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A fast method to sample real protein conformational space
1Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Proteins
|March 29, 2000
Summary
A new computer program, FOLDTRAJ, efficiently generates random protein structures. It overcomes computational challenges, producing valid protein models with realistic secondary structures and conformational diversity.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Biophysics
Background:
- Generating accurate random protein structures is crucial for understanding protein folding and function.
- Traditional build-up methods face computational challenges, including N-body scaling and exponential backtracking problems.
Purpose of the Study:
- To report a novel, fast computer program, FOLDTRAJ, for generating plausible random protein structures.
- To address and solve the computational limitations of existing protein structure generation methods.
Main Methods:
- Employs an N to C directed build-up approach with a pipelined residue addition (three residues at a time).
- Utilizes a multiway binary tree to optimize bump-checking (N log N scaling) and adaptive backtracking strategies.
- Relies on geometrical properties from known structures and Van der Waals radii, independent of energy potentials.
Main Results:
- FOLDTRAJ generates chirally and physically valid protein structures, confirmed by WHAT-CHECK.
- Generated random structures exhibit typical alpha-helical (5-15%) and beta-strand (approx. 20%) content.
- Ensembles of structures effectively sample conformational space and compare favorably with polymer theory and FRET data.
Conclusions:
- FOLDTRAJ offers an efficient and robust method for generating diverse and valid random protein structures.
- The program demonstrates capability in protein reconstruction, achieving low RMSD compared to existing methods.
- This tool advances computational approaches to protein structure prediction and analysis.