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Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis,
1Department of Biology, University of California at San Diego, La Jolla 92093-0116.
Microbiological Reviews
|March 1, 1994
Summary
Computer analysis aids in understanding solute transport protein structure and evolution. This review evaluates sequence-based methods and evolutionary events, suggesting independent evolution leading to similar protein structures.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Three-dimensional structures of integral membrane proteins are scarce.
- Computational methods offer insights into protein structure, function, and evolution.
- Transport proteins are crucial for cellular processes.
Purpose of the Study:
- To review the application of computer programs for analyzing transport protein families.
- To evaluate sequence-based analyses and evolutionary events in transport proteins.
- To explore the evolutionary relationships and convergence of transport protein structures.
Main Methods:
- Review of existing computer programs for protein analysis.
- Analysis of sequence conservation and topological predictions.
- Evaluation of evolutionary mechanisms like domain shuffling and gene duplication.
Main Results:
- Sequence-based analyses provide reliable topological and localization information.
- Domain shuffling, splicing, fusion, deletion, and duplication are key evolutionary events.
- Independent evolution of transport protein families can result in similar structures (topological convergence).
Conclusions:
- Computer methods are valuable tools for studying integral membrane proteins.
- Energy coupling is likely a later evolutionary addition to solute transport.
- Convergent evolution suggests common functional or structural constraints on transport proteins.