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Updated: Jul 13, 2026

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions
Published on: October 21, 2016
Evolution of function in the "two dinucleotide binding domains" flavoproteins
Sunil Ojha1, Elaine C Meng, Patricia C Babbitt
1Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, USA.
The conserved structure of cofactors in flavoproteins (tDBDF) dictates electron flow and protein interactions, driving functional evolution. This structural constraint enables diverse protein partners to bind, leading to new molecular functions.
Area of Science:
- Biochemistry
- Structural Biology
- Evolutionary Biology
Background:
- Proteins evolve at different rates, with conserved motifs revealing function.
- Flavoproteins with two dinucleotide binding domains (tDBDF) catalyze redox reactions via hydride transfer.
- Cofactor binding influences protein evolution and functional diversification.
Purpose of the Study:
- To investigate how cofactors constrain the evolution of new functions in the tDBDF flavoprotein superfamily.
- To analyze the structural and functional implications of cofactor configuration on enzyme evolution.
Main Methods:
- Sequence and structural analysis of over 1,600 tDBDF members.
- Comparative analysis of conserved cofactor configurations and amino acid interactions.
- Structural superposition to identify conserved protein-protein interaction faces.
Main Results:
- Cofactors adopt a conserved configuration for stereospecific hydride transfer across divergent tDBDF families.
- This conserved configuration restricts electron flow directionality (re-side to si-side).
- Directional electron flow constrains partner protein interactions to a specific face, aligning electron acceptors.
Conclusions:
- Conserved cofactor interactions in tDBDFs establish a foundation for functional evolution.
- Structural constraints on cofactor binding dictate conserved reaction mechanisms and protein interaction modes.
- Diversification of function arises from recruitment of diverse electron acceptors by conserved structural frameworks.
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