Flexibility and enzyme activity of NADH oxidase from Thermus thermophilus in the presence of monovalent cations of Hofmeister series

Specific anion effect on properties of HRV 3C protease

Specific salts effect is intensively studied from the prospective of modification of different physico-chemical properties of biomacromolecules. Limited knowledge of the specific salts effect on enzymes led us to address the influence of five sodium anions: sulfate, phosphate, chloride, bromide, and perchlorate, on catalytic and conformational properties of human rhinovirus-14 (HRV) 3C protease. The enzyme conformation was monitored by circular dichroism spectrum (CD) and by tyrosines fluorescence. Stability and flexibility of the enzyme have been analyzed by CD in the far-UV region, differential scanning calorimetry and molecular dynamics simulations, respectively. We showed significant influence of the anions on the enzyme properties in accordance with the Hofmeister effect. The HRV 3C protease in the presence of kosmotropic anions, in contrast with chaotropic anions, exhibits increased stability, rigidity. Correlations of stabilization effect of anions on the enzyme with their charge density and the rate constant of the enzyme with the viscosity B-coefficients of anions suggest direct interaction of the anions with HRV 3C protease. The role of stabilization and decreased fluctuation of the polypeptide chain of HRV 3C protease on its activation in the presence of kosmotropic anions is discussed within the frame of the macromolecular rate theory.

Perchlorate salts confer psychrophilic characteristics in α-chymotrypsin

Studies of salt effects on enzyme activity have typically been conducted at standard temperatures and pressures, thus missing effects which only become apparent under non-standard conditions. Here we show that perchlorate salts, which are found pervasively on Mars, increase the activity of α-chymotrypsin at low temperatures. The low temperature activation is facilitated by a reduced enthalpy of activation owing to the destabilising effects of perchlorate salts. By destabilising α-chymotrypsin, the perchlorate salts also cause an increasingly negative entropy of activation, which drives the reduction of enzyme activity at higher temperatures. We have also shown that α-chymotrypsin activity appears to exhibit an altered pressure response at low temperatures while also maintaining stability at high pressures and sub-zero temperatures. As the effects of perchlorate salts on the thermodynamics of α-chymotrypsin's activity closely resemble those of psychrophilic adaptations, it suggests that the presence of chaotropic molecules may be beneficial to life operating in low temperature environments.

Specific Buffer Effects on the Intermolecular Interactions among Protein Molecules at Physiological pH

BSA and lysozyme molecular motion at pH 7.15 is buffer-specific. Adsorption of buffer ions on protein surfaces modulates the protein surface charge and thus protein-protein interactions. Interactions were estimated by means of the interaction parameter k_D obtained from plots of diffusion coefficients at different protein concentrations (D_app = D₀[1 + k_DC_protein]) via dynamic light scattering and nuclear magnetic resonance. The obtained results agree with recent findings confirming doubts regarding the validity of the Henderson-Hasselbalch equation, which has traditionally provided a basis for understanding pH buffers of primary importance in solution chemistry, electrochemistry, and biochemistry.

Specific ion effects on the enzymatic activity of alcohol dehydrogenase fromSaccharomyces cerevisiae

The specific activity andV_max, but notK_m, of alcohol dehydrogenase fromSaccharomyces cerevisiaeare ion specific.

Functional Characterization and Structural Analysis of NADH Oxidase Mutants from Thermus thermophilus HB27: Role of Residues 166, 174, and 194 in the Catalytic Properties and Thermostability

The Thermus thermophilus strain HB27 NADH-oxidase (Tt27-NOX) catalyzes the oxidation of nicotinamide adenine dinucleotide (NAD(P)H) by reducing molecular oxygen to hydrogen peroxide in a two-electron transfer mechanism. Surprisingly, Tt27-NOX showed significant differences in catalytic properties compared to its counterpart from the strain HB8 (Tt8-NOX), despite a high degree of sequence homology between both variants. The sequence comparison between both enzymes revealed only three divergent amino acid residues at positions 166, 174, and 194. Motivated with these findings, in this work we performed mutagenesis experiments in the former three positions to study the specific role of these residues in the catalytic properties and thermostability of Tt27-NOX. We subjected five mutants, along with the wild-type enzyme, to biochemical characterization and thermal stability studies. As a result, we identified two more active and more thermostable variants than any Tt8-NOX variant reported in the literature. The most active and thermostable variant K166/H174/Y194 retained 90% of its initial activity after 5 h at pH 7 and 80 °C and an increase in melting temperature of 48.3 °C compared with the least active variant K166/R174/Y194 (inactivated after 15 min of incubation). These results, supported by structural analysis and molecular dynamics simulation studies, suggest that Lys at position 166 may stabilize the loop in which His174 is located, increasing thermal stability.

Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings-such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.

