Quo vadis, enzymology?

Khosla, Chaitan

doi:10.1038/nchembio.1844

Cited by 13 publications

(19 citation statements)

References 19 publications

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“…Perhaps the clearest discussion of these underlying issues is that by Jencks, 13,14 who outlined how sequential changes in ligand-binding affinity lead to profound changes in the overall free energy of ATP hydrolysis, and recognized the necessity for understanding what he called the “coupling rules.” As the structural landscape of transducing enzymes was as yet unknown, Jencks was mute about what mechanisms actually linked conformational changes to catalysis, and this issue remains unresolved 81 . Identifying 24,40 and mutating 29 key residues associated with the conformational transition state(s), together with modular thermodynamic cycles 44 to measure energetic coupling between domains, now enhance the understanding of how idiosyncratic structural and mechanistic details implement the coupling rules.…”

Section: Resultsmentioning

confidence: 99%

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

Carter

Chandrasekaran

Weinreb

et al. 2017

Structural Dynamics

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We measured and cross-validated the energetics of networks in Bacillus stearothermophilus Tryptophanyl-tRNA synthetase (TrpRS) using both multi-mutant and modular thermodynamic cycles. Multi-dimensional combinatorial mutagenesis showed that four side chains from this “molecular switch” move coordinately with the active-site Mg2+ ion as the active site preorganizes to stabilize the transition state for amino acid activation. A modular thermodynamic cycle consisting of full-length TrpRS, its Urzyme, and the Urzyme plus each of the two domains deleted in the Urzyme gives similar energetics. These dynamic linkages, although unlikely to stabilize the transition-state directly, consign the active-site preorganization to domain motion, assuring coupled vectorial behavior.

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Section: Resultsmentioning

confidence: 99%

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

Carter

Chandrasekaran

Weinreb

et al. 2017

Structural Dynamics

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“…Various applications can be envisioned, especially those related to synthetic biology and metabolic engineering in which cells are effectively considered as units of production for valuable products of bulk and fine chemicals . In addition, characterization of enzymes within their native (cellular) environment is an important goal in the field of enzymology . Our work shows that measurements of kinetic parameters such as K M , ϵ (app) , and [E] as a function of flow for whole‐cell catalysts is feasible for microorganisms immobilized within a microfluidic chamber.…”

Section: Figurementioning

confidence: 99%

A Generalized Kinetic Framework Applied to Whole‐Cell Bioelectrocatalysis in Bioflow Reactors Clarifies Performance Enhancements for Geobacter Sulfurreducens Biofilms

et al. 2019

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A common kinetic framework for studies of whole‐cell catalysis is vital for understanding and optimizing bioflow reactors. In this work, we demonstrate the applicability of a flow‐adapted version of Michaelis‐Menten kinetics to an electrocatalytic bacterial biofilm. A three‐electrode microfluidic biofilm flow reactor measured increased turnover rates by as much as 50 % from a Geobacter sulfurreducens biofilm as flow rate was varied. Based on parameters from the applied kinetic framework, flow‐induced increases to turnover rate, catalytic efficiency and device reaction capacity could be linked to an increase in catalytic biomass. This study demonstrates that a standardized kinetic framework is critical for quantitative measurements of new living catalytic systems in flow reactors and for benchmarking against well‐studied catalytic systems such as enzymes.

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“…With node attributes and the Control Panels, SSNs viewed with Cytoscape satisfy Khosla’s vision that genomic enzymology tools “could ideally capture the essence of an enzymologist’s judgment in layers of increasing sophistication, depending on the user’s actual needs”. 5 …”

Section: Sequence Similarity Network (Ssns)mentioning

confidence: 99%

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

2017

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The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of “genomic enzymology” web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence–function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems.

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Quo vadis, enzymology?

Abstract: Enzymology has been a vital link between chemistry and biology in the second half of the 20th century. A range of emerging scientific challenges is presenting the field with exciting opportunities to continue thriving in the future.

Cited by 13 publications

References 19 publications

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

A Generalized Kinetic Framework Applied to Whole‐Cell Bioelectrocatalysis in Bioflow Reactors Clarifies Performance Enhancements for Geobacter Sulfurreducens Biofilms

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

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