Synthetic Biology and Applied Biocatalysis

Beilstein Enzymology Symposium 2021

September 21 – 23, 2021

Online

This symposium took place online and brought together experts from biochemistry, biocatalysis, enzymology as well as from systems and synthetic biology.

 

Scientific Committee:

Jürgen Pleiss / University of Stuttgart
Roland Wohlgemuth / Lodz University of Technology
Ming-Daw Tsai / Academia Sinica, Taipei
Carsten Kettner / Beilstein-Institut

Topics

  • artificial biological systems
  • miniaturized bioreactors
  • high-throughput applied catalysis
  • insights in enzyme activities (using cryo EM and other techniques)
  • regulation and control of information transfer
  • systems biology and metabolic pathway analysis
  • computational biology

Overview

At a first glance, synthetic biology and applied biocatalysis do not seem to have much in common as they are considered two different research areas in biochemistry and molecular biology.

Synthetic biology studies the origin and development of minimal systems that comprise of the full cell machinery to maintain proliferation and metabolic pathways and looks for enhanced characteristics and traits through the design of chemically synthesized DNA. In addition, it aims at creating new building blocks for the assembly of larger synthetic biological circuits, new biological systems such as tissues or even organs as well as biological machines which are macromolecular components that carry out mechanical movement on a nanoscale.

Applied biocatalysis investigates chemical reactions by applying enzymes engineered for highest efficiency with regards to stability, catalytic activity, selectivity and substrate specificity. The combination of computational studies and  directed evolution leads to gene libraries that allow the targeted improvement of the properties of the enzymes and the conversion of cheap educts into valuable products. Process intensification by applying cascades of improved enzymes under optimized reaction conditions enables the upscaling from laboratory scale to industrial large scale.

However, a closer look reveals that synthetic biology and applied biocatalysis, as multidisciplinary fields of research, do have a lot in common. Here, engineering is key; engineering of enzymes that require a minimum of both chemical energy and building blocks to be assembled to catalyse chemical reactions in one or multiple steps under non-physiological conditions. Synthetic biology involves designing and redesigning biological systems for useful purposes by engineering them to have new abilities.

The Beilstein Enzymology Symposia embrace structural, computational, and biological disciplines, and bring established and young researchers  together to discuss the many and diverse roles of enzymes in biology, and to explore the limits and challenges of holistic studies that attempt to integrate microscopic views of protein function into complex biological behaviour.

This symposium takes synthetic biology and applied biocatalysis in perspective and addresses the insights in artificial biological systems, miniaturized bioreactors, high-throughput applied catalysis, structure-function relationships using cryo-EM and computational biology , the regulation and control of gene coded information transfer , and systems-wide analysis of metabolic pathways.

Under the guidance of the STRENDA Commission (www.beilstein-strenda.org), this conference series also provides a platform to present the results of this working group’s efforts, to discuss about the requirements for setting up standards in biochemistry and to address the needs making research data findable, accessible, interoperable and reusable. The mission of STRENDA is to establish guidelines for the reliable and accurate reporting of protein function data, and to maintain a database (STRENDA DB, www.beilstein-strenda-db.org) which stores this data after its validation on completeness and compliance with the STRENDA Guidelines.

We are looking forward to committed discussions about the latest results, approaches and methodologies presented in experimental, theoretic and bioinformatics biocatalysis.


Tuesday, Sept. 21

 


9.00 (CEST)
(2.00 CDT, 3 EDT, 8.00 BST, 15.00 CST, 16.00 KST/JST)

Opening and Introductory Remarks
Carsten Kettner

Session Chair: Ming-Daw Tsai

9.20
Synthetic Metabolism: From Evolution to Design, and Back to Evolution
James C. Liao

9.50
Enzymes from Non-model Organisms and their Gene Expression with "α-helix" and "Hydropathy Contradiction" Rules
Yasuhisha Asano