Refolding of horseradish peroxidase is enhanced in presence of metal cofactors and ionic liquids

The effects of various refolding additives, including metal cofactors, organic co-solvents, and ionic liquids, on the refolding of horseradish peroxidase (HRP), a well-known hemoprotein containing four disulfide bonds and two different types of metal centers, a ferrous ion-containing heme group and two calcium atoms, which provide a stabilizing effect on protein structure and function, were investigated. Both metal cofactors (Ca(2+) and hemin) and ionic liquids have positive impact on the refolding of HRP. For instance, the HRP refolding yield remarkably increased by over 3-fold upon addition of hemin and calcium chloride to the refolding buffer as compared to that in the conventional urea-containing refolding buffer. Moreover, the addition of ionic liquids [EMIM][Cl] to the hemin and calcium cofactor-containing refolding buffer further enhanced the HRP refolding yield up to 80% as compared to 12% in conventional refolding buffer at relatively high initial protein concentration (5 mg/ml). These results indicated that refolding method utilizing metal cofactors and ionic liquids could enhance the yield and efficiency for metalloprotein.

A coacervate-forming biodegradable polyester with elevated LCST based on bis-(2-methoxyethyl)amine

This work details a thermoresponsive, biodegradable coacervate-forming polyester, which exhibits tunable T_cp under various conditions.

A water-forming NADH oxidase from Lactobacillus pentosus suitable for the regeneration of synthetic biomimetic cofactors

The cell-free biocatalytic production of fine chemicals by oxidoreductases has continuously grown over the past years. Since especially dehydrogenases depend on the stoichiometric use of nicotinamide pyridine cofactors, an integrated efficient recycling system is crucial to allow process operation under economic conditions. Lately, the variety of cofactors for biocatalysis was broadened by the utilization of totally synthetic and cheap biomimetics. Though, to date the regeneration has been limited to chemical or electrochemical methods. Here, we report an enzymatic recycling by the flavoprotein NADH-oxidase from Lactobacillus pentosus (LpNox). Since this enzyme has not been described before, we first characterized it in regard to its optimal reaction parameters. We found that the heterologously overexpressed enzyme only contained 13% FAD. In vitro loading of the enzyme with FAD, resulted in a higher specific activity towards its natural cofactor NADH as well as different nicotinamide derived biomimetics. Apart from the enzymatic recycling, which gives water as a by-product by transferring four electrons onto oxygen, unbound FAD can also catalyze the oxidation of biomimetic cofactors. Here a two electron process takes place yielding H2O2 instead. The enzymatic and chemical recycling was compared in regard to reaction kinetics for the natural and biomimetic cofactors. With LpNox and FAD, two recycling strategies for biomimetic cofactors are described with either water or hydrogen peroxide as by-product.

Internal dynamics of F-actin and myosin subfragment-1 studied by quasielastic neutron scattering

Various biological functions related to cell motility are driven by the interaction between the partner proteins, actin and myosin. To obtain insights into how this interaction occurs, the internal dynamics of F-actin and myosin subfragment-1 (S1) were characterized by the quasielastic neutron scattering measurements on the solution samples of F-actin and S1. Contributions of the internal motions of the proteins to the scattering spectra were separated from those of the global macromolecular diffusion. Analysis of the spectra arising from the internal dynamics showed that the correlation times of the atomic motions were about two times shorter for F-actin than for S1, suggesting that F-actin fluctuates more rapidly than S1. It was also shown that the fraction of the immobile atoms is larger for S1 than for F-actin. These results suggest that F-actin actively facilitates the binding of myosin by utilizing the more frequent conformational fluctuations than those of S1.

Models and mechanisms of Hofmeister effects in electrolyte solutions, and colloid and protein systems revisited

Specific effects of electrolytes have posed a challenge since the 1880's. The pioneering work was that of Franz Hofmeister who studied specific salt induced protein precipitation. These effects are the rule rather the exception and are ubiquitous in chemistry and biology. Conventional electrostatic theories (Debye-Hückel, DLVO, etc.) cannot explain such effects. Over the past decades it has been recognised that additional quantum mechanical dispersion forces with associated hydration effects acting on ions are missing from theory. In parallel Collins has proposed a phenomenological set of rules (the law of matching water affinities, LMWA) which explain and bring to order the order of ion-ion and ion-surface site interactions at a qualitative level. The two approaches appear to conflict. Although the need for inclusion of quantum dispersion forces in one form or another is not questioned, the modelling has often been misleading and inappropriate. It does not properly describe the chemical nature (kosmotropic/chaotropic or hard/soft) of the interacting species. The success of the LMWA rules lies in the fact that they do. Here we point to the way that the two apparently opposing approaches might be reconciled. Notwithstanding, there are more challenges, which deal with the effect of dissolved gas and its connection to 'hydrophobic' interactions, the problem of water at different temperatures and 'water structure' in the presence of solutes. They take us to another dimension that requires the rebuilding of theoretical foundations.

