Time resolved data unveils the complex DOM dynamics in a Mediterranean river.

In this study, dissolved organic carbon (DOC) data and optical properties (absorbance and fluorescence) of DOM, weekly collected in the Arno River for 2 years, are used to investigate the main processes determining DOM temporal dynamics in a small Mediterranean river, with torrential hydrology and medium-high human impact, and to quantify the contribution of this river to Med Sea carbon budget. A clear seasonal cycle of DOM, with DOC values ranging between 170 and 490 µM, was observed. Optical properties indicates that DOM quality in the river is different depending on the season; terrestrial humic-like substances prevail in winter, when discharge and floods are the main drivers of DOM concentration and quality, whereas autochthonous protein-like substances prevail in spring and summer, when biological processes dominate. Our results provide a robust estimate of the DOC flux to the Med Sea (9.6 · 109 g DOC yr-1) and of its range of variability (12.95 · 109-5.12 · 109 g DOC yr-1). The 80% of this flux was generally delivered during autumn/winter with significant amounts ascribed to single flood events (up to 26% in 2014). This study, by providing a rich dataset on water quantity and quality and by quantifying the importance of the hydrological regime on DOC transport, represents an important step toward a quantitative modeling of the Arno River.

Chromophoric dissolved organic matter and microbial enzymatic activity. A biophysical approach to understand the marine carbon cycle.

This study reports the first information on extracellular enzymatic activity (EEA) combined with a study of DOM dynamics at the Arno River mouth. DOM dynamics was investigated from both a quantitative (dissolved organic carbon, DOC) and a qualitative (absorption and fluorescence of chromophoric DOM, CDOM) perspective. The data here reported highlight that the Arno River was an important source of both DOC and CDOM for this coastal area. CDOM optical properties suggested that terrestrial DOM did not undergo simple dilution at the river mouth but, other physical-chemical and biological processes were probably at work to change its molecular characteristics. This observation was further supported by the "potential" enzymatic activity of ß-glucosidase (BG) and leucine aminopeptidase (LAP). Their Vmax values were markedly higher in the river water than in the seawater and their ratio suggested that most of the DOM used by microbes in the Arno River was polysaccharide-like, while in the seawater it was mainly protein-like.

Influence of denaturants on native-state structural fluctuations in azurin probed by molecular size-dependent quenching of Trp phosphorescence.

Using azurin as a model protein, this study enquires on the nature of small and large amplitude structural fluctuations permitting the penetration of different size solutes within protein folds, as inferred from quenching of the phosphorescence of buried Trp residues. The work examines the effect that guanidinium hydrochloride and urea have on the migration of a range of quencher molecules of increasing molecular size (M(w) range = 32-206 Da). Using the quenching rate constant of Trp phosphorescence as a monitor, the results demonstrate that structural fluctuations linked to O(2) migration are not affected by denaturants, whereas larger amplitude structural fluctuations necessary to facilitate penetration of bulkier quencher molecules [acrylonitrile, acrylamide, N-(hydroxymethyl) acrylamide, N-[tris(hydroxymethyl) methyl]acrylamide, and 2-acrylamido-2-methyl-1-propanesulfonic acid] are clearly enhanced by the presence of denaturant. These data when interpreted in the context of the amount of new protein surface uncovered to solvent (ΔSASA(o)) by the underlying structural fluctuations show a direct correlation between the amplitude of these motions and ΔSASA(o). Denaturants also promote slow frequency (20-80 s(-1)) conformational transitions, not manifested in normal aqueous solutions, which provide extra migration pathways for acrylamide and its larger derivatives. The quencher-size dependence of the quenching rate provides evidence of multiple, independent quencher migration pathways to the azurin core, which are characterized by motions on different time scales, microseconds and milliseconds, and by a 3- to 5-fold difference in ΔSASA(o), respectively.

Amplitude spectrum of structural fluctuations in proteins from the internal diffusion of solutes of increasing molecular size: a Trp phosphorescence quenching study.

