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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures
András Szilágyi1, Yang Zhang, Péter Závodszky
1Institute of Enzymology, Hungarian Academy of Sciences, Karolina út 29, H-1113 Budapest, Hungary.
Journal of Molecular Biology
|November 15, 2011
Summary
New protein architectures evolve through segment swapping between similar domains. This process, identified in 32 segment-swapped proteins (SSPs), offers insights into protein evolution and function.
Area of Science:
- Structural biology
- Protein evolution
- Bioinformatics
Background:
- Multidomain proteins evolve via domain concatenation.
- Structural domains can consist of multiple chain segments.
- Novel evolutionary mechanisms for protein architecture are actively researched.
Purpose of the Study:
- To investigate the evolution of multidomain proteins through 3D segment swapping.
- To identify and characterize segment-swapped proteins (SSPs) in the Protein Data Bank (PDB).
- To elucidate the evolutionary mechanisms and functional implications of segment swapping.
Main Methods:
- Comprehensive structural search of the PDB.
- Identification of 32 well-defined segment-swapped proteins (SSPs).
- Large-scale comparative analyses using structural alignment and hidden Markov model methods.
Main Results:
- Identified 32 SSPs across 18 structural families.
- Estimated that nearly 13% of multidomain proteins may have segment-swapped precursors.
- Found that domain swapping and fusion (DSF) is the predominant evolutionary mechanism, with circular permutation (CP) being less common.
- Segment swapping imparts directed flexibility and contributes to new protein functions.
Conclusions:
- Inter-domain segment swapping is a novel mechanism for generating new protein folds and multidomain architectures.
- SSPs possess unique structural and functional properties warranting their classification as a distinct group.
- Segment swapping plays a significant role in protein evolutionary innovation.
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