Specific cation effects on hemoglobin aggregation below and at physiological salt concentration

Turbidity titrations are used to study the ion specific aggregation of hemoglobin (Hb) below and physiological salt concentration in the pH range 4.5-9.5. At a salt concentration 50 mM cations promote Hb aggregation according to the order Rb(+) > K(+) ~ Na(+) > Cs(+) > Li(+). The cation series changes if concentration is increased, becoming K(+) > Rb(+) > Na(+) > Li(+) > Cs(+) at 150 mM. We interpret the puzzling series by assuming that the kosmotropic Li(+) will bind to kosmotropic carboxylates groups-according to the law of matching water affinities (LMWA)-whereas the chaotropic Cs(+) will bind to uncharged protein patches due to its high polarizability. In fact, both mechanisms can be rationalized by invoking previously neglected ionic nonelectrostatic forces. This explains both adsorption to uncharged patches and the LMWA as a consequence of the simultaneous action of electrostatic and dispersion forces. The same interpretation applies to anions (with chaotropic anions binding to chaotropic amine groups). The implications extend beyond hemoglobin to other, still unexplained, ion specific effects in biological systems.

Effect of three trifluoromethanesulfonate ionic liquids on the activity, stability and conformation of laccase

The activity, stability and conformation of laccase were first investigated in an aqueous solution of ionic liquids 1-butyl-3-methylimidazolium trifluoromethanesulfonate ([Bmim]TfO), 1-butyl-1-methylpyrrolidinium trifluoromethanesulfonate ([Bmpyr]TfO) or tetramethylammonium trifluoromethanesulfonate ([TMA]TfO). Compared with control system, high level of [Bmim]TfO or [Bmpyr]TfO destabilizes laccase while [TMA]TfO stabilizes laccase. These effects are more pronounced with the extension of the incubation time. The activity variations are well correlated with the changes of the conformation of laccase evidenced by fluorescence and circular dichroism spectra under specified conditions. The effects of the three ionic liquids on laccase are associated with the chaotropicity of the cations in Hofmeister series. For laccase, [TMA]TfO is not a good activating agent but it greatly enhances the stability of laccase in addition to maintaining the catalytic efficiency of laccase, showing its great potential in real application.

Hofmeister challenges: ion binding and charge of the BSA protein as explicit examples

Experiments on bovine serum albumin (BSA) via potentiometric titration (PT) and electrophoretic light scattering (ELS) are used to study specific-ion binding. The effect is appreciable at a physiological concentration of 0.1 M. We found that anions bind to the protein surface at an acidic pH, where the protein carries a positive charge (Z(p) > 0), according to a Hofmeister series (Cl(-) < Br(-) < NO(3)(-) < I(-) < SCN(-)), as well as at the isoionic point (Z(p) = 0). The results obtained require critical interpretation. The measurements performed depend on electrostatic theories that ignore the very specific effects they are supposed to reveal. Notwithstanding this difficulty, we can still infer that different 1:1 sodium salts affect the BSA surface charge/pH curve because anions bind to the BSA surface with an efficiency which follows a Hofmeister series.

A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8

Using molecular dynamics simulations and steady-state fluorescence spectroscopy, we have identified a conformational change in the active site of a thermophilic flavoenzyme, NADH oxidase from Thermus thermophilus HB8 (NOX). The enzyme's far-UV circular dichroism spectrum, intrinsic tryptophan fluorescence, and apparent molecular weight measured by dynamic light scattering varied little between 25 and 75°C. However, the fluorescence of the tightly bound FAD cofactor increased approximately fourfold over this temperature range. This effect appears not to be due to aggregation, unfolding, cofactor dissociation, or changes in quaternary structure. We therefore attribute the change in flavin fluorescence to a temperature-dependent conformational change involving the NOX active site. Molecular dynamics simulations and the effects of mutating aromatic residues near the flavin suggest that the change in fluorescence results from a decrease in quenching by electron transfer from tyrosine 137 to the flavin.

Hofmeister effects on activity and stability of alkaline phosphatase

We have studied the effects on alkaline phosphatase of adding high concentrations (normally 1.0 M) of simple salts. It is necessary to allow for significant effects of salts on the extinction coefficient of the reaction product, and on the apparent pH of the buffer. Both activity and stability of the enzyme correlate well with the Hofmeister series in terms of the salt's kosmotropic/chaotropic properties, which are assessed by the Jones-Dole viscosity B coefficients (B(+) for cations and B(-) for anions). The catalytic activity or V(max)/K(m) of the enzyme showed a bell-shaped relationship with the (B(-)-B(+)) values of the salts present, being optimal with salts (such as NaCl, KCl, and KNO(3)) where the anion and cation have similar kosmotropic/chaotropic properties. This effect is believed to be enzyme-specific and relates to the impact of both cations and anions on the enzyme's surface pH, active site, and catalytic mechanism. Anions play a more predominant role than cations in affecting enzyme stability. The rate of irreversible thermal inactivation is strongly reduced by addition of kosmotropic anions like SO(4)(2-) (half-life increased from 8 to 580 min at 60 degrees C). This effect is general and the mechanism probably involves the ability of the ions to affect the water solvation layer around the enzyme molecule and to interact with both the surface and internal structure of the enzyme.