper study. Furthermore, at the doses examined, in contrast to haloperidol, clozapine bolsters frontal cortical glutamatergic but stabilizes D 1 dopaminergic pathways in a neurodevelopmental animal model of schizophrenia, possibly explaining the atypical clinical characteristics of this drug.

On‐column titration and investigation of metal complex formation for aminopolycarboxylate functionalised monoliths using scanning contactless conductivity detection

The application of scanning capacitively coupled contactless conductivity detection (SC(4)D) for the determination of pH dependant behaviour of two aminopolycarboxylates immobilised onto the surface of a monolithic capillary column is described. The use of SC(4)D to visualise changes in conductivity of the discrete zones of functional groups within monolithic capillary columns allows for the effects of immobilisation on the physicochemical properties of zones to be compared to that of the functional group in solution. The perturbation of the pK(a) values of the functional groups can be attributed to the change in chemical environment experienced by the functional group through the presence of local hydrogen bonding and surface induced effects. These bonds, both between adjacent functional groups and with the monolithic polymethacrylate scaffold, result in a modification of the electron density on the functional group and therefore a change in pK(a). Changes in the pK(a) of N-(2-acetamido)iminodiacetic acid (ADA) from 2.48 to 5.2 for one of the acidic protons, with little change in the pK(a) of the amine group, were observed, which correlates to similar changes in aggregated systems of aminopolycarboxylates. Similar results were obtained for the iminodiacetic acid (IDA) once immobilised onto the surface of the monolith. Furthermore, the ability to measure changes in the charge of such discrete zones of functional groups allows for the visualisation of complexation events occurring directly on-column, where such complexes result in a change in charge of the functional group. This potentially useful technique is illustrated within for the formation of aminopolycarboxylate complexes with a selection of metal ions.

Solution and Fluorescence Properties of Symmetric Dipicolylamine-Containing Dichlorofluorescein-Based Zn2+ Sensors

The mechanism by which dipicolylamine (DPA) chelate-appended fluorophores respond to zinc was investigated by the synthesis and study of five new analogues of the 2',7'-dichlorofluorescein-based Zn(2+) sensor Zinpyr-1 (ZP1). With the use of absorption and emission spectroscopy in combination with potentiometric titrations, a detailed molecular picture has emerged of the Zn(2+) and H(+) binding properties of the ZP1 family of sensors. The two separate N(3)O donor atom sets on ZP1 converge to form binding pockets in which all four heteroatoms participate in coordination to either Zn(2+) or protons. The position of the pyridyl group nitrogen atom, 2-pyridyl or 4-pyridyl, has a large impact on the fluorescence response of the dyes to protons despite relatively small changes in pK(a) values. The fluorescence quenching effects of such multifunctional electron-donating units are often taken as a whole. Despite the structural complexity of ZP1, however, we provide evidence that the pyridyl arms of the DPA appendages participate in the quenching process, in addition to the contribution from the tertiary nitrogen amine atom. Potentiometric titrations reveal ZP1 dissociation constants (K(d)) for Zn(2+) of 0.04 pM and 1.2 nM for binding to the first and second binding pockets of the ligand, respectively, the second of which correlates with the value observed by fluorescence titration. This result demonstrates that both binding pockets of this symmetric, ditopic sensor need to be occupied in order for full fluorescence turn-on to be achieved. These results have significant implications for the design and implementation of fluorescent sensors for studies of mobile zinc ions in biology.

Color-Changing Mutation in the E−F Loop of Proteorhodopsin

It is usually assumed that only amino acids located near the retinal chromophore are responsible for color tuning of rhodopsins. However, we recently found that replacement of Ala178 with Arg in the E-F loop of proteorhodopsin (PR), an archaeal-type rhodopsin in marine bacteria, shifts the lambda(max) from 525 to 545 nm at neutral pH [Yoshitsugu, M., Shibata, M., Ikeda, D., Furutani, Y., and Kandori, H. (2008) Angew. Chem., Int. Ed. 47, 3923-3926]. Since the location of Ala178 is distant from the retinal chromophore (approximately 25 A), the molecular mechanism of the unusual mutation effect on color tuning is intriguing. Here we studied this mechanism by using additional mutations and some analytical methods. Introduction of Arg into the corresponding amino acid in bacteriorhodopsin (BR, M163R mutant) does not change the absorption spectra, indicating that the effect is specific to PR. Introduction of Arg into the A-B or C-D loop yields little (3 nm) or no color change, respectively. T177R and P180R mutants exhibited absorption spectra identical to that of the wild type, while N176R and S179R mutants exhibit lambda(max) values of 528 and 535 nm, respectively. Therefore, the observed color change is position-specific, being fully effective at position 178 and half-effective at position 179. Salt affects the absorption spectra of wild-type and A178R PR similarly. FTIR spectroscopy at 77 K indicated similar chromophore structures for wild-type and A178R PR, and A178R PR pumps protons normally. We infer that the E-F loop has a unique structure in PR and the mutation of Ala178 disrupts the structure that includes the transmembrane region, leading to the observed changes in color and pK(a).

