Blog
About

7
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Inverse Thio Effects in the Hepatitis Delta Virus Ribozyme Reveal that the Reaction Pathway Is Controlled by Metal Ion Charge Density

      Read this article at

      ScienceOpenPublisherPMC
      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

          The hepatitis delta virus (HDV) ribozyme self-cleaves in the presence of a wide range of monovalent and divalent ions. Prior theoretical studies provided evidence that self-cleavage proceeds via a concerted or stepwise pathway, with the outcome dictated by the valency of the metal ion. In the present study, we measure stereospecific thio effects at the nonbridging oxygens of the scissile phosphate under a wide range of experimental conditions, including varying concentrations of diverse monovalent and divalent ions, and combine these with quantum mechanical/molecular mechanical (QM/MM) free energy simulations on the stereospecific thio substrates. The R P substrate gives large normal thio effects in the presence of all monovalent ions. The S P substrate also gives normal or no thio effects, but only for smaller monovalent and divalent cations, such as Li +, Mg 2+, Ca 2+, and Sr 2+; in contrast, sizable inverse thio effects are found for larger monovalent and divalent cations, including Na +, K +, NH 4 +, and Ba 2+. Proton inventories are found to be unity in the presence of the larger monovalent and divalent ions, but two in the presence of Mg 2+. Additionally, rate–pH profiles are inverted for the low charge density ions, and only imidazole plus ammonium ions rescue an inactive C75Δ variant in the absence of Mg 2+. Results from the thio effect experiments, rate–pH profiles, proton inventories, and ammonium/imidazole rescue experiments, combined with QM/MM free energy simulations, support a change in the mechanism of HDV ribozyme self-cleavage from concerted and metal ion-stabilized to stepwise and proton transfer-stabilized as the charge density of the metal ion decreases.

          Related collections

          Most cited references 55

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

          Advances in methods and algorithms in a modern quantum chemistry program package.

          Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Tertiary contacts distant from the active site prime a ribozyme for catalysis.

            Minimal hammerhead ribozymes have been characterized extensively by static and time-resolved crystallography as well as numerous biochemical analyses, leading to mutually contradictory mechanistic explanations for catalysis. We present the 2.2 A resolution crystal structure of a full-length Schistosoma mansoni hammerhead ribozyme that permits us to explain the structural basis for its 1000-fold catalytic enhancement. The full-length hammerhead structure reveals how tertiary interactions occurring remotely from the active site prime this ribozyme for catalysis. G-12 and G-8 are positioned consistent with their previously suggested roles in acid-base catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosphate, and previously unexplained roles of other conserved nucleotides become apparent within the context of a distinctly new fold that nonetheless accommodates the previous structural studies. These interactions permit us to explain the previously irreconcilable sets of experimental results in a unified, consistent, and unambiguous manner.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              A widespread self-cleaving ribozyme class is revealed by bioinformatics

              Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs.
                Bookmark

                Author and article information

                Journal
                Biochemistry
                Biochemistry
                bi
                bichaw
                Biochemistry
                American Chemical Society
                0006-2960
                1520-4995
                23 March 2015
                31 March 2015
                : 54
                : 12
                : 2160-2175
                Affiliations
                []Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
                []Department of Chemistry, University of Illinois at Urbana−Champaign , Urbana, Illinois 61801, United States
                Author notes
                [* ](S.H.-S.) Telephone: (217) 300-0335; e-mail: shs3@ 123456illinois.edu .
                [* ](P.C.B.) Telephone: (814) 863-3812; fax: (814) 865-2927; e-mail: pcb5@ 123456psu.edu .
                Article
                10.1021/acs.biochem.5b00190
                4824481
                25799319
                Copyright © 2015 American Chemical Society

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                Funding
                National Institutes of Health, United States
                Categories
                Article
                Custom metadata
                bi5b00190
                bi-2015-00190y

                Biochemistry

                Comments

                Comment on this article