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Solitons and collapse in the lambda-repressor protein
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, no 2, 021923- p.Article in journal (Refereed) Published
Abstract [en]

The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding lambda-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability, and folding pathways of the lambda-repressor protein, which controls the transition from the lysogenic to the lytic state. We first investigate the supersecondary helix-loop helix composition of its backbone. We use a discrete Frenet framing to resolve the backbone spectrum in terms of bond and torsion angles. Instead of four, there appears to be seven individual loops. We model the putative loops using an explicit soliton Ansatz. It is based on the standard soliton profile of the continuum nonlinear Schrodinger equation. The accuracy of the Ansatz far exceeds the B-factor fluctuation distance accuracy of the experimentally determined protein configuration. We then investigate the folding pathways and dynamics of the lambda-repressor protein. We introduce a coarse-grained energy function to model the backbone in terms of the C-alpha atoms and the side chains in terms of the relative orientation of the C-beta atoms. We describe the folding dynamics in terms of relaxation dynamics and find that the folded configuration can be reached from a very generic initial configuration. We conclude that folding is dominated by the temporal ordering of soliton formation. In particular, the third soliton should appear before the first and second. Otherwise, the DNA binding turn does not acquire its correct structure. We confirm the stability of the folded configuration by repeated heating and cooling simulations.

Place, publisher, year, edition, pages
2012. Vol. 86, no 2, 021923- p.
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Physical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-182527DOI: 10.1103/PhysRevE.86.021923ISI: 000308132900001OAI: oai:DiVA.org:uu-182527DiVA: diva2:560289
Available from: 2012-10-12 Created: 2012-10-11 Last updated: 2017-12-07Bibliographically approved

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Krokhotin, AndreyLundgren, MartinNiemi, Antti J.

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