Hairpin and hammerhead ribozymes: how different are they?

2002 ◽  
Vol 30 (6) ◽  
pp. 1116-1119 ◽  
Author(s):  
J. M. Burke
Keyword(s):  
Metal Ions ◽  
Conformational Changes ◽  
Experimental Work ◽  
Hammerhead Ribozyme ◽  
Active Conformation ◽  
Hairpin Ribozyme ◽  
Hammerhead Ribozymes ◽  
Active Structure ◽  
Catalytic Function ◽  
Recent Experimental Work

Recent experimental work on the hairpin and hammerhead ribozymes suggests that they have more similarities than previously suspected. Notably, each is now known to function as a true RNA catalyst, not requiring metal ions for folding or catalytic function. The active conformation of the hairpin ribozyme has been established by crystallography, and is well supported by biochemical and biophysical evidence that has identified conformational changes and key nucleotides required for catalysis. Analogous work is under way to establish the active structure of the hammerhead ribozyme.

scholarly journals Physiological Metals Can Induce Conformational Changes in Transthyretin Structure: Neuroprotection or Misfolding Induction?

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 354
Author(s):  
Lidia Ciccone ◽  
Nicolò Tonali ◽  
William Shepard ◽  
Susanna Nencetti ◽  
Elisabetta Orlandini
Keyword(s):  
Cerebrospinal Fluid ◽  
Metal Ions ◽  
Conformational Change ◽  
Conformational Changes ◽  
Binding Proteins ◽  
Active Conformation ◽  
Pathological Conditions ◽  
High Concentrations ◽  
Partially Unfolded

Transthyretin (TTR) is a plasma homotetrameric protein that transports thyroxine and retinol. TTR itself, under pathological conditions, dissociates into partially unfolded monomers that aggregate and form fibrils. Metal ions such as Zn2+, Cu2+, Fe2+, Mn2+ and Ca2+ play a controversial role in the TTR amyloidogenic pathway. TTR is also present in cerebrospinal fluid (CSF), where it behaves as one of the major Aβ-binding-proteins. The interaction between TTR and Aβ is stronger in the presence of high concentrations of Cu2+. Crystals of TTR, soaked in solutions of physiological metals such as Cu2+ and Fe2+, but not Mn2+, Zn2+, Fe3+, Al3+, Ni2+, revealed an unusual conformational change. Here, we investigate the effects that physiological metals have on TTR, in order to understand if metals can induce a specific and active conformation of TTR that guides its Aβ-scavenging role. The capability of certain metals to induce and accelerate its amyloidogenic process is also discussed.

Chemical reactivities of tetrapyrrole pigments: a comparison of experimental behaviour with the results of s.c.f.-π-m.o. calculations

1976 ◽  
Vol 273 (924) ◽  
pp. 335-352 ◽  
Keyword(s):  
Metal Ions ◽  
Metal Complexes ◽  
Experimental Work ◽  
Oxidation Potential ◽  
Central Metal ◽  
Reversible Reactions ◽  
Specific Reactivity ◽  
Cleavage Reactions ◽  
Recent Experimental Work ◽  
Experimental Behaviour

Porphyrins are highly σ-electron donating bases and very weak π-acids. Hence they increase the electron density on central metal ions, e.g. iron, which leads to the specific reactivity of haem cytochromes, haemoglobin and oxidizing enzymes. The macrocyclic chlorin ligand behaves similarly but to a lesser degree which explains the comparably low oxidation potential of chlorophyll. Phlorins, oxophlorins, oxa- and aza-porphyrins, tetradehydrocorrins, corrins and biliverdins all produce metal complexes which have a similar geometry to that of metalloporphyrins, but their reactivity patterns are different. In contrast to themetalloporphyrins which undergo many fully reversible reactions, these compounds tend to irreversible addition and cleavage reactions. These tetrapyrrole ligands are stronger π-acids than porphyrins. Results of some recent experimental work and π-electron s.c.f. calculations are presented in support of these generalizations.

