STRENDA DB: enabling the validation and sharing of enzyme kinetics data

Swainston, Neil; Baici, Antonio; Bakker, Barbara M.; Cornish‐Bowden, Athel; Fitzpatrick, Paul F.; Halling, Peter J.; Leyh, Thomas S.; O′Donovan, Claire; Raushel, Frank M.; Reschel, Udo; Rohwer, Johann M.; Schnell, Santiago; Schomburg, Dietmar; Tipton, Keith F.; Tsai, Ming‐Daw; Westerhoff, Hans V.; Wittig, Ulrike; Wohlgemuth, Roland; Kettner, Carsten

doi:10.1111/febs.14427

Cited by 44 publications

(42 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is probably best demonstrated by the BioBrick System [62] and the multitude of standardized genetic elements that are available for the assembly of complex genetic networks. The STRENDA standard [63–64] might provide a good blue print, how enzyme data could be organized and reported by enzymologists in the future so that the synthetic biologist could better compare and evaluate different enzymes in respect to their suitability for a given pathway.…”

Section: Reviewmentioning

confidence: 99%

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

Erb¹

2019

Beilstein J. Org. Chem.

View full text Add to dashboard Cite

Biology is turning from an analytical into a synthetic discipline. This is especially apparent in the field of metabolic engineering, where the concept of synthetic metabolism has been recently developed. Compared to classical metabolic engineering efforts, synthetic metabolism aims at creating novel metabolic networks in a rational fashion from bottom-up. However, while the theoretical design of synthetic metabolic networks has made tremendous progress, the actual realization of such synthetic pathways is still lacking behind. This is mostly because of our limitations in enzyme discovery and engineering to provide the parts required to build synthetic metabolism. Here I discuss the current challenges and limitations in synthetic metabolic engineering and elucidate how modern day enzymology can help to build a synthetic metabolism of the future.

show abstract

Section: Reviewmentioning

confidence: 99%

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

Erb¹

2019

Beilstein J. Org. Chem.

View full text Add to dashboard Cite

show abstract

“…This fine quality control is crucial for the success of quantitative kinetic analysis since important mechanistic nuances "may play a subordinated role with respect to even modest mistakes in reagent handling, (...) instrumental noise and others" [48]. In line with current initiatives to improve enzymology data reporting [49,50], this new method is expected to contribute in improving the reproducibility of kinetic data, thus increasing the impact of fundamental and applied research in fields such as enzyme engineering, systems biology and drug discovery.…”

Section: Discussionmentioning

confidence: 93%

A simple linearization method unveils hidden enzymatic assay interferences

Pinto

Ripoll‐Rozada

Ramos

et al. 2019

Preprint

View full text Add to dashboard Cite

Enzymes are among the most important drug targets in the pharmaceutical industry. The bioassays used to screen enzyme modulators can be affected by unaccounted interferences such as time-dependent inactivation and inhibition effects. Using procaspase-3, caspase-3, and α-thrombin as model enzymes, we show that some of these effects are not eliminated by merely ignoring the reaction phases that follow initial-rate measurements. We thus propose a linearization method (LM) for detecting spurious changes of enzymatic activity based on the representation of progress curves in modified coordinates. This method is highly sensitive to signal readout distortions, thereby allowing rigorous selection of valid kinetic data. The method allows the detection of assay interferences even when their occurrence is not suspected a priori. By knowing the assets and liabilities of the bioassay, enzymology results can be reported with enhanced reproducibility and accuracy. Critical analysis of full progress curves is expected to help discriminating experimental artifacts from true mechanisms of enzymatic inhibition.

show abstract

“…Biotechnology, bioengineering, and the universe of enzymes contain large gold mines for developing and improving existing enzyme functions for applications as well as for discovering enzymes with novel functions. The enzymatic reaction diversity, the molecular elucidation of metabolic pathways, their information retrieval, and advanced bioinformatics tools are growing continuously and will have, undoubtedly, a major influence on the further growth of bioeconomies.…”

Section: New Value Chains and Widening Connections Between Industriesmentioning

confidence: 99%

Bioeconomy for Sustainable Development

Aguilar,

Twardowski,

Wohlgemuth

2019

Biotechnology Journal

Self Cite

128

View full text Add to dashboard Cite

Bioeconomy is an emerging paradigm under which the creation, development, and revitalization of economic systems based on a sustainable use of renewable biological resources in a balanced way is rapidly spreading globally. Bioeconomy is building bridges between biotechnology and economy as well as between science, industry, and society. Biotechnology, from its ancient origins up to the present is at the core of the scientific and innovative foundation of bioeconomy policies developed in numerous countries. The challenges and perspectives of bioeconomies are immense, from resource‐efficient large‐scale manufacturing of products such as chemicals, materials, food, pharmaceuticals, polymers, flavors, and fragrances to the production of new biomaterials and bioenergy in a sustainable and economic way for a growing world population. Key success factors for different countries working on the bioeconomy vary widely from high‐tech bioeconomies, emerging diversified or diversified bioeconomies to advanced and basic primary sector bioeconomies. Despite the large variety of bioeconomies, several common elements are identified, which are simultaneously needed altogether.

show abstract

STRENDA DB: enabling the validation and sharing of enzyme kinetics data

Cited by 44 publications

References 28 publications

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

A simple linearization method unveils hidden enzymatic assay interferences

Bioeconomy for Sustainable Development

Contact Info

Product

Resources

About