Etsuko Nishimoto

Multiple conformational state of human serum albumin around single tryptophan residue at various pH revealed by time-resolved fluorescence spectroscopy

Human serum albumin (HSA) plays important roles in transport of fatty acids and binding a variety of drugs and organic compounds in the circulatory system. This protein experiences several conformational transitions by the change of pH, and the resulting conformations were essential for completing the physiological roles in vivo. Steady-state and time-resolved fluorescence spectroscopy was applied to single tryptophan residue solely arranged in HSA to study subtle conformational change around single tryptophan residue in HSA at various pH. The results showed the characteristic feature of local conformation around tryptophan residue in domain II responding to the change in entire structure. The study of time-resolved area-normalized fluorescence emission spectra (TRANES) also showed the peculiar dielectric property of water molecule trapped nearby tryptophan residue depending on pH. These results suggested that microenvironment around tryptophan residue was tightly packed at acidic and basic pH although entire conformation was loosened.

Fluorescence decay characteristics of indole compounds revealed by time-resolved area-normalized emission spectroscopy.

Time-resolved fluorescence spectroscopy of tryptophan residue has been extensively applied to the studies on structure-function relationships of protein. Regardless of this, the fluorescence decay mechanism and kinetics of tryptophan residue in many proteins still remains unclear. Previous studies have demonstrated that conformational heterogeneity and relaxation dynamics are both involved in the peculiar multiexponential decay kinetics in subnanosecond resolution. In the present study, we characterized the fluorescence decay property of six indole compounds in glycerol by resolving the contribution of conformational heterogeneity and relaxation dynamics. We applied the time-resolved area-normalized fluorescence emission spectrum (TRANES) method for the fluorescence decay analysis. The results of TRANES, time-dependent shift of fluorescence spectral center of gravity, and fluorescence decay simulation demonstrated that the dielectric relaxation process independent of intrinsic rotamer/conformer and the individual fluorescence lifetime gives the peculiarity to the fluorescence decay of indole compounds. These results confirmed that TRANES and time-dependent spectral shift analysis are potent methods to resolve the origin of multiexponential decay kinetics of tryptophyl fluorescence in protein.

The Unfolding of α-Momorcharin Proceeds Through the Compact Folded Intermediate

The unfolding of alpha-momorcharin was systematically investigated using steady-state and time-resolved tryptophan fluorescence, circular dichroism and 8-anilino-1-naphthalenesulfonic acid (ANS) binding. These spectroscopic studies demonstrated that alpha-momorcharin unfolded through a compact folded intermediate state. The content of alpha-helix was increased, Trp192 approached closer to the side of active site and its rotational motion was restricted by being equilibrated with 2-3 M of guanidine hydrochloride. Furthermore, the binding of ANS with alpha-momorcharin was more suppressed to show that the hydrophobic parts would not be accessed to the protein surface but rather be sealed off in this specific conformation state. These results suggest that the structure of alpha-momorcharin holds the more compact conformation as an incipient state for unfolding, which is the sharp contrast to beta-momorcharin that gives the characteristics of the generally known molten globule state.

Protein-protein interaction on lysozyme crystallization revealed by rotational diffusion analysis.

Intermolecular interactions between protein molecules diffusing in various environments underlie many biological processes as well as control protein crystallization, which is a crucial step in x-ray protein structure determinations. Protein interactions were investigated through protein rotational diffusion analysis. First, it was confirmed that tetragonal lysozyme crystals containing fluorescein-tagged lysozyme were successfully formed with the same morphology as that of native protein. Using this nondisruptive fluorescent tracer system, we characterized the effects of sodium chloride and ammonium sulfate concentrations on lysozyme-lysozyme interactions by steady-state and time-resolved fluorescence anisotropy measurements and the introduction of a novel interaction parameter, k(rot). The results suggested that the specific attractive interaction, which was reflected in the retardation of the protein rotational diffusion, was induced depending on the salt type and its concentration. The change in the attractive interactions also correlated with the crystallization/precipitation behavior of lysozyme. Moreover, we discuss the validity of our rotational diffusion analysis through comparison with the osmotic second virial coefficient, B(22), previously reported for lysozyme and those estimated from k(rot).

The structural mechanism of the inhibition of archaeal RelE toxin by its cognate RelB antitoxin

The archaeal toxin, aRelE, in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 inhibits protein synthesis, whereas its cognate antitoxin, aRelB, neutralizes aRelE activity by forming a non-toxic complex, aRelB-aRelE. The structural mechanism whereby aRelB neutralizes aRelE activity was examined by biochemical and biophysical analyses. Overexpression of aRelB with an aRelE mutant (ΔC6), in which the C-terminal residues critical for aRelE activity were deleted, in Escherichia coli allowed a stable complex, aRelB-ΔC6, to be purified. Isothermal titration of aRelE or ΔC6 with aRelB indicated that the association constant (Ka) of wild-type aRelB-aRelE is similar to that of aRelB-ΔC6, demonstrating that aRelB makes little contact with the C-terminal active site of aRelE. Overexpression of deletion mutants of aRelB with aRelE indicated that either the N-terminal (pos. 1-27) or C-terminal (pos. 50-67) fragment of aRelB is sufficient to counteract the toxicity of aRelE in E. coli cells and the second α-helix (α2) in aRelB plays a critical role in forming a stable complex with aRelE. The present results demonstrate that aRelB, as expected from its X-ray structure, precludes aRelE from entering the ribosome, wrapping around the molecular surface of aRelE.