The accessibility of O(2), acrylamide, and four acrylamide derivatives of increasing molecular size {N-(hydroxymethyl)acrylamide, N,N'-methylene-bisacrylamide, N-[tris(hydroxymethyl)methyl]acrylamide, and 2-acrylamido-2-methyl-1-propanesulfonic acid} to buried Trp residues in four proteins, as determined by dynamic quenching of their phosphorescence emission, was utilized for probing the amplitude range of structural fluctuations in these macromolecules. The quenching rate constant of each solute, k(q), was determined (at 25 and -5 °C) for liver alcohol dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, azurin, and alkaline phosphatase. The results show that high-frequency small amplitude motions pervade the protein globular fold, permitting relatively unhindered diffusion of small diatomic molecules all the way to compact cores of the macromolecule. For larger solutes, the access to deep regions drops sharply with molecular size, with acrylamide probably representing a threshold for diffusion of a solute through homogeneous compact domains, on the long second time scale. The results emphasize the variability in the amplitude of protein motions between deep cores and more superficial regions of the globular fold and unveil the existence of unexpectedly large amplitude low-activation barrier fluctuations permitting the penetration of solutes with comparatively large M(w) values.

Acrylonitrile quenching of trp phosphorescence in proteins: a probe of the internal flexibility of the globular fold.

Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O(2) and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) =k(0) exp[-(r -r(0))/r(e)], with an attenuation length r(e) = 0.03 nm and a contact rate k(0) = 3.6 x 10(10) s(-1). At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 x 10(9) M(-1)s(-1) for free Trp in water, in proteins kq ranged from 6.5 x 10(6) M(-1)s(-1) for superficial sites to 1.3 x 10(2) M(-1)s(-1) for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.

Protein phosphorescence quenching: distinction between quencher penetration and external quenching mechanisms.

The accessibility of quenching solutes, Q, of various molecular sizes to buried Trp residues in proteins, as attested by dynamic quenching of their phosphorescence emission, is instrumental for probing structural fluctuations in these macromolecules. However, interpretation of quenching rates in terms of Q migration through the globular fold requires that alternative reaction pathways, such as long-range interactions with Q in the solvent, be ruled out. In theory, the external quenching rate can be estimated from the distance dependence of the through-space interaction by assuming compliance with the rapid diffusion limit regime. To validate the applicability of theoretical predictions to external quenching of protein phosphorescence, we compared the rate of quenching of the buried Trp residues of RNase T1 and parvalbumin by acrylamide and the bigger double-headed derivative bisacrylamide. The results showed that larger bisacrylamide is twice as efficient a quencher as acrylamide, implying that for these superficially buried residues the reaction is dominated by long-range interactions with acrylamide in the aqueous phase. To test the dependence of the quenching rate constant, k(q), on solvent viscosity, quenching studies were extended to glycerol-water solutions ranging in bulk viscosity from 1 to 120 cP. Apart from an initial about 2-fold increase, k(q) was found to be independent of solvent viscosity, thus demonstrating that external quenching rigorously complies with the rapid diffusion limit regime. Experiments were extended to larger acrylamide derivatives to evaluate the impact of Q size on the external quenching rate.

Fluorescence quenching of buried Trp residues by acrylamide does not require penetration of the protein fold.

The accessibility of acrylamide to buried Trp residues in proteins, as attested by dynamic quenching of their fluorescence emission, is often interpreted in terms of migration of the quencher (Q) through the globular fold. The quencher penetration mechanism, however, has long been debated because, on one hand, solutes the size of acrylamide are not expected to diffuse within the protein matrix on the nanosecond time scale of fluorescence and, on the other hand, alternative reactions pathways where Q remains in the solvent cannot be ruled out. To test the Q penetration hypothesis, we compared the quenching rates of acrylamide analogs of increasing molecular size (acrylonitrile, acrylamide, and bis-acrylamide) on the buried Trp residues of RNaseT1 and parvalbumin. The results show that the largest molecule, bis-acrylamide, is also the most efficient quencher and that in general the quenching rate is not correlated to quencher size, as expected for a penetration mechanism. Whereas these results rule out significant internal Q migration in the times of fluorescence, it is also demonstrated that up to a depth of burial of 3 A, through-space interactions with acrylamide in the solvent satisfactorily account for the small rate constants reported for these proteins. More generally, this analysis emphasizes that reduced dynamic quenching of protein fluorescence by acrylamide rather than reporting on the structural rigidity of the globular fold reflects the distance of closest approach between the internal chromophore and Q in the aqueous phase.

Structure and dynamics of cold-adapted enzymes as investigated by phosphorescence spectroscopy and molecular dynamics studies. 2. The case of an esterase from Pseudoalteromonas haloplanktis.

