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Rational Engineering of Enzyme Allosteric Regulation through SequenceEvolution Analysis
- Source :
- PLOS COMPUTATIONAL BIOLOGY(8): 7, PLoS Computational Biology, Vol 8, Iss 7, p e1002612 (2012), PLoS Computational Biology
- Publication Year :
- 2012
-
Abstract
- Control of enzyme allosteric regulation is required to drive metabolic flux toward desired levels. Although the three-dimensional (3D) structures of many enzyme-ligand complexes are available, it is still difficult to rationally engineer an allosterically regulatable enzyme without decreasing its catalytic activity. Here, we describe an effective strategy to deregulate the allosteric inhibition of enzymes based on the molecular evolution and physicochemical characteristics of allosteric ligand-binding sites. We found that allosteric sites are evolutionarily variable and comprised of more hydrophobic residues than catalytic sites. We applied our findings to design mutations in selected target residues that deregulate the allosteric activity of fructose-1,6-bisphosphatase (FBPase). Specifically, charged amino acids at less conserved positions were substituted with hydrophobic or neutral amino acids with similar sizes. The engineered proteins successfully diminished the allosteric inhibition of E. coli FBPase without affecting its catalytic efficiency. We expect that our method will aid the rational design of enzyme allosteric regulation strategies and facilitate the control of metabolic flux.<br />Author Summary Design of allosterically regulatable enzyme is essential to develop a highly efficient metabolite production. However, mutations on allosteric ligand binding sites often disrupt the catalytic activity of enzyme. To aid the design process of allosterically controllable enzymes, we develop an effective computational strategy to deregulate the allosteric inhibition of enzymes based on sequence evolution analysis of allosteric ligand-binding sites. We analyzed the molecular evolution and amino acid composition of catalytic and allosteric sites of enzymes, and discovered that allosteric sites are evolutionarily variable and comprised of more hydrophobic residues than catalytic sites. We then experimentally tested our strategy of enzyme allosteric regulation and found that the designed mutations effectively deregulated allosteric inhibition of FBPase. We believe that our method will aid the rational design of enzyme allosteric regulation and help to facilitate control of metabolic flux.
- Subjects :
- Models, Molecular
Evolutionary Processes
QH301-705.5
Allosteric regulation
Molecular Sequence Data
Evolutionary Selection
Glucose-6-Phosphate
Bioengineering
Protein Engineering
Evolution, Molecular
Cellular and Molecular Neuroscience
Enzyme activator
Engineering
Allosteric Regulation
Sequence Analysis, Protein
Catalytic Domain
Genetics
Biological Systems Engineering
Amino Acid Sequence
Biology (General)
Molecular Biology
Biology
Ecology, Evolution, Behavior and Systematics
chemistry.chemical_classification
Evolutionary Biology
Ecology
biology
Escherichia coli Proteins
Rational design
Computational Biology
Genomics
Enzyme structure
Adenosine Monophosphate
Amino acid
Fructose-Bisphosphatase
Enzyme
Computational Theory and Mathematics
chemistry
Allosteric enzyme
Biochemistry
Modeling and Simulation
Mutation
biology.protein
Structural Genomics
Synthetic Biology
Flux (metabolism)
Hydrophobic and Hydrophilic Interactions
Research Article
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- PLOS COMPUTATIONAL BIOLOGY(8): 7, PLoS Computational Biology, Vol 8, Iss 7, p e1002612 (2012), PLoS Computational Biology
- Accession number :
- edsair.doi.dedup.....d9ba839bf554e3ca2c58e44e03513ce0