scholarly journals Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction

Biochemistry ◽  
2015 ◽  
Vol 54 (41) ◽  
pp. 6369-6381 ◽  
Author(s):  
Aamir Mir ◽  
Ji Chen ◽  
Kyle Robinson ◽  
Emma Lendy ◽  
Jaclyn Goodman ◽  
...  
Keyword(s):  
Metal Ions ◽  
Conformational Changes ◽  
Hammerhead Ribozyme ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Cleavage Reaction

X-ray photoemission studies of the interaction of metals and metal ions with DNA

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Esha Mishra ◽  
Subrata Majumder ◽  
Shikha Varma ◽  
Peter A. Dowben
Keyword(s):  
Heavy Metal ◽  
Metal Ions ◽  
Conformational Changes ◽  
Photoelectron Spectroscopy ◽  
X Ray ◽  
Surface Sensitivity ◽  
Metal Interaction ◽  
The Status ◽  
Sensitivity And Selectivity ◽  
Insight Into

Abstract X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.

scholarly journals Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

1999 ◽  
Vol 32 (3) ◽  
pp. 241-284 ◽  
Author(s):  
William G. Scott
Keyword(s):  
Metal Ions ◽  
Conformational Change ◽  
Large Scale ◽  
Enzyme Inhibitor ◽  
Hammerhead Ribozyme ◽  
Three Dimensional ◽  
Chemical Mechanism ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hammerhead Rna

1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?

Taxonomic studies on Archigetes Leuckart, 1878 (Cestoda: Caryophyllaeidae)

Parasitology ◽  
1965 ◽  
Vol 55 (3) ◽  
pp. 439-451 ◽  
Author(s):  
C. R. Keneedy
Keyword(s):  
Life History ◽  
Experimental Work ◽  
Nature Conservancy ◽  
The Family ◽  
Single Genus ◽  
Biological Characters ◽  
Taxonomic Studies ◽  
Relationship Of ◽  
Recent Experimental Work ◽  
The Relationship

Recent experimental work has indicated that species of Archigetes are capable of infecting and maturing in fishes in addition to tubificids.The genus Archigetes is re-defined on the basis of morphological and biological characters, with particular emphasis on recent life history studies. All species capable of neotenic development have been re-united in a single genus.A description of all species of Archigetes together with a key for their identification are included. New synonomies are discussed.The relationship of Archigetes to other genera of the family is briefly considered, and it is concluded that it forms the terminal stage in a series showing the attainment of neotenic development.I wish to thank Professor R. J. Pumphrey in whose Department the work was carried out, and Dr J. C. Chubb for advice and help in the preparation of this manuscript. I am also grateful to Professor K. Berg and Dr R. L. Calentine for the loan of specimens. The work was carried out during the tenure of a Nature Conservancy Research Studentship.

ChemInform Abstract: Investigation of Metal Ions Induced Conformational Changes in N-Acetyl Alanine Methyl Ester

ChemInform ◽  
1987 ◽  
Vol 18 (3) ◽  
Author(s):  
S. U. KOKPOL ◽  
S. V. HANNONGBUA ◽  
B.-M. RODE ◽  
J. LIMTRAKUL
Keyword(s):  
Methyl Ester ◽  
Metal Ions ◽  
Conformational Changes

Acceptability ratings cannot be taken at face value

2020 ◽  
pp. 189-214
Author(s):  
Carson T. Schütze
Keyword(s):  
Rate Of Convergence ◽  
Experimental Work ◽  
Rates Of Convergence ◽  
Original Method ◽  
Journal Articles ◽  
True Rate ◽  
Acceptability Judgments ◽  
Critical Words ◽  
Recent Experimental Work

This chapter addresses how linguists’ empirical (syntactic) claims should be tested with non-linguists. Recent experimental work attempts to measure rates of convergence between data presented in journal articles and the results of large surveys. Three follow-up experiments to one such study are presented. It is argued that the original method may underestimate the true rate of convergence because it leaves considerable room for naïve subjects to give ratings that do not reflect their true acceptability judgments of the relevant structures. To understand what can go wrong, the experiments were conducted in two parts. The first part had visually presented sentences rated on a computer, replicating previous work. The second part was an interview where the experimenter asked the participants about the ratings they gave to particular items, in order to determine what interpretation or parse they had assigned, whether they had missed any critical words, and so on.

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