Enzymes from psychrophiles display high catalytic efficiency at low temperatures. As a consequence, there is a lot of academic and industrial interest in investigating the molecular strategies adopted from these enzymes to work in conditions where other enzymes are almost inactive. Recently, a novel esterase activity was identified and isolated from the cold-adapted organism Pseudoalteromonas haloplanktis. The enzyme, named PhEST, is a dimer with a molecular mass of 60 kDa composed of two identical subunits. PhEST possesses four tryptophan residues that are homogenously dispersed in the protein tertiary organization. In this work, we used phosphorescence spectroscopy and molecular dynamics experiments to investigate the structural properties of PhEST. The obtained model structure of PhEST indicates that the environments of tryptophan residues W14 and W50 are characterized by limited conformational freedom. On the contrary, the environments of the tryptophan residues W181 and W197 are relatively mobile owing to enhanced fluctuations of residues 93-99 and 192-195, respectively, flexible loops that join segments of the protein secondary structure. The high-resolution phosphorescence spectrum in low-temperature glasses distinguishes two classes of Trp environments in PhEST structure: one class that is typical of compact internal hydrophobic sites, and the other class that is characteristic of disordered and/or partly solvent exposed regions. The phosphorescence lifetime of PhEST registered in fluid solution is invariably short, indicating that some Trp residues are in rather flexible superficial sites of the globular fold, whereas internal chromophores are strongly quenched by the proximity to Cys residues. Acrylamide and O(2) quenching studies pointed out that the internal protein site is compact and rigid, typical of beta-barrel core structures. Every spectroscopic feature described in this work is well accounted for by the proposed model structure of PhEST.

Acrylamide quenching of Trp phosphorescence in liver alcohol dehydrogenase: evidence of gated quencher penetration.

Notwithstanding the relevance of their biological function, slow motions in proteins, beyond the microsecond range, are still poorly understood and often elusive. We propose that acrylamide quenching of Trp phosphorescence of deeply buried residues, when extended over the entire accessible range of lifetime measurements (tau > 10 micros), may help to unveil low-frequency protein motions that allow penetration of solute into the protein interior. The work examines in some detail acrylamide quenching of Trp phosphorescence in a model protein (liver alcohol dehydrogenase) over an extended submillimolar to molar acrylamide concentration range. The results, which encompass a >10(4)-fold variation in the quenching rate, provide the first evidence of a downward-curving lifetime Stern-Volmer plot, indicative of a nonlinear dependence of the quenching rate on the quencher concentration. From an analysis of saturation effects in terms of a protein-gated acrylamide diffusion mechanism, we infer two main routes for acrylamide to penetrate the globular fold and come into the proximity of internal W314: a low-frequency gate [36 s(-1) (at 25 degrees C)] tentatively assigned to partial opening of the dimer interface and a higher-frequency one (11800 s(-1)) tentatively assigned to a channel blocked by the side chains of V276 and L307. These motions are sharply inhibited in the rigid protein complexes formed with the coenzyme NAD(+) and the coenzyme analogue adenine diphosphate ribose, as well as by the frictional drag of the solvent in viscous glycerol solutions, evidence that rules out an alternative quenching mechanism involving acrylamide binding to the protein.

No effect of covalently linked poly(ethylene glycol) chains on protein internal dynamics.

Poly(ethylene glycol) or PEG is a hydrophilic polymer that covalently linked to therapeutical proteins may significantly increase their pharmacological properties. Despite the extensive production of PEG-conjugated proteins the effects of the polymer on the protein structure and dynamics is poorly understood, making the production of active biomaterials a largely unpredictable process. The present investigation examines the effects of 5 k and 20 k PEG on the internal flexibility of Ribonuclease T1, the mutant C112S of azurin from Pseudomonas aeruginosa, alcohol dehydrogenase and alkaline phosphatase, native and Zn-depleted. These systems encompass structural domains that range from rather superficial, flexible sites to deeply buried, rigid cores. The approach is based on three sensitive parameters related to the phosphorescence emission of internal Trp residues, namely, the intrinsic room-temperature phosphorescence lifetime (tau(0)) that reports on the local flexibility of the protein matrix around the chromophore and the bimolecular rate constant (k(q)) for the quenching of phosphorescence by O(2) and by acrylamide in solution, which are related to the diffusion of these solutes through the protein fold. The results obtained by these three independent, intrinsic probes of protein structure-dynamics concur that mono-PEGylation does not detectably perturb the conformation and dynamics of the protein native fold, over a wide temperature range. The implication is that protein motions are essentially not coupled to the polymer and that adverse effects of chemical modification on biological function are presumably owed to steric hindrance by PEG units blocking the access to sites critical for molecular recognition.

