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Journal of Biochemistry 2005 138(1):79-88; doi:10.1093/jb/mvi101
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© 2005 The Japanese Biochemical Society

Regular Paper

Improved Estimation of the Secondary Structures of Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy

Koichi Matsuo1, Ryuta Yonehara1 and Kunihiko Gekko1,2,*

1 Department of Mathematical and Life Sciences, Graduate School of Science, and 2 Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan

* To whom correspondence should be addressed. E-mail: gekko{at}sci.hiroshima-u.ac.jp

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°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, ß-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 ß-strand segments, which were calculated from the distorted {alpha}-helix and ß-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.


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