Related Experiment Video
Updated: Jun 13, 2026
08:58
Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow
Published on: October 17, 2025
Hierarchical Design Synergizing Local Dynamics Optimization and Global Rigidification Unlocks the Catalytic Potential
Chunxiang Pu1, Tenghe Wang1, Yu Lv1
1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
Journal of Agricultural and Food Chemistry
|June 11, 2026
Summary
Enzyme engineering was improved by optimizing local dynamics and global structure. This strategy enhanced d-erythrose-4-phosphate dehydrogenase (Epd) activity and stability, boosting vitamin B6 production.
Area of Science:
- Biocatalysis and enzyme engineering
- Protein structure-function relationships
- Metabolic engineering
Background:
- Enzyme engineering faces challenges in balancing catalytic activity with structural stability.
- d-erythrose-4-phosphate dehydrogenase (Epd) is crucial for vitamin B6 biosynthesis.
- Optimizing enzyme performance requires understanding the interplay between local and global protein dynamics.
Purpose of the Study:
- To develop a hierarchical strategy for enzyme engineering by integrating local active-site dynamics optimization with global scaffold rigidification.
- To enhance the activity and stability of d-erythrose-4-phosphate dehydrogenase (Epd) using this strategy.
- To establish a generalizable framework for engineering industrial biocatalysts.
Main Methods:
- Employing evolutionary and conformational network analyses to guide enzyme engineering.
- Engineering local active-site dynamics through specific mutations (G14A/A234S).
- Implementing global scaffold rigidification via additional mutations (T31I/V17I) and validating with molecular dynamics simulations.
Main Results:
- A double mutant (G14A/A234S) showed a 3-fold increase in catalytic rate (kcat) and improved thermostability.
- A quadruple mutant (G14A/A234S/T31I/V17I) exhibited an 11.2-fold higher kcat and further enhanced thermostability.
- Molecular dynamics revealed that rigidification suppresses nonproductive fluctuations, enriching active conformations.
- Engineered Epd boosted vitamin B6 production by 3.9-fold.
Conclusions:
- A hierarchical strategy combining local dynamics optimization and global rigidification effectively enhances enzyme activity and stability.
- The developed 'inner flexibility, outer rigidity' architecture provides a powerful paradigm for biocatalyst design.
- This approach offers a generalizable framework for engineering enzymes for industrial applications, particularly in vitamin synthesis.
Related Concept Videos
01:24Other Glycolytic Pathways
The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
01:07Catalytically Perfect Enzymes
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
01:41The Supercomplexes in the Crista Membrane
The mitochondrial cristae membrane is the primary site for the oxidative phosphorylation (OXPHOS) process of energy conversion mediated through respiratory complexes I to V. These complexes have been widely studied for decades, and it has been proven that they form supramolecular structures called respiratory supercomplexes (SC). These higher-order complexes may be crucial in maintaining the biochemical structure and improving the physiological activity of the individual complexes while...
01:31ATP Energy Storage and Release
ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP and inorganic phosphate (Pi), and the free energy released during this process is lost as heat. The energy released by ATP hydrolysis is used to perform work inside the cell and depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed.
One example of energy coupling using ATP involves a...
One example of energy coupling using ATP involves a...
01:22Amplifying Signals via Enzymatic Cascade
When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze the...
01:43Electron Transport Chain: Complex III and IV
During the electron transport chain, electrons from NADH and FADH2 are first transferred to complexes I and II, respectively. These two complexes then transfer the electrons to ubiquinol, which carries them further to complex III. Complex III passes the electrons across the intermembrane space to Cyt c, which carries them further to complex IV. Complex IV donates electrons to oxygen and reduces it to water. As electrons pass through complexes I, III, and IV, the energy released aids the pumping...