Mutations in transhydrogenase change the fluorescence emission state of TRP72 from 1La to 1Lb.

The dI component of Rhodospirillum rubrum transhydrogenase has a single Trp residue (Trp(72)), which has distinctive optical properties, including short-wavelength fluorescence emission with clear vibrational fine structure, and long-lived, well-resolved phosphorescence emission. We have made a set of mutant dI proteins in which residues contacting Trp(72) are conservatively substituted. The room-temperature fluorescence-emission spectra of our three Met(97) mutants are blue shifted by approximately 4 nm, giving them a shorter-wavelength emission than any other protein described in the literature, including azurin from Pseudomonas aeruginosa. Fluorescence spectra in low-temperature glasses show equivalent well-resolved vibrational bands in wild-type and the mutant dI proteins, and in azurin. Substitution of Met(97) in dI changes the relative intensities of some of these vibrational bands. The analysis supports the view that fluorescence from the Met(97) mutants arises predominantly from the (1)L(b) excited singlet state of Trp(72), whereas (1)L(a) is the predominant emitting state in wild-type dI. It is suggested that the sulfur atom of Met(97) promotes greater stabilization of (1)L(a) than either (1)L(b) or the ground state. The phosphorescence spectra of Met(97) mutants are also blue-shifted, indicating that the sulfur atom decreases the transition energy between the (3)L(a) state of the Trp and the ground state.

Specific anions effects of on the stability of azurin in ice.

This investigation represents a first attempt to gain a quantitative estimate of the effects of the anions sulfate, citrate, acetate, chloride and thiocyanate on the thermodynamic stability (DeltaG degrees) of a model globular protein in ice at -15 degrees C. The method, based on guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, distinguishes between the effects of cooling to subfreezing temperatures from those induced specifically by the formation of a solid ice phase. The results confirm that, both in liquid and frozen states, kosmotropes (sulfate, citrate and acetate) increase significantly protein stability, relative to chloride, whereas the chaotrope thiocyanate decreases it. Throughout, their stabilizing efficacy was found to rank according to the Hofmeister series, sulfate>citrate>acetate>chloride>thiocyanate, although the magnitude of Delta(DeltaG degrees) exhibited a distinct sensitivity among the anions to low temperature and to ice formation. In the liquid state, lowering the temperature from +20 to -15 degreesC weakens considerably the stabilizing efficacy of the organic anions citrate and acetate. Among the anions sulfate stands out as the only strong stabilizer at subfreezing temperatures while SCN- becomes an even stronger denaturant. Freezing of the solution in the presence the "neutral" salt NaCl destabilizes the protein, DeltaG degrees progressively decreasing up to 3-4 kcal/mol as the fraction of liquid water in equilibrium with ice (VL) is reduced to less than 1%. Kosmotropes do attenuate the decrease in protein stability in ice although in the case of citrate and acetate, their efficacy diminishes sharply as the liquid fraction shrinks to below 2.7%. On the contrary, sulfate is remarkable for it maintains constantly high the stability of azurin in liquid and frozen solutions, down to the smallest VL (0.5%) examined. Throughout, the reduction in DeltaG degrees caused by the solidification of water correlates with the decrease in the denaturant m value, an indirect indication that protein-ice interactions generally lead to partial unfolding of the native state. It is proposed that binding of the kosmotropes to the ice interface may inhibit protein adsorption to the solid phase and thereby counter the ice perturbation.

Effects of sugars and polyols on the stability of azurin in ice.

