16
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

      review-article
      Biophysics and Physicobiology
      The Biophysical Society of Japan (BSJ)
      amino acids, nucleic acids, proteins, saccharides, structural analysis

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

          Related collections

          Most cited references147

          • Record: found
          • Abstract: found
          • Article: not found

          Knowledge-based protein secondary structure assignment.

          We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard-of-truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 22:2577-2637, 1983) shows that STRIDE and DSSP assign secondary structural states in 58 and 31% of 226 protein chains in our data sample, respectively, in greater agreement with the specific residue-by-residue definitions provided by the discoverers of the structures while in 11% of the chains, the assignments are the same. STRIDE delineates every 11th helix and every 32nd strand more in accord with published assignments.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Prediction of protein secondary structure at better than 70% accuracy.

            We have trained a two-layered feed-forward neural network on a non-redundant data base of 130 protein chains to predict the secondary structure of water-soluble proteins. A new key aspect is the use of evolutionary information in the form of multiple sequence alignments that are used as input in place of single sequences. The inclusion of protein family information in this form increases the prediction accuracy by six to eight percentage points. A combination of three levels of networks results in an overall three-state accuracy of 70.8% for globular proteins (sustained performance). If four membrane protein chains are included in the evaluation, the overall accuracy drops to 70.2%. The prediction is well balanced between alpha-helix, beta-strand and loop: 65% of the observed strand residues are predicted correctly. The accuracy in predicting the content of three secondary structure types is comparable to that of circular dichroism spectroscopy. The performance accuracy is verified by a sevenfold cross-validation test, and an additional test on 26 recently solved proteins. Of particular practical importance is the definition of a position-specific reliability index. For half of the residues predicted with a high level of reliability the overall accuracy increases to better than 82%. A further strength of the method is the more realistic prediction of segment length. The protein family prediction method is available for testing by academic researchers via an electronic mail server.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins.

                Bookmark

                Author and article information

                Journal
                Biophys Physicobiol
                Biophys Physicobiol
                Biophysics and Physicobiology
                The Biophysical Society of Japan (BSJ)
                2189-4779
                2019
                06 February 2019
                : 16
                : 41-58
                Affiliations
                Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
                Author notes
                Corresponding author: Kunihiko Gekko, Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan. e-mail: gekko@ 123456hiroshima-u.ac.jp
                Article
                16_41
                10.2142/biophysico.16.0_41
                6435020
                30923662
                6736c480-6183-49d6-8f85-06b491fc0f6c
                2019 © The Biophysical Society of Japan

                This article is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.

                History
                : 06 November 2018
                : 13 January 2019
                Categories
                Review Article

                amino acids,nucleic acids,proteins,saccharides,structural analysis

                Comments

                Comment on this article