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  1. Article: Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme.

    Scott, W G

    Quarterly reviews of biophysics

    2001  Volume 32, Issue 3, Page(s) 241–284

    MeSH term(s) Base Sequence ; Biophysical Phenomena ; Biophysics ; Kinetics ; Metals/metabolism ; Models, Molecular ; Mutagenesis ; Nucleic Acid Conformation ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Catalytic/metabolism
    Chemical Substances Metals ; RNA, Catalytic
    Language English
    Publishing date 2001-01-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
    ZDB-ID 209912-3
    ISSN 1469-8994 ; 0033-5835
    ISSN (online) 1469-8994
    ISSN 0033-5835
    DOI 10.1017/s003358350000353x
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  2. Article: Ribozyme catalysis via orbital steering.

    Scott, W G

    Journal of molecular biology

    2001  Volume 311, Issue 5, Page(s) 989–999

    Abstract: Orbital steering is invoked to explain how the three-dimensional structure of a small self-cleaving RNA, the hammerhead ribozyme, both prevents and enhances RNA autocatalysis. Within the conserved catalytic core of the ribozyme, the position of the 2' ... ...

    Abstract Orbital steering is invoked to explain how the three-dimensional structure of a small self-cleaving RNA, the hammerhead ribozyme, both prevents and enhances RNA autocatalysis. Within the conserved catalytic core of the ribozyme, the position of the 2' oxygen atom of the G8 ribose is observed to be aligned almost perfectly with the phosphorus atom and the 5' oxygen atom of the adjacent A9 phosphate group for self-cleavage via an in-line attack mechanism. Despite this apparent near-perfect atomic positioning, no cleavage takes place. The explanation proposed is that a network of hydrogen bonds in the ribozyme core orients or steers the orbitals containing the electron lone pairs of the attacking nucleophile (the 2' oxygen atom) away from the A9 phosphorus atom, eliminating overlap with the vacant phosphorus d-orbitals despite the near-perfect in-line positioning of the oxygen atom, thus preventing catalysis. Because of the near-perfect atomic positioning of the 2' oxygen atom relative to the phosphate group, orbital steering effects in this case are fortuitously uncoupled from conformational, distance and orientation effects, allowing an assessment of the catalytic power due purely to orbital steering. In contrast, a conformational change at the cleavage site is required to bring the 2' oxygen atom and the scissile phosphate group into atomic positions amenable to an in-line attack mechanism. In addition, the conformationally changed structure must then steer the lone-pair orbitals of the correctly positioned 2' oxygen atom toward the scissile phosphorus atom in order for cleavage to take place. We estimate that fulfillment of each of these two required changes may contribute separately an approximately 1000-fold rate enhancement, potentially accounting for a significant fraction of the catalytic power of this ribozyme. Orbital steering therefore appears to be a general phenomenon that may help to explain catalysis in both ribozymes and protein enzymes in a unified manner.
    MeSH term(s) Base Sequence ; Binding Sites ; Catalysis ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Oxygen/chemistry ; Oxygen/metabolism ; Phosphates/metabolism ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Catalytic/metabolism
    Chemical Substances Phosphates ; RNA, Catalytic ; Oxygen (S88TT14065)
    Language English
    Publishing date 2001-08-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1006/jmbi.2001.4886
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  3. Article: RNA structure, metal ions, and catalysis.

    Scott, W G

    Current opinion in chemical biology

    1999  Volume 3, Issue 6, Page(s) 705–709

    Abstract: Several new and unexpected insights into the metalloenzymology of ribozymes have been achieved in the past year. From a mechanistic point of view, the NMR and crystal structures of a small Pb(2+)-dependent ribozyme have been particularly revealing. ...

    Abstract Several new and unexpected insights into the metalloenzymology of ribozymes have been achieved in the past year. From a mechanistic point of view, the NMR and crystal structures of a small Pb(2+)-dependent ribozyme have been particularly revealing.
    MeSH term(s) Catalysis ; Metals/chemistry ; Metals/metabolism ; RNA, Catalytic/chemistry ; RNA, Catalytic/metabolism
    Chemical Substances Metals ; RNA, Catalytic
    Language English
    Publishing date 1999-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/s1367-5931(99)00029-0
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  4. Article: RNA catalysis.