This study represents the first attempt to gain a quantitative estimate of the protective influence of sugars (sucrose and trehalose) and polyols (sorbitol and glycerol) on the thermodynamic stability (DeltaG degrees ) of a protein in low-temperature part-frozen aqueous solutions. The method, based on guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, distinguishes between the effects of cooling to subfreezing temperatures from those induced specifically by the formation of a solid ice phase. The results point out that in the liquid state the generally stabilizing effect (at molar concentrations) of these polyhydric compounds is markedly attenuated on cooling to subfreezing temperatures such that at -15 degrees C, only sucrose still exerts a significant increase in DeltaG degrees . At this temperature, and in the absence of additives, the formation of ice caused a progressive destabilization of the native fold, DeltaG degrees decreasing up to 3-4 kcal/mol as the fraction of liquid water in equilibrium with ice (V(L) was reduced to less than 1%. Unexpectedly, denaturation profiles in ice at selected V(L) demonstrate that none of the above sugars and polyols counters effectively the decrease in protein stability at small V(L). Only trehalose was able to partly attenuate the ice perturbation, raising DeltaG degrees by a modest 0.6-0.8 kcal/mol relative to the salt reference. In all cases the reduction in DeltaG degrees caused by the solidification of water correlates with the decrease in m-value. The implication is that DeltaASA of unfolding is smaller in ice because protein-ice interactions either increase the solvent-accessible surface area (ASA) of the native fold (partial unfolding) or reduce the ASA of the denatured state (compaction), or both. Information on the protein tertiary structure in ice, in the absence and in the presence of sucrose or glycerol, suggests that these osmolytes play an important role in maintaining a compact native state that in their absence is expanded and partly unfolded. Thus, it appears that the prevailing mechanism by which these osmolytes act as cryoprotectants is through preservation of the native conformation in the liquidus rather than by increasing the thermodynamic stability of the native fold.

Singular efficacy of trimethylamine N-oxide to counter protein destabilization in ice.

This study reports the first quantitative estimate of the thermodynamic stability (Delta G degrees ) of a protein in low-temperature partly frozen aqueous solutions in the presence of the protective osmolytes trimethylamine N-oxide (TMAO), glycine betaine, and sarcosine. The method, based on guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, distinguishes between the deleterious effects of subfreezing temperatures from those due specifically to the formation of a solid ice phase. The results point out that in the liquid state molar concentrations of these osmolytes stabilize significantly the native fold and that their effect is maintained on cooling to -15 degrees C. At this temperature, freezing of the solution in the absence of any additive causes a progressive destabilization of the protein, Delta G degrees decreasing up to 3-4 kcal/mol as the fraction of liquid water in equilibrium with ice ( V L) is reduced to less than 1%. The ability of the three osmolytes to prevent the decrease in protein stability at small V L varies significantly among them, ranging from the complete inertness of sarcosine to full protection by TMAO. The singular effectiveness of TMAO among the osmolytes tested until now is maintained high even at concentrations as low as 0.1 M when the additive stabilization of the protein in the liquid state is negligible. In all cases the reduction in Delta G degrees caused by the solidification of water correlates with the decrease in m-value entailing that protein-ice interactions generally conduct to partial unfolding of the native state. It is proposed that the remarkable effectiveness of TMAO to counter the ice perturbation is owed to binding of the osmolyte to ice, thereby inhibiting protein adsorption to the solid phase.

The tryptophan phosphorescence of porcine and mutant bovine odorant-binding proteins: a probe for the local protein structure and dynamics.

Vertebrate odorant-binding proteins (OBPs) are small extracellular proteins belonging to the lipocalin superfamily. They have been supposed to play a role in events of odorant molecules detection by carrying, deactivating, and/or selecting odorant molecules. The OBPs share a conserved folding pattern, an eight-stranded beta-barrel flanked by an alpha-helix at the C-terminal end of the polypeptide chain. The beta-barrel creates a central nonpolar cavity whose role is to bind and transport hydrophobic odorant molecules. These proteins reversibly bind odorant molecules with dissociation constants ranging from nanomolar to micromolar range. In this work, we have studied the structural features of the OBP from pig and from cow by phosphorescence spectroscopy. The obtained results demonstrate that the indolic phosphorescence of the two studied proteins can be readily detected at ambient temperature solutions and that it is owed exclusively to the internal tryptophan residue located next to the ligand binding cavity, which is generally conserved in the mammalian OBPs. In addition, while both the phosphorescence spectrum and the lifetime yield a picture of the fold of the studied protein in good agreement with the protein crystallographic structures, the triplet probe points out that in solution the polypeptide structure of the both investigated OBPs exists as a multiplicity of slowly interconverting protein conformations. Finally, this work also demonstrates that it is possible to directly detect the binding of the ligands to OBPs as variations of the protein luminescence features, thus, representing the very first observation reported in the literature so far that a fast and direct assay can be used for monitoring the binding of ligands to OBPs.

The differences in the microenvironment of the two tryptophan residues of the glutamine-binding protein from Escherichia coli shed light on the binding properties and the structural dynamics of the protein.

