https://link.springer.com/content/pdf/10.1097%2FWOX.0b013e3182439613.pdf

Oxidative Stress and Antioxidant Defense

Background: Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, wellorganized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. Results: We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems. Conclusions: This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site [http://www.rna.icmb.utexas.edu] . In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.

/pdf/the-comparative-rna-web-crw-site-an-online-database-of-3qqlqybxhe.pdf

The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

This paper is the first part of a trilogy, which comprises a detailed study of a special type of functional organization and demonstrates its relevance with respect to the origin and evolution of life. Self-replicative macromolecules, such as RNA or DNA in a suitable environment exhibit a behavior, which we may call Darwinian and which can be formally represented by the concept of the quasi-species. A quasi-species is defined as a given distribution of macromolecular species with closely interrelated sequences, dominated by one or several (degenerate) master copies. External constraints enforce the selection of the best adapted distribution, commonly referred to as the wild-type. Most important for Darwinian behavior are the criteria for internal stability of the quasi-species. If these criteria are violated, the information stored in the nucleotide sequence of the master copy will disintegrate irreversibly leading to an error catastrophy. As a consequence, selection and evolution of RNA or DNA molecules is limited with respect to the amount of information that can be stored in a single replicative unit. An analysis of experimental data regarding RNA and DNA replication at various levels of organization reveals, that a sufficient amount of information for the build up of a translation machinery can be gained only via integration of several different replicative units (or reproductive cycles) through functional linkages. A stable functional integration then will raise the system to a new level of organization and thereby enlarge its information capacity considerably. The hypercycle appears to be such a form of organization.

The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle.

Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.

https://science.sciencemag.org/content/sci/273/5282/1678.full.pdf

Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

This article is about the current status of the mfold package for RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules. The details of the free energy rules and of the latest version 3.0 software are described. Future plans are also discussed.

Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide

The structure of a tRNA has been determined by isomorphous replacement. Some of the interactions which maintain the tertiary structure are of a novel type. Our model differs significantly from one which has recently been proposed.

Structure of yeast phenylalanine tRNA at 3 A resolution.

Influence of globin structure on the state of the heme. I. Human deoxyhemoglobin

The x-ray analysis of the monoclinic form of yeast tRNAPhe has been taken to a resolution of 2.5 A by the method of isomorphous replacement. The model proposed at 3 A has been confirmed and extended to reveal additional features of the tertiary structure and of the stereochemistry. An extensive hydrogen bonding network is described involving specific interactions between bases and the ribose-phosphate backbone. The structure of a G-U base pair has been solved.

Structure of yeast phenylalanine transfer RNA at 2.5 A resolution.

Influence of globin structure on the state of the heme. III. Changes in heme spectra accompanying allosteric transitions in methemoglobin and their implications for heme-heme interaction

The class kappa glutathione (GSH) transferase is an enzyme that resides in the mitochondrial matrix. Its relationship to members of the canonical GSH transferase superfamily has remained an enigma. The three-dimensional structure of the class kappa enzyme from rat (rGSTK1-1) in complex with GSH has been solved by single isomorphous replacement with anomalous scattering at a resolution of 2.5 A. The structure reveals that the enzyme is more closely related to the protein disulfide bond isomerase, dsbA, from Escherichia coli than it is to members of the canonical superfamily. The structures of rGSTK1-1 and the canonical superfamily members indicate that the proteins folds have diverged from a common thioredoxin/glutaredoxin progenitor but did so by different mechanisms. The mitochondrial enzyme, therefore, represents a fourth protein superfamily that supports GSH transferase activity. The thioredoxin domain functions in a manner that is similar to that seen in the canonical enzymes by providing key structural elements for the recognition of GSH. The hydroxyl group of S16 is within hydrogen-bonding distance of the sulfur of bound GSH and is, in part, responsible for the ionization of the thiol in the E*GSH complex (pKa = 6.4 +/- 0.1). Preequilibrium kinetic experiments indicate that the k(on) for GSH is 1 x 10(5) M(-1) s(-1) and k(off) for GS- is approximately 8 s(-1) and relatively slow with respect to turnover with 1-chloro-2, 4-dinitrobenzene (CDNB). As a result, the KM(GSH) (11 mM) is much larger than the apparent Kd(GSH) (90 microM). The active site has a relatively open access channel that is flanked by disordered loops that may explain the relatively high turnover number (280 s(-1) at pH 7.0) toward CDNB. The disordered loops form an extensive contiguous patch on one face of the dimeric enzyme, a fact that suggests that the protein surface may interact with a membrane or other protein partner.

Jane E. Ladner

Papers

Structure of yeast phenylalanine tRNA at 3 A resolution.

Influence of globin structure on the state of the heme. I. Human deoxyhemoglobin

Structure of yeast phenylalanine transfer RNA at 2.5 A resolution.

Influence of globin structure on the state of the heme. III. Changes in heme spectra accompanying allosteric transitions in methemoglobin and their implications for heme-heme interaction

Parallel evolutionary pathways for glutathione transferases: structure and mechanism of the mitochondrial class kappa enzyme rGSTK1-1.