The vacuum-ultraviolet circular dichroism (VUVCD) spectra of 16 globular proteins (insulin, lactate dehydrogenase, glucose isomerase, lipase, conalbumin, transferrin, catalase, subtilisin A, alpha-amylase, staphylococcal nuclease, papain, thioredoxin, carbonic anhydrase, elastase, avidin, and xylanase) were successfully measured in aqueous solutions at 25 degrees C from 260 to 160 nm under a high vacuum using a synchrotron-radiation VUVCD spectrophotometer. These proteins exhibited characteristic CD spectra below 190 nm that were related to their different secondary structures, which could not be detected with a conventional CD spectrophotometer. The component spectra of alpha-helices, beta-strands, turns, and unordered structures were obtained by deconvolution analysis of the VUVCD spectra of 31 reference proteins including the 15 proteins reported in our previous paper [Matsuo, K. et al. (2004) J. Biochem. 135, 405-411]. Prediction of the secondary-structure contents using the SELCON3 program was greatly improved, especially for alpha-helices, by extending the short-wavelength limit of CD spectra to 160 nm and by increasing the number of reference proteins. The numbers of alpha-helix and beta-strand segments, which were calculated from the distorted alpha-helix and beta-strand contents, were close to those obtained on X-ray crystallography. These results demonstrate the usefulness of synchrotron-radiation VUVCD spectroscopy for the secondary structure analysis of proteins.

The vacuum ultraviolet circular dichroism (VUVCD) spectra of 15 globular proteins (myoglobin, hemoglobin, human serum albumin, cytochrome c, peroxidase, alpha-lactalbumin, lysozyme, ovalbumin, ribonuclease A, beta-lactoglobulin, pepsin, trypsinogen, alpha-chymotrypsinogen, soybean trypsin inhibitor, and concanavalin A) were measured in aqueous solutions at 25 degrees C in the wavelength region from 260 to 160 nm under a high vacuum, using a synchrotron-radiation VUVCD spectrophotometer. The VUVCD spectra below 190 nm revealed some characteristic bands corresponding to different secondary structures. The contents of alpha-helices, beta-strands, turns, and unordered structures were estimated using the SELCON3 program with VUVCD spectra data on the 15 proteins. Prediction of the secondary-structure contents was greatly improved by extending the circular dichroism spectra to 165 nm. The numbers of alpha-helix and beta-strand segments calculated from the distorted alpha-helix and beta-strand contents did not differ greatly from those obtained from X-ray crystal structures. These results demonstrate that synchrotron-radiation VUVCD spectroscopy is a powerful tool for analyzing the secondary structures of proteins.

To elucidate the structure of denatured proteins, we measured the vacuum-ultraviolet circular dichroism (VUVCD) spectra from 260 to 172 nm of three proteins (metmyoglobin, staphylococcal nuclease, and thioredoxin) in the native and the acid-, cold-, and heat-denatured states, using a synchrotron-radiation VUVCD spectrophotometer. The circular dichroism spectra of proteins fully unfolded by guanidine hydrochloride (GdnHCl) were also measured down to 197 nm for comparison. These denatured proteins exhibited characteristic VUVCD spectra that reflected a considerable amount of residual secondary structures. The contents of alpha-helices, beta-strands, turns, poly-L-proline type II (PPII), and unordered structures were estimated for each denatured state of the three proteins using the SELCON3 program with Protein Data Bank data and the VUVCD spectra of 31 reference proteins reported in our previous study. Based on these contents, the characteristics of the four types of denaturation were discussed for each protein. In all types of denaturation, a decrease in alpha-helices was accompanied by increases in beta-strands, PPII, and unordered structures. About 20% beta-strands were present even in the proteins fully unfolded by GdnHCl in which beta-sheets should be broken. From these results, we propose that denatured proteins constitute an ensemble of residual alpha-helices and beta-sheets, partly unfolded (or distorted) alpha-helices and beta-strands, PPII, and unordered structures.

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The unusual ascidian ability to accumulate high levels of vanadium ions at concentrations of up to 350 mM, a 10(7)-fold increase over that found in seawater, has been attracting interdisciplinary attention for a century. Accumulated V(V) is finally reduced to V(III) via V(IV) in ascidian vanadocytes. Reducing agents must therefore participate in the reduction. Previously, we identified a vanadium-binding protein, Vanabin2, in which all 18 cysteines form nine disulfide bonds. Here, we report that Vanabin2 is a novel vanadium reductase because partial cleavage of its disulfide bonds results in the reduction of V(V) to V(IV). We propose that Vanabin2 forms a possible electron transfer cascade from the electron donor, NADPH, via glutathione reductase, glutathione, and Vanabin2 to the acceptor, and vanadium ions conjugated through thiol-disulfide exchange reactions.

Synchrotron-radiation vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy can significantly improve the predictive accuracy of the contents and segment numbers of protein secondary structures by extending the short-wavelength limit of the spectra. In the present study, we combined VUVCD spectra down to 160 nm with neural-network (NN) method to improve the sequence-based prediction of protein secondary structures. The secondary structures of 30 target proteins (test set) were assigned into alpha-helices, beta-strands, and others by the DSSP program based on their X-ray crystal structures. Combining the alpha-helix and beta-strand contents estimated from the VUVCD spectra of the target proteins improved the overall sequence-based predictive accuracy Q(3) for three secondary-structure components from 59.5 to 60.7%. Incorporating the position-specific scoring matrix in the NN method improved the predictive accuracy from 70.9 to 72.1% when combining the secondary-structure contents, to 72.5% when combining the numbers of segments, and finally to 74.9% when filtering the VUVCD data. Improvement in the sequence-based prediction of secondary structures was also apparent in two other indices of the overall performance: the correlation coefficient (C) and the segment overlap value (SOV). These results suggest that VUVCD data could enhance the predictive accuracy to over 80% when combined with the currently best sequence-prediction algorithms, greatly expanding the applicability of VUVCD spectroscopy to protein structural biology.

The electronic circular dichoism (ECD) of L-alanine in the vacuum-ultraviolet region was calculated for various optimized structures using time-dependent density functional theory (TDDFT) to assign the CD spectrum observed experimentally in aqueous solution down to 140 nm [Matsuo, et al. Chem. Lett. 2002, 826]. The structure of L-alanine in vacuo was optimized using density functional theory (DFT) at the B3LYP/6-31G* level. Its hydrated structure was optimized with nine water molecules (six and three around carboxyl and amino groups, respectively) using DFT and a continuum model (Onsager model). The dihedral angles of carboxyl and amino groups in the optimized hydrated structure differed greatly from those in the crystal and in nonhydrated structures optimized using a continuum model only. The ECD spectrum calculated for the hydrated structure had two successive positive peaks with molar ellipticities of about 2000 deg cm2 dmol(-1) at around 205 and 185 nm, which were close to those observed experimentally. These positive peaks were attributable to n pi* transitions of the carboxyl group, with the latter peak also influenced by the pi pi* transition of the carboxyl group that originates below 175 nm. A small negative peak observed at around 252 nm was also predicted from the hydrated structure. These results demonstrate that the hydrated water molecules around the zwitterions play a crucial role in stabilizing the conformation of L-alanine in aqueous solution and that TDDFT is useful for the ab initio assignment of ECD spectra down to the vacuum-ultraviolet region.