Extending the PRIME model for protein aggregation to all 20 amino acids
- 8 September 2010
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 78 (14), 2950-2960
- https://doi.org/10.1002/prot.22817
Abstract
We extend PRIME, an intermediate‐resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, to the description of the geometry and energetics of peptides containing all 20 amino acid residues. The 20 amino acid side chains are classified into 14 groups according to their hydrophobicity, polarity, size, charge, and potential for side chain hydrogen bonding. The parameters for extended PRIME, called PRIME 20, include hydrogen‐bonding energies, side chain interaction range and energy, and excluded volume. The parameters are obtained by applying a perceptron‐learning algorithm and a modified stochastic learning algorithm that optimizes the energy gap between 711 known native states from the PDB and decoy structures generated by gapless threading. The number of independent pair interaction parameters is chosen to be small enough to be physically meaningful yet large enough to give reasonably accurate results in discriminating decoys from native structures. The most physically meaningful results are obtained with 19 energy parameters. Proteins 2010.Keywords
Funding Information
- National Institutes of Health, USA (GM56766, EB006006)
- National Creative Research Initiatives (Center for Proteome Biophysics) of National Research Foundation/Ministry of Education, Science and Technology, Korea (2008-0061984)
This publication has 72 references indexed in Scilit:
- CHARMM: The biomolecular simulation programJournal of Computational Chemistry, 2009
- Protein aggregation in silicoTrends in Biotechnology, 2007
- Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanismProceedings of the National Academy of Sciences of the United States of America, 2007
- Structure of the cross-β spine of amyloid-like fibrilsNature, 2005
- Inferring ideal amino acid interaction forms from statistical protein contact potentialsProteins-Structure Function and Bioinformatics, 2005
- Protein folding and misfoldingNature, 2003
- Statistical potentials for fold assessmentProtein Science, 2002
- Are proteins ideal mixtures of amino acids? Analysis of energy parameter setsProtein Science, 1995
- A new approach to protein fold recognitionNature, 1992
- Selection of representative protein data setsProtein Science, 1992