Glutamine-binding protein (GlnBP) from Escherichia coli is a monomer (26 kDa) that is responsible for the first step in the active transport of L-glutamine across the cytoplasmic membrane. GlnBP consists of two domains (termed large and small) linked by two antiparallel beta-strands. The large domain is similar to the small domain but it contains two additional alpha-helices and three more short antiparallel beta-strands. The deep cleft formed between the two domains contains the ligand-binding site. The binding of L-glutamine leads to cleft closing and a significant structural change with the formation of the so-called "closed form" structure. The protein contains two tryptophan residues (W32 and W220) and 10 tyrosine residues. We used phosphorescence spectroscopy measurements to characterize the role of the two tryptophan residues in the protein structure in the absence and the presence of glutamine. Our results pointed out that the phosphorescence of GlnBP is easily detected in fluid solutions where the emission of the two tryptophan residues is readily discriminated by the drastic difference in the phosphorescence lifetime allowing the assignments of the short lifetime to W220 and the long lifetime to W32. In addition, our results showed that the triplet lifetime of the superficial W220 is unusually short because of intramolecular quenching by the proximal Y163. On the contrary, the lifetime of W32 is several hundred milliseconds long, implicating a well-ordered, compact fold of the surrounding polypeptide. The spectroscopic data were analyzed and discussed together with a detailed inspection of the 3D structure of GlnBP.

Tryptophan phosphorescence studies of the D-galactose/D-glucose-binding protein from Escherichia coli provide a molecular portrait with structural and dynamics features of the protein.

The D-galactose/D-glucose-binding protein (GGBP) from E. coli serves as an initial component for both chemotaxis toward glucose and high-affinity active transport of the sugar. In this work, we have used phosphorescence spectroscopy to investigate the effects of glucose and calcium on the dynamics and stability of GGBP. We found that GGBP exhibits a phosphorescence spectrum composed of two energetically distinct 0,0-vibrational bands centered at 404.43 and 409.61 nm; the large energy separation between them indicates two classes of chromophores making distinct dipolar interactions with their surrounding. Interestingly, the high-energy spectral component (404.43 nm) is one of the bluest spectra reported to date in proteins. Considering the ground state dipole direction, low-energy configurations for the indole side chain in proteins leading to blue-shifted spectra can arise from negative charges in proximity to the imidazole-ring nitrogen and/or positive charges near C4-C5 of the benzene ring. Among the five tryptophan residues of GGBP, Trp-284, located at the N-terminal domain of the protein, and Trp-183, located in the protein hinge region, make strong attractive charge interactions with surrounding side chains. Regarding Trp-284, the indole ring nitrogen is in contact with the negative charge of the Asp-267, whereas Trp-183 is next to the Glu-149 residue. In the latter, the ground state energy is further lowered by the proximity of the Arg-158 to the negative end (near C6) of the indole dipole. Regarding the red spectral component (409.61 nm), it is more intense than the blue component, presumably because more residues contribute to it. lambda 0,0 is typical of environments that are weakly polar or characterized by charges positioned near 90 degrees from the ground state dipole direction (the case of W195 and W127). The binding of glucose modifies the phosphorescence lifetime values as well as the spectrum of GGBP, shifting the blue band 0.54 nm to the blue and the red band 1 nm to the red. Finally, the removal of the calcium from GGBP structure causes variations in lifetime values and spectral shifts similar to those induced by glucose binding to the native protein. Aided by a detailed inspection of the three-dimensional structure of GGBP, these results contribute to a better understanding of the structure/function relationship of this protein.

Protein stability in ice.

This study presents an experimental approach, based on the change of Trp fluorescence between native and denatured states of proteins, which permits to monitor unfolding equilibria and the thermodynamic stability (DeltaG degrees ) of these macromolecules in frozen aqueous solutions. The results obtained by guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, in the temperature range from -8 to -16 degrees C, demonstrate that the stability of the native fold may be significantly perturbed in ice depending mainly on the size of the liquid water pool (V(L)) in equilibrium with the solid phase. The data establish a threshold, around V(L)=1.5%, below which in ice DeltaG degrees decreases progressively relative to liquid state, up to 3 kcal/mole for V(L)=0.285%. The sharp dependence of DeltaG degrees on V(L) is consistent with a mechanism based on adsorption of the protein to the ice surface. The reduction in DeltaG degrees is accompanied by a corresponding decrease in m-value indicating that protein-ice interactions increase the solvent accessible surface area of the native fold or reduce that of the denatured state, or both. The method opens the possibility for examining in a more quantitative fashion the influence of various experimental conditions on the ice perturbation and in particular to test the effectiveness of numerous additives used in formulations to preserve labile pharmaco proteins.

