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A Search for Energy Minimized Sequences of Proteins (2009)
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@MISC{Jha09asearch,
author = {Anupam Nath Jha and G. K. Ananthasuresh and Saraswathi Vishveshwara},
title = {A Search for Energy Minimized Sequences of Proteins},
year = {2009}
}
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Abstract
In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from nonredundant protein sequence database that are similar to ours with an E-value of the order of 10-7. In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energyminimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the
Keyphrases
energy minimized sequence energy-minimizing sequence sequence space protein data bank diverse sequence edge-weighted connectivity graph different inter-residue energy matrix basic local alignment search tool target conformation efficient method minimum energy reduced amino acid alphabet energy matrix inter-residue interaction tight upper bound different consideration global energyminimizing sequence residue site continuous optimization nonredundant protein sequence database protein environment numerical evidence real protein
