Protein loops, solitons and side-chain visualization with applications to the left-handed helix region
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, Vol. 85, no 6, 061909- p.Article in journal (Refereed) Published
Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha helices and beta strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C-alpha atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C-beta carbons on the two-sphere. We show that the residue independent localization extends to C gamma and C-delta carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed beta turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.
Place, publisher, year, edition, pages
2012. Vol. 85, no 6, 061909- p.
Condensed Matter Physics Structural Biology
IdentifiersURN: urn:nbn:se:uu:diva-172355DOI: 10.1103/PhysRevE.85.061909ISI: 000305128000007OAI: oai:DiVA.org:uu-172355DiVA: diva2:514149