    Scott, W G

    Current opinion in structural biology

    1998  Volume 8, Issue 6, Page(s) 720–726

    Abstract: Our understanding of the relationship between the structure of RNA and its catalytic activity has advanced significantly in the past year. These advances include time-resolved crystallographic studies on the hammerhead ribozyme, as well as new structures ...

    Abstract Our understanding of the relationship between the structure of RNA and its catalytic activity has advanced significantly in the past year. These advances include time-resolved crystallographic studies on the hammerhead ribozyme, as well as new structures of a group I intron, a lead(II)-cleavage ribozyme, a hepatitis delta virus ribozyme, and components of the spliceosome machinery and the peptidyl transferase center of the ribosome and, most significantly, the structure of the ribosome itself.
    MeSH term(s) Catalysis ; Crystallography, X-Ray ; Magnetic Resonance Spectroscopy ; Protein Conformation ; RNA Splicing ; RNA, Catalytic/chemistry ; RNA, Catalytic/metabolism
    Chemical Substances RNA, Catalytic
    Language English
    Publishing date 1998-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 0959-440X
    ISSN 0959-440X
    DOI 10.1016/s0959-440x(98)80091-2
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  5. Article: Crystallographic analyses of chemically synthesized modified hammerhead RNA sequences as a general approach toward understanding ribozyme structure and function.

    Scott, W G

    Methods in molecular biology (Clifton, N.J.)

    1997  Volume 74, Page(s) 387–391

    MeSH term(s) Crystallization ; Crystallography, X-Ray ; Methods ; Molecular Structure ; Nucleic Acid Conformation ; RNA/chemical synthesis ; RNA/chemistry ; RNA/metabolism ; RNA, Catalytic/chemical synthesis ; RNA, Catalytic/chemistry ; RNA, Catalytic/metabolism
    Chemical Substances RNA, Catalytic ; RNA (63231-63-0)
    Language English
    Publishing date 1997
    Publishing country United States
    Document type Journal Article
    ISSN 1064-3745
    ISSN 1064-3745
    DOI 10.1385/0-89603-389-9:387
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  6. Article: Molecular palaeontology: understanding catalytic mechanisms in the RNA world by excavating clues from a ribozyme three-dimensional structure.

    Scott, W G

    Biochemical Society transactions

    1996  Volume 24, Issue 3, Page(s) 604–608

    MeSH term(s) Base Sequence ; Catalysis ; Conserved Sequence ; Evolution, Molecular ; Models, Molecular ; Molecular Structure ; Nucleic Acid Conformation ; Paleontology ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Catalytic/metabolism
    Chemical Substances RNA, Catalytic ; RNA (63231-63-0)
    Language English
    Publishing date 1996-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 184237-7
    ISSN 1470-8752 ; 0300-5127
    ISSN (online) 1470-8752
    ISSN 0300-5127
    DOI 10.1042/bst0240604
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    Zs.A 944: Show issues Location:
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  7. Article: Food safety knowledge and practices in ready-to-eat food establishments.

    Kramer, J / Scott, W G

    International journal of environmental health research

    2004  Volume 14, Issue 5, Page(s) 343–350

    Abstract: Safe food handling in ready-to-eat food establishments is a basic element in the reduction of foodborne illness. The aim of this research was to investigate (using a questionnaire), knowledge and attitudes about food safety held by management and staff ... ...

