Soliton concepts and protein structure
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, Vol. 85, no 3, 031906- p.Article in journal (Refereed) Published
Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.
Place, publisher, year, edition, pages
APS , 2012. Vol. 85, no 3, 031906- p.
Research subject Theoretical Physics
IdentifiersURN: urn:nbn:se:uu:diva-196716DOI: 10.1103/PhysRevE.85.031906OAI: oai:DiVA.org:uu-196716DiVA: diva2:610847