title: Using genome-wide protein sequence data to predict amino acid conservation.
abstract: For most proteins, multiple sequence alignments are a viable method to identify functionally and structurally important amino acids, but for most organisms, there is a subset of proteins that are unique or found in a few closely related organisms. For these proteins, it is not possible to produce sequence alignments that are useful in identifying functionally or structurally important amino acids. We have investigated the relationship between amino acid conservation and five factors (the amino acid's identity, N-terminal neighbor, C-terminal neighbor, the local hydropathy of surrounding amino acids, and the local expected net charge of the surrounding amino acids based on the primary sequence) in Escherichia coli proteins. For four of the factors examined (all but the amino acid's identity), there is a significant relationship with conservation for some of the standard 20 amino acids. Using the combination of all five factors, we show that it is possible to calculate a score based on the primary sequences of a subset of E. coli proteins that has statistically significant predictive value with respect to predicting conserved amino acids in other E. coli proteins and Saccharomyces cerevisiae proteins. As these five variables show significant relationships with conservation, we have termed them conservation factors.
authors.affiliation: Department of Chemistry, Rutgers University, 315 Penn St, Camden, NJ 08102-1411, USA. peterpal@crab.rutgers.edu
authors.forename: Peter
authors.initials: P
authors.lastname: Palenchar
authors.forename: Mathew
authors.initials: M
authors.lastname: Mount
authors.forename: Douglas
authors.initials: D
authors.lastname: Cusato
authors.forename: Jeffery
authors.initials: J
authors.lastname: Dougherty
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D017124:Conserved Sequence; D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D029968:Escherichia coli Proteins; D029701:Saccharomyces cerevisiae Proteins
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