12 results on '"Chad R. Bernier"'
Search Results
2. Translation: The Universal Structural Core of Life
- Author
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Chad R Bernier, Anton S Petrov, Nicholas A Kovacs, Petar I Penev, and Loren Dean Williams
- Published
- 2018
- Full Text
- View/download PDF
3. ProteoVision: web server for advanced visualization of ribosomal proteins
- Author
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Maria Ahmad, Vasanta L Chivukula, Caeden D. Meade, Aparna Maddala, Holly M McCann, Aakash Sharma, Anton S. Petrov, Burak Gulen, Claudia Alvarez-Carreño, Chad R. Bernier, Loren Dean Williams, and Petar I. Penev
- Subjects
Models, Molecular ,Ribosomal Proteins ,Internet ,Web server ,Multiple sequence alignment ,Information retrieval ,AcademicSubjects/SCI00010 ,Protein Conformation ,Protein domain ,Sequence alignment ,Peptide Elongation Factor Tu ,Biology ,computer.software_genre ,Visualization ,Acetolactate Synthase ,Upload ,Protein structure ,Bacterial Proteins ,Scripting language ,Web Server Issue ,Genetics ,Sequence Alignment ,computer ,Software - Abstract
ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/., Graphical Abstract Graphical AbstractProteoVision is a webserver designed to visualize phylogenetic, structural, and physicochemical properties of proteins by integration of four mutually synchronized applets that visually represent map data for each amino-acid simultaneously on levels of a (i) multiple sequence alignment; (ii) secondary structure; (iii) 3D structure and (iv) frequency box plot graph.
- Published
- 2021
4. Secondary structures of rRNAs from all three domains of life.
- Author
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Anton S Petrov, Chad R Bernier, Burak Gulen, Chris C Waterbury, Eli Hershkovits, Chiaolong Hsiao, Stephen C Harvey, Nicholas V Hud, George E Fox, Roger M Wartell, and Loren Dean Williams
- Subjects
Medicine ,Science - Abstract
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).
- Published
- 2014
- Full Text
- View/download PDF
5. RNA folding and catalysis mediated by iron (II).
- Author
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Shreyas S Athavale, Anton S Petrov, Chiaolong Hsiao, Derrick Watkins, Caitlin D Prickett, J Jared Gossett, Lively Lie, Jessica C Bowman, Eric O'Neill, Chad R Bernier, Nicholas V Hud, Roger M Wartell, Stephen C Harvey, and Loren Dean Williams
- Subjects
Medicine ,Science - Abstract
Mg²⁺ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA folding and function can indeed be served by Fe²⁺. The results of quantum mechanical calculations show that the geometry of coordination of Fe²⁺ by RNA phosphates is similar to that of Mg²⁺. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4-P6 domain RNA is conserved between complexes with Fe²⁺ or Mg²⁺. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg²⁺, and the hammerhead ribozyme are enhanced in the presence of Fe²⁺ compared to Mg²⁺. All chemical footprinting and ribozyme assays in the presence of Fe²⁺ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe²⁺. The combined biochemical and paleogeological data are consistent with a role for Fe²⁺ in an RNA World. RNA and Fe²⁺ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg²⁺ alone.
- Published
- 2012
- Full Text
- View/download PDF
6. Translation: The Universal Structural Core of Life
- Author
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Petar I. Penev, Chad R. Bernier, Anton S. Petrov, Loren Dean Williams, and Nicholas A. Kovacs
- Subjects
0301 basic medicine ,last universal common ancestor ,Computational biology ,Biology ,Ribosome ,Genome ,Evolution, Molecular ,03 medical and health sciences ,Escherichia coli ,Methods ,Genetics ,Animals ,Humans ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Sequence (medicine) ,Genes, Essential ,Phylum ,Universality (philosophy) ,Translation (biology) ,structural bioinformatics ,Ribosomal RNA ,030104 developmental biology ,Genetic Techniques ,ribosome ,tree of life ,RNA, Ribosomal ,Protein Biosynthesis ,multiple sequence alignment ,ribosomal RNA - Abstract
The Universal Gene Set of Life (UGSL) is common to genomes of all extant organisms. The UGSL is small, consisting of
- Published
- 2018
7. Evolution of the ribosome at atomic resolution
- Author
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Nicholas A. Kovacs, Chad R. Bernier, Ashlyn M. Norris, Anton S. Petrov, Victor G. Stepanov, George E. Fox, Chiaolong Hsiao, Stephen C. Harvey, Roger M. Wartell, Nicholas V. Hud, Loren Dean Williams, and Chris C. Waterbury
- Subjects
5S ribosomal RNA ,Multidisciplinary ,Ribosomal protein ,Eukaryotic Large Ribosomal Subunit ,Evolutionary biology ,5.8S ribosomal RNA ,30S ,Biological Sciences ,Ribosomal RNA ,Biology ,Eukaryotic Ribosome ,Molecular biology ,18S ribosomal RNA - Abstract
The origins and evolution of the ribosome, 3–4 billion years ago, remain imprinted in the biochemistry of extant life and in the structure of the ribosome. Processes of ribosomal RNA (rRNA) expansion can be “observed” by comparing 3D rRNA structures of bacteria (small), yeast (medium), and metazoans (large). rRNA size correlates well with species complexity. Differences in ribosomes across species reveal that rRNA expansion segments have been added to rRNAs without perturbing the preexisting core. Here we show that rRNA growth occurs by a limited number of processes that include inserting a branch helix onto a preexisting trunk helix and elongation of a helix. rRNA expansions can leave distinctive atomic resolution fingerprints, which we call “insertion fingerprints.” Observation of insertion fingerprints in the ribosomal common core allows identification of probable ancestral expansion segments. Conceptually reversing these expansions allows extrapolation backward in time to generate models of primordial ribosomes. The approach presented here provides insight to the structure of pre-last universal common ancestor rRNAs and the subsequent expansions that shaped the peptidyl transferase center and the conserved core. We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel.
