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Residue coevolution reveals functionally important intramolecular interactions in formamidopyrimidine-DNA glycosylase
Anton V Endutkin1, Simeon S Koptelov2, Alexander V Popov1
1SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia.
DNA Repair
|July 23, 2018
Summary
Coevolution analysis reveals conserved polar bridges in formamidopyrimidine-DNA glycosylase (Fpg) are crucial for DNA binding and protein stability. These interactions are vital for DNA repair enzyme function.
Area of Science:
- Protein evolution
- Molecular biology
- Biochemistry
Background:
- Functionally important intramolecular interactions in proteins, like polar bridges, are often conserved during evolution.
- The formamidopyrimidine-DNA glycosylase (Fpg) is a key DNA repair enzyme.
Purpose of the Study:
- To analyze coevolution of physicochemical properties in Fpg protein residues.
- To identify and investigate the roles of conserved polar bridges in Fpg function and stability.
Main Methods:
- Coevolution analysis of amino acid residue properties.
- Site-directed mutagenesis.
- Structural and molecular dynamic modeling.
- Biochemical assays (DNA binding, thermal stability).
Main Results:
- Identified three conserved polar bridges in Fpg: Arg54-Glu131, Gln234-Arg244, and Tyr170-Ser208.
- The Arg54-Glu131 bridge is critical for DNA binding affinity.
- Mutations in Gln234-Arg244 decreased protein melting temperature, indicating a role in thermal stability.
- Tyr170 and Ser208 interactions influence Fpg binding and stability through alternative hydrogen bonding.
Conclusions:
- Coevolution analysis combined with experimental and computational methods is powerful for understanding intramolecular interactions in DNA repair enzymes.
- Conserved polar bridges play distinct roles in Fpg's DNA binding, stability, and overall function.
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