10.20
Kinetics of Enzymatic De-symmetrisation of Prochiral Substrates
Peter Hallling

10.50
Multi-scale Modelling of Host-microbe Co-metabolism
Ines Thiele

11.20
Discussion and Networking Session

12.20
Poster Flash Talk Session 1
Chaired by: Ming-Daw Tsai


13.00
Break


Session Chair: Joelle N. Pelletier

15.00 (CEST)
(8.00 CDT, 9.00 EDT, 14.00 BST, 21.00 CST, 22.00 KST/JST)

Structure-guided Insight into Function, Mechanism and Evolution of Enzymes in Bacterial Glycoconjugate Synthesis
Karen N. Allen

15.30
Multiplexing Small-molecule Metabolism
Thomas S. Leyh

16.00
Biosynthesis of the Capsular Polysaccharide from Campylobacter jejuni
Frank M. Raushel

16.30
De novo Enzyme Cascades for Organic Synthesis
Sabine Flitsch

17.00
Discussion and Networking Session

18.00
Close

 


Wednesday, Sept. 22


Session Chair: Roland Wohlgemuth

9.00 (CEST)
(2.00 CDT, 3 EDT, 8.00 BST, 15.00 CST, 16.00 KST/JST)

Opening

9.10
Watching a DNA Photolyse Undergoing Photoactivation and DNA Repair by Time-resolved Serial Femtosecond X-ray Crystallography

Ming-Daw Tsai

9.40
High-resolution CryoEM of Energy-converting Membrane Protein Complexes
Werner Kühlbrandt

10.10
How do we Find New Functional Proteins in Sequence Space?
Florian Hollfelder

10.40
Deploying Directed Evolution for Synthetic Biology: Case Studies in Material and Menthol Biosynthesis
Andrew Currin

11.10
Discussion and Networking Session

12.10
Poster Flash Talk Session 2
Chaired by: Roland Wohlgemuth


12.45
Break


Session Chair: Jürgen Pleiss

15.00 (CEST)
(8.00 CDT, 9.00 EDT, 14.00 BST, 21.00 CST, 22.00 KST/JST)

Development of Biocatalytic Reactions - an Engineering Approach
Zvjezdana Findrik Blazevic

15.30
From Raspberry Flavor to Anti-cancer Drugs: Teaching Nature's Catalysts New Tricks
Joelle N. Pelletier

16.00
Kinetic Modelling of Beta-lactam Synthesizing Enzymes
Andreas S. Bommarius

16.30
DNA-dynamics-driven Mutagenesis: How DNA Directs its own Copying Errors
Hashim Murthada Al-Hashimi

17.00
Time Travel to the Past and Future - Evolution of Energy Landscapes for Enzyme Catalysis
Dorothee Kern

17.30
Discussion and Networking Session

18.30
Close


Thursday, Sept. 23


Session Chair: Zvjezdana Findrik Blazevic

9.00 (CEST)
(2.00 CDT, 3 EDT, 8.00 BST, 15.00 CST, 16.00 KST/JST)

Opening

9.10
Oxidoreducatases for Isoflavonoid Bioconversion
Byung-Gee Kim

9.40
Photoenzymatic Decarboxylation Reactions - Scope and (Current) Limitations
Frank Hollmann

10.10
Reaction Engineering Challenges with Oxidases
John M. Woodley

10.40
Applications of Systems Biocatalysis for the Synthesis of Metabolites
Roland Wohlgemuth

11.10
Discussion and Networking Session


12.15
Break


Session Chair: Andreas Bommarius

15.00 (CEST)
(8.00 CDT, 9.00 EDT, 14.00 BST, 21.00 CST, 22.00 KST/JST)

The Imprecise Reproducibility of the Michaelis Constant Measurements in Enzyme Kinetics
Santiago Schnell

15.30
Integrating Knowledge on Enzymes and Analysis Tools
Maria-Jesus Martin

16.00
The EnzymeML Toolbox: F.A.I.R. Management and Modelling of Enzymatic Data
Jürgen Pleiss

16.30
Discussion and Networking Session

17.30
Conclusions and close

 

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