title: Statistical analysis of intrahelical ionic interactions in alpha-helices and coiled coils.
abstract: There are many controversies concerning whether ionic interactions in alpha-helices and coiled coils actually contribute to the stabilisation and formation of these structures. Here we used a statistical approach to probe this question. We extracted unique alpha-helical and coiled coil structures from the protein database and analysed the ionic interactions between positively and negatively charged residues. The ionic interactions were categorized according to the type, spacing and order of the residues involved. Separate datasets were produced depending on the number of alpha-helices in the coiled coils and the mutual orientation of the helices. We compared the frequency of residue configurations able to form ionic interactions with their probability to form the interaction. We found a correlation between the two variables in alpha-helices, antiparallel two-stranded coiled coils and parallel two-stranded coiled coils. This indicates that some ionic interactions are indeed important for the formation and stabilisation of alpha-helices and coiled coils. We concluded that the configurations, which have simultaneously a large probability to form the ionic interaction and a frequent occurrence, are those, which have the most stabilising effect. These are the 4RE, 3ER and 4ER interactions.
authors.affiliation: The Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Storrs, CT 06269-3136, USA. markus.meier@uconn.edu
authors.forename: Markus
authors.initials: M
authors.lastname: Meier
authors.forename: Peter
authors.initials: P
authors.lastname: Burkhard
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D007477:Ions / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013223:Statistics as Topic / Q000379:methods*
chemical_list: D000596:Amino Acids; D007477:Ions