The Experts below are selected from a list of 91671 Experts worldwide ranked by ideXlab platform

Adrian J Mulholland - One of the best experts on this subject based on the ideXlab platform.

  • combined quantum mechanics molecular mechanics qm mm methods in computational Enzymology
    Biochemistry, 2013
    Co-Authors: Marc W Van Der Kamp, Adrian J Mulholland
    Abstract:

    Computational Enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in Enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications...

  • Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational Enzymology
    Biochemistry, 2013
    Co-Authors: Marc W Van Der Kamp, Adrian J Mulholland
    Abstract:

    Computational Enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in Enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications...

  • Computational Enzymology.
    Chemical communications (Cambridge England), 2010
    Co-Authors: Richard Lonsdale, Kara E Ranaghan, Adrian J Mulholland
    Abstract:

    Molecular simulations and modelling are changing the science of Enzymology. Calculations can provide detailed, atomic-level insight into the fundamental mechanisms of biological catalysts. Computational Enzymology is a rapidly developing area, and is testing theories of catalysis, challenging 'textbook' mechanisms, and identifying novel catalytic mechanisms. Increasingly, modelling is contributing directly to experimental studies of enzyme-catalysed reactions. Potential practical applications include interpretation of experimental data, catalyst design and drug development.

Marc W Van Der Kamp - One of the best experts on this subject based on the ideXlab platform.

  • combined quantum mechanics molecular mechanics qm mm methods in computational Enzymology
    Biochemistry, 2013
    Co-Authors: Marc W Van Der Kamp, Adrian J Mulholland
    Abstract:

    Computational Enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in Enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications...

  • Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational Enzymology
    Biochemistry, 2013
    Co-Authors: Marc W Van Der Kamp, Adrian J Mulholland
    Abstract:

    Computational Enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in Enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications...

Gerard D. Wright - One of the best experts on this subject based on the ideXlab platform.

  • The Genomic Enzymology of Antibiotic Resistance
    Annual review of genetics, 2010
    Co-Authors: Mariya Morar, Gerard D. Wright
    Abstract:

    The need for new antibiotic therapies is acute and growing in large part because of the emergence of drug-resistant pathogens. A vast number of resistance determinants are, however, found in nonpathogenic micro-organisms. The resistance totality in the global microbiota is the antibiotic resistome and includes not only established resistance genes but also genes that have the potential to evolve into resistance elements. We term these proto-resistance genes and hypothesize that they share common ancestry with other functional units known as housekeeping genes. Genomic Enzymology is the study of protein structure–function in light of genetic context and evolution of protein superfamilies. This concept is highly applicable to study of antibiotic resistance evolution from proto-resistance elements. In this review, we summarize some of the genomic Enzymology evidence for resistance enzymes pointing to common ancestry with genes of other metabolic functions. Genomic Enzymology plays a key role in understanding...

Brian D. Ames - One of the best experts on this subject based on the ideXlab platform.

  • Structural Enzymology of polyketide synthases.
    Methods in enzymology, 2009
    Co-Authors: Shiou-chuan Sheryl Tsai, Brian D. Ames
    Abstract:

    This chapter describes structural and associated enzymological studies of polyketide synthases, including isolated single domains and multidomain fragments. The sequence–structure–function relationship of polyketide biosynthesis, compared with homologous fatty acid synthesis, is discussed in detail. Structural Enzymology sheds light on sequence and structural motifs that are important for the precise timing, substrate recognition, enzyme catalysis, and protein–protein interactions leading to the extraordinary structural diversity of naturally occurring polyketides.

Matthew Wallenstein - One of the best experts on this subject based on the ideXlab platform.

  • Integrating genomics, transcriptomics, proteomics, and metabolomics into environmental Enzymology: the next frontier or fool's gold?
    Nature Precedings, 2011
    Co-Authors: Matthew Wallenstein
    Abstract:

    Extracellular enzymes are widely measured as indices of microbial activity, resource allocation, and substrate availability. However, interpretation of enzyme activities is hampered by a limited understanding of controls on enzyme production, turnover, and in-situ activity. In part, this is the consequence of methodological limitations, which require artificial substrates and are conducted under conditions that differ from in situ conditions. Recently, new tools have emerged that have potential to provide new insights into microbial Enzymology. Will these methods open a new frontier in Enzymology research, or will they only result in the discovery of fool’s gold? I will highlight how genomic, transcriptomic, proteomic, and metabolomic tools might be used to gain new insights into the controls on enzyme production, turnover, and in-situ activity. I will also discuss the potential for significant advancements even without the use of emerging tools. Each of these techniques offers the potential to provide new pieces to the puzzle of environmental Enzymology, but progress is most likely through a multi-faceted approach.

  • Integrating genomics, transcriptomics, proteomics, and metabolomics into environmental Enzymology: the next frontier or fool’s gold?
    Nature Precedings, 2011
    Co-Authors: Matthew Wallenstein
    Abstract:

    Extracellular enzymes are widely measured as indices of microbial activity, resource allocation, and substrate availability. However, interpretation of enzyme activities is hampered by a limited understanding of controls on enzyme production, turnover, and in-situ activity. In part, this is the consequence of methodological limitations, which require artificial substrates and are conducted under conditions that differ from in situ conditions. Recently, new tools have emerged that have potential to provide new insights into microbial Enzymology. Will these methods open a new frontier in Enzymology research, or will they only result in the discovery of fool’s gold? I will highlight how genomic, transcriptomic, proteomic, and metabolomic tools might be used to gain new insights into the controls on enzyme production, turnover, and in-situ activity. I will also discuss the potential for significant advancements even without the use of emerging tools. Each of these techniques offers the potential to provide new pieces to the puzzle of environmental Enzymology, but progress is most likely through a multi-faceted approach