- Published
- 2014
8. RiboVision suite for visualization and analysis of ribosomes
- Author
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Zachary Wartell, Jessica C. Bowman, Fengbo Li, Larry Freil, Chris C. Waterbury, Chad R. Bernier, Chiaolong Hsiao, Eli Hershkovits, James Jett, Anton S. Petrov, Stephen C. Harvey, Xiao Xiong, Martha A. Grover, Blacki Li Rudi Migliozzi, Lan Wang, Yuzhen Xue, and Loren Dean Williams
- Subjects
Ribosomal Proteins ,Complex data type ,biology ,Computer science ,Saccharomyces cerevisiae ,Context (language use) ,Computational biology ,Ribosomal RNA ,Thermus thermophilus ,biology.organism_classification ,Ribosome ,Crystallography ,Haloarcula marismortui ,RNA, Ribosomal ,Ribosomal protein ,Nucleic Acid Conformation ,Physical and Theoretical Chemistry ,Ribosomes ,Software - Abstract
RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component of life responsible for the synthesis of proteins in all living organisms. RiboVision is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. Preloaded information includes 1D, 2D, and 3D structures augmented by base-pairing, base-stacking, and other molecular interactions. RiboVision is preloaded with rRNA secondary structures, rRNA domains and helical structures, phylogeny, crystallographic thermal factors,etc.RiboVision contains structures of ribosomal proteins and a database of their molecular interactions with rRNA. RiboVision contains preloaded structures and data for two bacterial ribosomes (Thermus thermophilusandEscherichia coli), one archaeal ribosome (Haloarcula marismortui), and three eukaryotic ribosomes (Saccharomyces cerevisiae,Drosophila melanogaster, andHomo sapiens). RiboVision revealed several major discrepancies between the 2D and 3D structures of the rRNAs of the small and large subunits (SSU and LSU). Revised structures mapped with a variety of data are available in RiboVision as well as in a public gallery (http://apollo.chemistry.gatech.edu/RibosomeGallery). RiboVision is designed to allow users to distill complex data quickly and to easily generate publication-quality images of data mapped onto secondary structures. Users can readily import and analyze their own data in the context of other work. This package allows users to import and map data from CSV files directly onto 1D, 2D, and 3D levels of structure. RiboVision has features in rough analogy with web-based map services capable of seamlessly switching the type of data displayed and the resolution or magnification of the display. RiboVision is available at http://apollo.chemistry.gatech.edu/RiboVision.
- Published
- 2014
9. Secondary structure and domain architecture of the 23S and 5S rRNAs
- Author
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Chiaolong Hsiao, Yuzhen Xue, Roger M. Wartell, Nicholas V. Hud, Stephen C. Harvey, Victor G. Stepanov, Anton S. Petrov, Chris C. Waterbury, Martha A. Grover, Eric A. Gaucher, George E. Fox, Eli Hershkovits, Loren Dean Williams, and Chad R. Bernier
- Subjects
RNA Folding ,Architecture domain ,RNA Stability ,5.8S ribosomal RNA ,Computational biology ,Biology ,Bioinformatics ,Domain (software engineering) ,Evolution, Molecular ,Structure-Activity Relationship ,23S ribosomal RNA ,Three-domain system ,Genetics ,Escherichia coli ,Protein secondary structure ,Base Pairing ,Phylogeny ,Base Sequence ,RNA, Ribosomal, 5S ,Domain model ,Ribosomal RNA ,RNA, Bacterial ,RNA, Ribosomal, 23S ,RNA ,Nucleic Acid Conformation ,Ribosomes - Abstract
We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).
