Acrylamide Quenching of Trp Phosphorescence in Liver Alcohol Dehydrogenase: Evidence of Gated Quencher Penetration

Heat and cold denaturation of yeast frataxin: The effect of pressure

Yfh1 is a yeast protein with the peculiar characteristic to undergo, in the absence of salt, cold denaturation at temperatures above the water freezing point. This feature makes the protein particularly interesting for studies aiming at understanding the rules that determine protein fold stability. Here, we present the phase diagram of Yfh1 unfolding as a function of pressure (0.1-500 MPa) and temperature 278-313 K (5-40°C) both in the absence and in the presence of stabilizers using Trp fluorescence as a monitor. The protein showed a remarkable sensitivity to pressure: at 293 K, pressures around 10 MPa are sufficient to cause 50% of unfolding. Higher pressures were required for the unfolding of the protein in the presence of stabilizers. The phase diagram on the pressure-temperature plane together with a critical comparison between our results and those found in the literature allowed us to draw conclusions on the mechanism of the unfolding process under different environmental conditions.

Room temperature fluorescence and phosphorescence study on the interactions of iodide ions with single tryptophan containing serum albumins

In this study, the influence of heavy-atom perturbation, induced by the addition of iodide ions, on the fluorescence and phosphorescence decay parameters of some single tryptophan containing serum albumins isolated from: human (HSA), equine (ESA) and leporine (LSA) has been studied. The obtained results indicated that, there exist two distinct conformations of the proteins with different exposure to the quencher. In addition, the Stern-Volmer plots indicated saturation of iodide ions in the binding region. Therefore, to determine quenching parameter, we proposed alternative quenching model and we have performed a global analysis of each conformer to define the effect of iodide ions in the cavity by determining the value of the association constant. The possible quenching mechanism may be based on long-range through-space interactions between the buried chromophore and quencher in the aqueous phase. The discrepancies of the decay parameters between the albumins studied may be related with the accumulation of positive charge at the main and the back entrance to the Drug Site 1 where tryptophan residue is located.

Room temperature phosphorescence study on the structural flexibility of single tryptophan containing proteins

In this study, we have undertaken efforts to find correlation between phosphorescence lifetimes of single tryptophan containing proteins and some structural indicators of protein flexibility/rigidity, such as the degree of tryptophan burial or its exposure to solvent, protein secondary and tertiary structure of the region of localization of tryptophan as well as B factors for tryptophan residue and its immediate surroundings. Bearing in mind that, apart from effective local viscosity of the protein/solvent matrix, the other factor that concur in determining room temperature tryptophan phosphorescence (RTTP) lifetime in proteins is the extent of intramolecular quenching by His, Cys, Tyr and Trp side chains, the crystallographic structures derived from the Brookhaven Protein Data Bank were also analyzed concentrating on the presence of potentially quenching amino acid side chains in the close proximity of the indole chromophore. The obtained results indicated that, in most cases, the phosphorescence lifetimes of tryptophan containing proteins studied tend to correlate with the above mentioned structural indicators of protein rigidity/flexibility. This correlation is expected to provide guidelines for the future development of phosphorescence lifetime-based method for the prediction of structural flexibility of proteins, which is directly linked to their biological function.

Substituted tryptophans at amyloid-β(1-40) residues 19 and 20 experience different environments after fibril formation

Amyloid-β protein (Aβ) is the principal component of the neuritic plaques found in Alzheimer's disease. The predominant Aβ morphology in the plaques is fibrillar which has prompted substantial in vitro work to better understand the molecular organization of Aβ fibrils. In the current study, tryptophan substitutions were made at Aβ(1-40) position 19 (F19W) or 20 (F20W) to ascertain environmental differences between the two residues in the fibril structure. Kinetic studies revealed similar rates of fibril formation between Aβ(1-40) F19W and F20W and both peptides formed typical amyloid fibril structures. Aβ(1-40) F19W fibrils displayed a significant tryptophan fluorescence blue-shift in λ(max) (33nm) compared to monomer while Aβ(1-40) F20W fibrils had a much smaller shift (9nm). Fluorescence quenching experiments with water-soluble acrylamide and KI demonstrated that both W19 and W20 were much less accessible to quenching in fibrils compared to monomer. Lipid-soluble TEMPO quenched the fluorescence of Aβ(1-40) F19W fibrils more effectively than F20W fibrils in agreement with the fluorescence blue-shift results. These findings demonstrate distinct environments between Aβ(1-40) residues 19 and 20 fibrils and indicate that while W20 accessibility is compromised in Aβ fibrils it resides in a much less hydrophobic environment than W19.

Electrostatically directed visual fluorescence response of DNA-functionalized monolithic hydrogels for highly sensitive Hg²+ detection

Hydrogels are cross-linked hydrophilic polymer networks with low optical background and high loading capacity for immobilization of biomolecules. Importantly, the property of hydrogel can be precisely controlled by changing the monomer composition. This feature, however, has not been investigated in the rational design of hydrogel-based optical sensors. We herein explore electrostatic interactions between an immobilized mercury binding DNA, a DNA staining dye (SYBR Green I), and the hydrogel backbone. A thymine-rich DNA was covalently functionalized within monolithic hydrogels containing a positive, neutral, or negative backbone. These hydrogels can be used as sensors for mercury detection since the DNA can selectively bind Hg(2+) between thymine bases inducing a hairpin structure. SYBR Green I can then bind to the hairpin to emit green fluorescence. For the neutral or negatively charged gels, addition of the dye in the absence of Hg(2+) resulted in intense yellow background fluorescence, which was attributed to SYBR Green I binding to the unfolded DNA. We found that, by introducing 20% positively charged allylamine monomer, the background fluorescence was significantly reduced. This was attributed to the repulsion between positively charged SYBR Green I by the gel matrix as well as the strong binding between the DNA and the gel backbone. The signal-to-background ratio and detection limit was, respectively, improved by 6- and 9-fold using the cationic gel instead of neutral polyacrylamide gel. This study helps understand the electrostatic interaction within hydrogels, showing that hydrogels can not only serve as a high capacity matrix for sensor immobilization but also can actively influence the interaction between involved molecules.

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 dynamics and pressure: what can high pressure tell us about protein structural flexibility?

After a brief overview of NMR and X-ray crystallography studies on protein flexibility under pressure, we summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of the globular fold and modulation of its dynamical structure is analyzed both in terms of a reduction of internal cavities and of the hydration of the polypeptide. The study of the effect of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (ΔV(0)) of azurin and on the internal dynamics of the protein fold under pressure demonstrate that the creation of an internal cavity will enhance the plasticity and lower the stability of the globular structure. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.