The quenching-resolved fluorescence spectrum and its application to studies of the folding/unfolding of trypsin inhibitor from seeds of the bitter gourd.

With reference to the local conformation of a protein, it is interesting to differentiate the individual fluorescence properties of included tryptophan residues without modification. The fluorescence spectrum of bitter gourd trypsin inhibitor (BGTI) was separated into two emission bands by the quenching-resolved fluorescence method. One emission band was given as a fraction with the Stern-Volmer quenching constant, 44.9×10−3 M−1, against the fluorescence quenching by KI, and it showed an emission maximum intensity at 341 nm. The fluorescence quenching constant of the other band was 1.58×10−3 M−1, and the maximum wavelength was found at 337 nm. These separated emissions were due to the fluorescence of Trp54 and Trp9 of BGTI. The quenching resolved-fluorescence spectrum was effectively applied to the precise description of the polar circumstances surrounding the Trp residues in the unfolding intermediate state of BGTI. The results suggested that the molten globule-like state of BGTI adopted such a peculiar conformation that the helix domain including Trp9 was packed more densely while the other loop domain partially unfolded.

Rotational diffusion analysis of polyethylene glycol induced protein interactions

Protein intermolecular depletion interactions induced by polyethylene glycol (PEG) depend largely on its concentration and molecular weight. Herein, we investigated the effects of various concentrations and molecular weights of PEG on lysozyme interactions through the analysis of protein rotational diffusion, which is susceptible to intermolecular interactions at short range. To this end, we measured fluorescence anisotropy of fluorescein-tagged lysozyme added as a tracer in concentrated native lysozyme solutions and introduced a protein concentration-dependent interaction parameter, k(rot). The results show the nonmonotonic changes in k(rot) as the concentrations of PEG10000 and 6000 are increased. The depletion attractions are characterized by the decrease in k(rot), indicating an increase of a degree at which protein rotational diffusion slows down. The influences of temperature on the lysozyme rotational diffusion and k(rot) were also measured, and the validity of this approach was checked through comparison with the colloidal theory.

Conformational Change Near the Redox Center of Dihydrolipoamide Dehydrogenase Induced by NAD+ to Regulate the Enzyme Activity

Dihydrolipoamide dehydrogenase (LipDH) transfers two electrons from dihydrolipoamide (DHL) to NAD+ mediated by FAD. Since this reaction is the final step of a series of catalytic reaction of pyruvate dehydrogenase multi-enzyme complex (PDC), LipDH is a key enzyme to maintain the fluent metabolic flow. We reported here the conformational change near the redox center of LipDH induced by NAD+ promoting the access of the DHL to FAD. The increase in the affinity of DHL to redox center was evidenced by the decrease in KM responding to the increase in the concentration of NAD+ in Lineweaver-Burk plots. The fluorescence intensity of FAD transiently reduced by the addition of DHL was not recovered but rather reduced by the binding of NAD+ with LipDH. The fluorescence decay lifetimes of FAD and Trp were prolonged in the presence of NAD+ to show that FAD would be free from the electron transfer from the neighboring Tyrs and the resonance energy transfer efficiency between Trp and FAD lowered. These results consistently reveal that the conformation near the FAD and the surroundings would be so rearranged by NAD+ to allow the easier access of DHL to the redox center of LipDH.

Steady-State and Time-Resolved Fluorescence Spectroscopic Studies on Interaction of the N-terminal Region with the Hairpin Loop of the Phytocystain Scb

The steady-state and time-resolved fluorescece spectroscopy is one of the most powerful method to detect and analyze subtle conformation change and interaction between peptide elements in protein. Phytocystatin Scb isolated from sunflower seeds includes a single Trp residue at position 85. In an attempt to investigate the interaction of the N-terminal region of Scb with the first and second hairpin loops by fluorescence spectroscopy of Trp residue, two Scb mutants in which single Trp locates at position 52 and 58, respectively, and their N-terminal removed mutants were generated. The N-terminal truncation changed the fluorescence decay kinetics of Trp52 from the triple exponential to double. Furthermore, the time-resolved fluorescence anisotropy residue indicated that the segmental motion of Trp52 was significantly enhanced by its N-terminal truncation. In contrast, Trp58 and Trp85 had little influence. The N-terminal successive truncations of Scb and its mutants resulted in the weaken inhibitors to papain. These results suggested that the N-terminal region of Scb interacts with the peptide segment preceding the first hairpin loop, thereby stabilizing the conformation of the hairpin loop structure.

Heterogeneous Packing in the Folding/Unfolding Intermediate State of Bitter Gourd Trypsin Inhibitor

The conformation and dynamics of a protein are essential in characterizing the protein folding/unfolding intermediate state. They are closely involved in the packing and site-specific interactions of peptide elements to build and stabilize the tertiary structure of the protein. In this study, it was confirmed that trypsin inhibitor obtained from seeds of bitter gourd (BGTI) adopted a peculiar but plausible conformation and dynamics in the unfolding intermediate state. The fluorescence spectrum of one of two tryptophan residues of BGTI, Trp9, shifted to the blue side in the presence of 2–3 M guanidine hydrochloride, although the other, Trp54, did not show this spectral shift. At the same time, the motional freedom of Trp9 revealed by a time-resolved fluorescence study decreased, suggesting that the segmental motion of this residue was more restricted. These results indicate that BGTI takes such a conformation state that the hydrophobic core and loop domains arranging Trp9 and Trp54 respectively are heterogeneously packed in the unfolding intermediate state.