Crystal Structure Analysis and in Silico pKa Calculations Suggest Strong pKa Shifts of Ligands as Driving Force for High‐Affinity Binding to TGT

A novel ligand series is presented to inhibit tRNA-guanine transglycosylase (TGT), a protein with a significant role in the pathogenicity mechanism of Shigella flexneri, the causative agent of Shigellosis. The enzyme exchanges guanine in the wobble position of tRNA(Asn,Asp,His,Tyr) against a modified base. To prevent the base-exchange reaction, several series of inhibitors have already been designed, synthesized, and tested. One aim of previous studies was to address a hydrophobic pocket with different side chains attached to the parent skeletons. Disappointingly, no significant increase in binding affinity could be observed that could be explained by the disruption of a conserved water cluster. The ligand series examined in this study are based on the known scaffold lin-benzoguanine. Different side chains were introduced leading to 2-amino-lin-benzoguanines, which address a different pocket of the protein and avoid disruption of the water cluster. With the introduction of an amino group in the 2-position, a dramatic increase in binding affinity can be experienced. To explain this significant gain in binding affinity, Poisson-Boltzmann calculations were performed to explore pK(a) changes of ligand functional groups upon protein binding, they can differ significantly on going from aqueous solution to protein environment. For all complexes, a permanent protonation of the newly designed ligands is suggested, leading to a charge-assisted hydrogen bond in the protein-ligand complex. This increased strength in hydrogen bonding takes beneficial effect on binding affinity of the ligands, resulting in low-nanomolar binders. Crystal structures and docking emphasize the importance of the newly created charge-assisted hydrogen bond. A detailed analysis of the crystal structures in complex with substituted 2-amino-lin-benzoguanines indicate pronounced disorder of the attached side chains addressing the ribose 33 binding pocket. Docking suggests multiple orientations of these side chains. Obviously, an entropic advantage of the residual mobility experienced by these ligands in the bound state is beneficial and reveals an overall improved protein binding.

Kinetics of an Acid‐Base Catalyzed Reaction (Aspartame Degradation) as Affected by Polyol‐Induced Changes in Buffer pH and pKa Values

The kinetics of an acid-base catalyzed reaction, aspartame degradation, were examined as affected by the changes in pH and pK(a) values caused by adding polyols (sucrose, glycerol) to phosphate buffer. Sucrose-containing phosphate buffer solutions had a lower pH than that of phosphate buffer alone, which contributed, in part, to reduced aspartame reactivity. A kinetic model was introduced for aspartame degradation that encompassed pH and buffer salt concentrations, both of which change with a shift in the apparent pK(a) value. Aspartame degradation rate constants in sucrose-containing solutions were successfully predicted using this model when corrections (that is, lower pH, lower apparent pK(a) value, buffer dilution from the polyol) were applied. The change in buffer properties (pH, pK(a)) from adding sucrose to phosphate buffer does impact food chemical stability. These effects can be successfully incorporated into predictive kinetic models. Therefore, pH and pK(a) changes from adding polyols to buffer should be considered during food product development.

A Long-Lived M-Like State of Phoborhodopsin that Mimics the Active State

Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II) is a seven transmembrane helical retinal protein. ppR forms a signaling complex with pharaonis Halobacterial transducer II (pHtrII) in the membrane that transmits a light signal to the sensory system in the cytoplasm. The M-state during the photocycle of ppR ( λ max = 386 nm) is one of the active (signaling) intermediates. However, progress in characterizing the M-state at physiological temperature has been slow because its lifetime is very short (decay half-time is ∼1 s). In this study, we identify a highly stable photoproduct that can be trapped at room temperature in buffer solution containing n-octyl- β- d-glucoside, with a decay half-time and an absorption maximum of ∼2 h and 386 nm, respectively. HPLC analysis revealed that this stable photoproduct contains 13- cis-retinal as a chromophore. Previously, we reported that water-soluble hydroxylamine reacts selectively with the M-state, and we found that this stable photoproduct also reacts selectively with that reagent. These results suggest that the physical properties of the stable photoproduct (named the M-like state) are very similar with the M-state during the photocycle. By utilizing the high stability of the M-like state, we analyzed interactions of the M-like state and directly estimated the pK a value of the Schiff base in the M-like state. These results suggest that the dissociation constant of the ppR M-like/pHtrII complex greatly increases (to 5 μM) as the pK a value greatly decreases (from 12 to 1.5). The proton transfer reaction of ppR from the cytoplasmic to the extracellular side is proposed to be caused by this change in pK a.