Topological solitons and folded proteins
2010 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 82, no 1, 011916- p.Article in journal (Refereed) Published
We argue that protein loops can be described by topological domain-wall solitons that interpolate between ground states which are the alpha helices and beta strands. We present an energy function that realizes loops as soliton solutions to its equation of motion, and apply these solitons to model a number of biologically active proteins including 1VII, 2RB8, and 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to numerically construct soliton solutions that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 1.0 angstrom or less for the central alpha-carbons, i.e., close to the limits of current experimental accuracy.
Place, publisher, year, edition, pages
2010. Vol. 82, no 1, 011916- p.
IdentifiersURN: urn:nbn:se:uu:diva-135760DOI: 10.1103/PhysRevE.82.011916ISI: 000280175700006OAI: oai:DiVA.org:uu-135760DiVA: diva2:375587