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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Stylus: a system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional
Douglas D Axe1, Brendan W Dixon, Philip Lu
1Biologic Institute, Redmond, Washington, United States of America. daxe@biologicinstitute.org
Plos One
|June 5, 2008
Summary
This study introduces a novel protein evolution model using written language characters as a proxy for biological function. The developed software, Stylus, simulates protein evolution, offering a life-like system for biological comparisons.
Area of Science:
- Computational Biology
- Evolutionary Modeling
- Bioinformatics
Background:
- Protein evolution studies are complex due to vast sequence/structure space and intricate sequence-structure-function relationships.
- Existing lattice models for protein folding lack direct incorporation of biological function, using arbitrary structural criteria instead.
- There is a need for protein-like models that incorporate real structure-function relationships to accurately study evolution.
Purpose of the Study:
- To develop a novel protein-like model based on real structure-function relationships.
- To introduce open-source software (Stylus) for implementing this model.
- To demonstrate the model's utility in simulating protein evolution and generating homologous sequences.
Main Methods:
- A vector-world model was created, using Chinese characters as a basis for structure and written language meaning for function.
- Twenty coplanar vectors, encoded by base triplets, represent amino acids in forming character structures.
- The Stylus software was developed for Unix systems to implement and simulate this vector-world model.
Main Results:
- The vector-world model successfully captures key aspects of real proteins, including sequence, structure (secondary, tertiary, quaternary), genetic code, and functional complexity.
- Generated homologous vector proteins through simulated evolution exhibited sequence and structure divergence comparable to natural homologues.
- The Stylus software provides a full-featured implementation for exploring this model.
Conclusions:
- The developed model and Stylus software offer a life-like system for studying protein evolution by integrating real structure-function principles.
- This approach provides a valuable complement to experimental studies, enabling informative comparisons with biological systems.
- The model's ability to mimic evolutionary divergence suggests its potential for advancing our understanding of protein evolution.
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