- Published
- 2013
10. RNA–Magnesium–Protein Interactions in Large Ribosomal Subunit
- Author
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Chiaolong Hsiao, Anton S. Petrov, Emmanuel Tannenbaum, C. Denise Okafor, Eric A. Gaucher, Nicholas V. Hud, Chad R. Bernier, Loren Dean Williams, Joshua G. Stern, Stephen C. Harvey, and Dana M. Schneider
- Subjects
Models, Molecular ,Magnesium ,RNA ,chemistry.chemical_element ,Ribosomal RNA ,Crystallography, X-Ray ,Ribosome ,Surfaces, Coatings and Films ,Crystallography ,chemistry ,Ribosomal protein ,Ribosome Subunits ,Large ribosomal subunit ,Materials Chemistry ,Biophysics ,Ribosome Subunits, Large ,Physical and Theoretical Chemistry ,Magnesium ion - Abstract
Some of the magnesium ions in the ribosome are coordinated by multiple rRNA phosphate groups. These magnesium ions link distal sequences of rRNA, primarily by incorporating phosphate groups into the first coordination shell. Less frequently, magnesium interacts with ribosomal proteins. Ribosomal protein L2 appears to be unique by forming specific magnesium-mediated interactions with rRNA. Using optimized models derived from X-ray structures, we subjected rRNA/magnesium/water/rProtein L2 assemblies to quantum mechanical analysis using the density functional theory and natural energy decomposition analysis. The combined results provide estimates of energies of formation of these assemblies, and allow us to decompose the energies of interaction. The results indicated that RNA immobilizes magnesium by multidentate chelation with phosphate, and that the magnesium ions in turn localize and polarize water molecules, increasing energies and specificities of interaction of these water molecules with L2 protein. Thus, magnesium plays subtle, yet important, roles in ribosomal assembly beyond neutralization of electrostatic repulsion and direct coordination of RNA functional groups.
- Published
- 2012
11. History of the ribosome and the origin of translation
- Author
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Ashlyn M. Norris, Kathryn A. Lanier, Stephen C. Harvey, Nicholas A. Kovacs, George E. Fox, Burak Gulen, Roger M. Wartell, Loren Dean Williams, Chad R. Bernier, Nicholas V. Hud, and Anton S. Petrov
- Subjects
Models, Molecular ,molecular growth ,Biology ,insertion ,Evolution, Molecular ,RNA, Transfer ,accretion ,Ribosomal protein ,Large ribosomal subunit ,ad hocness ,Escherichia coli ,Ribosome Subunits ,Eukaryotic Small Ribosomal Subunit ,Molecular Biosciences ,RNA, Messenger ,rRNA ,cladistics ,50S ,Genetics ,Multidisciplinary ,Eukaryotic Large Ribosomal Subunit ,General Commentary ,molecular evolution ,homoplasy ,Ribosomal RNA ,Evolutionary biology ,RNA, Ribosomal ,Protein Biosynthesis ,Biocatalysis ,Nucleic Acid Conformation ,Eukaryotic Ribosome ,Ribosomes - Abstract
We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.
- Published
- 2015
12. Secondary Structures of rRNAs from All Three Domains of Life
- Author
-
Chris C. Waterbury, Loren Dean Williams, Burak Gulen, Stephen C. Harvey, Nicholas V. Hud, Chiaolong Hsiao, George E. Fox, Chad R. Bernier, Anton S. Petrov, Eli Hershkovits, and Roger M. Wartell
- Subjects
Models, Molecular ,Haloarcula marismortui ,Base pair ,Origin of Life ,Molecular Sequence Data ,Biophysics ,lcsh:Medicine ,Yeast and Fungal Models ,Computational biology ,RNA, Archaeal ,Saccharomyces cerevisiae ,Biophysics Theory ,Model Organisms ,Animals ,Humans ,Nucleic acid structure ,lcsh:Science ,RNA structure ,Biology ,Base Pairing ,Phylogeny ,Genetics ,Evolutionary Biology ,Escherichia Coli ,Multidisciplinary ,biology ,Phylogenetic tree ,Drosophila Melanogaster ,Thermus thermophilus ,lcsh:R ,Fungal genetics ,RNA, Fungal ,Animal Models ,Ribosomal RNA ,biology.organism_classification ,Nucleic acids ,Macromolecular structure analysis ,RNA, Bacterial ,RNA, Ribosomal ,RNA ,Prokaryotic Models ,Nucleic Acid Conformation ,lcsh:Q ,Pseudoknot ,Research Article - Abstract
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).
- Published
- 2014
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