    Abstract Safe food handling in ready-to-eat food establishments is a basic element in the reduction of foodborne illness. The aim of this research was to investigate (using a questionnaire), knowledge and attitudes about food safety held by management and staff in ready-to-eat food establishments. Fieldwork was conducted in 2002 in Wellington City, New Zealand. Managers rated 'staff with good food safety knowledge' the most important aspect of ensuring safe food. Half of these managers were prepared to pay higher wages to staff holding a current food safety certificate. Although respondents considered that closure of the establishment was the most serious business consequence of a breakdown in safe food handling, less than half (49%) were prepared to pay an additional insurance premium to cover this risk. All food handling workers should be encouraged to obtain and maintain a current food safety certificate. Environmental health officers who inspect ready-to-eat food establishments play an important role in guiding and assisting owners and staff in improving food handling standards.
    MeSH term(s) Certification ; Data Collection ; Food Contamination/prevention & control ; Food Handling ; Food Services/standards ; Health Knowledge, Attitudes, Practice ; New Zealand ; Risk Factors ; Safety
    Language English
    Publishing date 2004-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 1104887-6
    ISSN 1369-1619 ; 0960-3123
    ISSN (online) 1369-1619
    ISSN 0960-3123
    DOI 10.1080/09603120400004022
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    Zs.A 3517: Show issues Location:
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  8. Article ; Online: Features and development of Coot.

    Emsley, P / Lohkamp, B / Scott, W G / Cowtan, K

    Acta crystallographica. Section D, Biological crystallography

    2010  Volume 66, Issue Pt 4, Page(s) 486–501

    Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual ... ...

    Abstract Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
    MeSH term(s) Crystallography, X-Ray/methods ; DNA/analysis ; DNA/chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; Proteins/analysis ; Proteins/chemistry ; RNA/analysis ; RNA/chemistry ; Software Design
    Chemical Substances Proteins ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2010-03-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020492-9
    ISSN 1399-0047 ; 0907-4449
    ISSN (online) 1399-0047
    ISSN 0907-4449
    DOI 10.1107/S0907444910007493
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  9. Article: Conventional and time-resolved ribozyme X-ray crystallography.

    Scott, W G / Murray, J B

    Methods in enzymology

    2000  Volume 317, Page(s) 180–198

    MeSH term(s) Chromatography, High Pressure Liquid ; Crystallography, X-Ray ; RNA, Catalytic/chemistry ; Time Factors
    Chemical Substances RNA, Catalytic
    Language English
    Publishing date 2000
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ISSN 0076-6879
    ISSN 0076-6879
    DOI 10.1016/s0076-6879(00)17015-6
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  10. Article: Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?

    Murray, J B / Scott, W G

    Journal of molecular biology

    2000  Volume 296, Issue 1, Page(s) 33–41

    Abstract: We have constructed a model structure that we believe represents the strongest possible physically and chemically reasonable representation of a hypothesized catalytically active hammerhead ribozyme structure in which a single divalent metal ion bridges ... ...

    Abstract We have constructed a model structure that we believe represents the strongest possible physically and chemically reasonable representation of a hypothesized catalytically active hammerhead ribozyme structure in which a single divalent metal ion bridges the A9 and scissile phosphate groups. It has been proposed that such a structure arises from a conformational change in which the so-called ground-state structure (as observed by X-ray crystallography) rearranges in such a way that the pro-R oxygen atoms of both the A9 and scissile phosphate groups are directly coordinated by a single divalent metal ion in the transition-state of the hammerhead ribozyme cleavage reaction. We show that even the small subset of possible model structures that are consistent with these requirements, and that are stereochemically and sterically reasonable, are contradicted by experimental evidence. We also demonstrate that even a minimal subset of assumptions, i.e. that stems I and II are helical and that the two phosphate groups are coordinated by a divalent metal ion in the standard octahedral geometry, are sufficient to lead to this contradiction. We therefore conclude that such a mechanism of hammerhead ribozyme catalysis is untenable, at least in its present formulation.
    MeSH term(s) Base Sequence ; Binding Sites ; Catalysis ; Cations, Divalent/metabolism ; Crystallization ; Crystallography, X-Ray ; Enzyme Activation ; Manganese/metabolism ; Metals/chemistry ; Metals/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Oxygen/metabolism ; Phosphates/metabolism ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Catalytic/metabolism ; Reproducibility of Results ; Thermodynamics
    Chemical Substances Cations, Divalent ; Metals ; Phosphates ; RNA, Catalytic ; Manganese (42Z2K6ZL8P) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2000-02-11
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1006/jmbi.1999.3428
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