Related Experiment Video
Updated: Jan 22, 2026
10:58
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
17.6K
Phosphoester hydrolysis using a de novo designed protein: A combined experimental and computational study
Dona Imanga Upamadi Edirisinghe1, Prerana Dash2, Jiawen Yang3
1Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States of America.
Journal of Inorganic Biochemistry
|January 20, 2026
Summary
This study investigated how different metal ions affect the hydrolytic activity of the Due Ferri single chain (DFsc) model protein. Manganese-bound DFsc (Mn2-DFsc) demonstrated the highest catalytic efficiency, suggesting potential for designing artificial enzymes.
Area of Science:
- Biochemistry
- Enzyme kinetics
- Bioinorganic chemistry
Background:
- Metallohydrolases are enzymes that utilize metal ions for substrate hydrolysis.
- Understanding metal ion influence is crucial for enzyme design and function.
Purpose of the Study:
- To investigate the impact of different metal ions (Mn-Mn and Zn-Zn) on the reactivity of a model protein, Due Ferri single chain (DFsc).
- To elucidate the mechanism of phosphoester hydrolysis catalyzed by Mn2-DFsc.
Main Methods:
- Inductively Coupled Plasma - Optical Emission Spectrometry (ICP-OES) for metal ion quantification.
- Electron Paramagnetic Resonance (EPR) spectroscopy to analyze the electronic state of manganese ions.
- Kinetic assays to determine catalytic efficiency (kcat/Km).
- Computational modeling to propose a reaction mechanism.
Main Results:
- ICP-OES confirmed successful metal ion binding to DFsc.
- Mn2-DFsc exhibited the highest hydrolytic activity with a catalytic efficiency of 6.5 M⁻¹ min⁻¹.
- EPR analysis revealed antiferromagnetic coupling between manganese ions in Mn2-DFsc, resulting in a S=0 ground state.
Conclusions:
- A mechanism for phosphoester hydrolysis involving substrate binding to manganese and a bridging hydroxide nucleophile was proposed.
- The DFsc scaffold shows promise for developing artificial enzymes for bioremediation applications.
More Related Videos
Related Concept Videos
01:08Hydrolysis of ATP
81.1K
The bonds of adenosine triphosphate (ATP) can be broken through the addition of water, releasing one or two phosphate groups in an exergonic process called hydrolysis. This reaction liberates the energy in the bonds for use in the cell—for instance, to synthesize proteins from amino acids.
If one phosphate group is removed, a molecule of ADP—adenosine diphosphate—remains, along with inorganic phosphate. ADP can be further hydrolyzed to AMP—adenosine...
If one phosphate group is removed, a molecule of ADP—adenosine diphosphate—remains, along with inorganic phosphate. ADP can be further hydrolyzed to AMP—adenosine...
81.1K
01:15Hydrolysis
121.6K
Overview
Hydrolysis is a chemical reaction in which the addition of water breaks down a polymer into its simpler monomer units. For example, peptides break into amino acids, carbohydrates into simple sugars, and DNA into nucleotides. Enzymes often facilitate these processes.
Hydrolysis Reverses Dehydration Synthesis
Complex carbohydrates can be broken down by breaking the bonds between individual sugar units. The reaction breaks a glycosidic bond as water is added to the compound. The...
Hydrolysis is a chemical reaction in which the addition of water breaks down a polymer into its simpler monomer units. For example, peptides break into amino acids, carbohydrates into simple sugars, and DNA into nucleotides. Enzymes often facilitate these processes.
Hydrolysis Reverses Dehydration Synthesis
Complex carbohydrates can be broken down by breaking the bonds between individual sugar units. The reaction breaks a glycosidic bond as water is added to the compound. The...
121.6K
01:16Experimental Designs
16.7K
An experimental design is a systematic process that allows researchers to evaluate the relationship between dependent and independent variables. There are three widely used types of experimental design - pre-experimental design, true experimental design, and quasi-experimental design. In pre-experimental design, the researcher compares the data before and after some interventions or treatments. The true-experimental design has more than one purposefully created group, a commonly measured...
16.7K
01:20Bioequivalence Experimental Study Designs: Completely Randomized and Randomized Block Designs
241
Body:Bioequivalence experimental study designs are crucial methodologies used in evaluating and comparing the bioavailability of different drug products. These designs are categorized into various types: completely randomized, randomized block, repeated measures, cross and carry-over, and Latin square designs.Completely randomized designs involve randomly allocating treatments to all subjects participating in the experiment. This allocation is achieved by assigning unique random numbers to...
241
01:25Design Example: Traverse Angle Computations
311
Traverse angle computations are a critical component of surveying, used to compute the internal angles within a closed traverse. A traverse consists of a series of connected lines forming a closed loop, often used for land boundary delineation or mapping. Calculating the internal angles ensures accuracy in the traverse geometry and is essential for checking survey data integrity.The process begins with known azimuths and bearings of the traverse sides. Internal angles at each vertex are...
311
01:15Bioequivalence Experimental Study Designs: Repeated Measures, Cross-Over, Carry-Over, and Latin Square Designs
194
Body:Bioequivalence experimental study designs play a pivotal role in testing the effectiveness of various treatments. Key among these are the repeated measures, cross-over, carry-over, and Latin square designs. In the repeated measures design, each subject receives all treatments, allowing for temporal comparisons. This type of design is useful in reducing variability but requires careful planning to avoid bias.The cross-over design, an economical method, involves sequential administration of...
194