Intramolecular quenching of tryptophan phosphorescence in short peptides and proteins.

The phosphorescence lifetime (tau) of tryptophan (Trp) residues in proteins in aqueous solutions at ambient temperature can vary several orders of magnitude depending on the flexibility of the local structure and the rate of intramolecular quenching reactions. For a more quantitative interpretation of tau in terms of the local protein structure, knowledge of all potential quenching moieties in proteins and of their reaction rates is required. The quenching effectiveness of each amino acid (X) side chain and of the peptide backbone was investigated by monitoring their intramolecular quenching rate (k(obs)) in tripeptides of the form acetyl-Trp-Gly-X-CONH2 (WGX), where Trp is joined to X by a flexible Gly link. The results indicate that among the various groups present in proteins only the side chains of Cys, His, Tyr and Phe are able to quench Trp phosphorescence at a detectable rate (k(obs) > 40 s(-1)), with the quenching effectiveness for rotationally unrestricted side chains ranking in the order Cys >> His+ > Tyr >> Phe approximately His. For the aromatic side chains the corresponding contact rate at 20 degrees C is estimated to be between 3-4 x 10(9) s(-1) for Cys (as determined by Lapidus et al.), 0.8-8 x 10(6) s(-1) for His+, 0.37-3.7 x 10(6) s(-1) for Tyr and 0.2-2 x 10(5) s(-1) for Phe and His. In the cases of His and Tyr, k(obs) drops sharply with increasing pH, with midpoint transitions about 1 pH unit above the pKa, indicating that quenching is almost exclusive to the protonated form. From the temperature dependence of the rate, obtained in 50/50 propylene glycol/water between -20 degrees C and 20 degrees C, the reaction is characterized by activation energies of about 5 kcal.M(-1) for His+ and Tyr and 8 kcal.M(-1) for Phe. An analysis of the groups in contact with Trp residues in proteins that exhibit long phosphorescence lifetimes at ambient temperature leads to the conclusion that the contact rate of the peptide group and of the remaining side chains is lower than 0.1 s(-1), showing that these moieties are practically inert with respect to the triplet-state lifetime. It shows further that the immobilization of the aromatic side chains within the globular fold cuts their quenching effectiveness drastically to contact rates < 2 s(-1), a phenomenon attributed to the low probability of forming a stacked exciplex with the indole ring. All evidence suggests that, except in the case of nearby Cys or Trp residues, whose interaction with the triplet state reaches beyond van der Waals contact, the emission of buried Trp residues is unlikely to be quenched by surrounding protein groups.

The triplet-state lifetime of indole derivatives in aqueous solution.

An important feature of tryptophan phosphorescence, crucial for probing protein structure and dynamics, is the drastic reduction of the lifetime (tau) in fluid solutions. Initial reports of indole and derivatives showed that tau decreases from 6 s in rigid glasses to about 1 ms in aqueous solutions at ambient temperature. Recently a report by Fischer et al. questioned the validity of the millisecond lifetime, claiming that in millimolar electrolyte solutions tau is about 40 micros, similar to the 12-30 micros of earlier determinations based on flash photolysis. Longer lived phosphorescence was detected in pure water but because it exhibited an initial growing phase and an anomalously large triplet yield, the emission was attributed to an artifact arising from the slow, first-order, geminate recombination of the radical cation and electron generated by photochemistry. In this study, we reexamine both the phosphorescence lifetime and the triplet quantum yield of indole, N-acetyl tryptophanamide (NATA), N-methyl tryptophan and the tryptophan-glycine-glycine tripeptide under the same conditions adopted by Fischer et al. as well as over a wider range of electrolyte and buffering salts concentrations, pH, solvent and temperature. Throughout, the results show that the phosphorescence decay is slow and uniform down to the 12 micros resolution of the instrument, with no evidence of short-lived, 40 micros-like components. Most compelling was the similarity between the fluorescence-normalized triplet yield of indole derivatives in water and that of W59 in the protein ribonuclease T1 or of NATA in rigid glasses. Its invariance over experimental conditions that varied the production of photoproducts several fold and the characteristic susceptibility of the triplet lifetime to O2, proton and ground state quenching demonstrated that the triplet state was formed predominantly through normal intersystem crossing and that its unquenched lifetime was at least 9 ms.