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Long range correlations and folding angle with applications to alpha-helical proteins
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 9, 095103- p.Article in journal (Refereed) Published
Abstract [en]

The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. Unlike particles, chains can bend, twist, and even become knotted. Thus chains might also display a much richer phase structure. Unfortunately, it is not very easy to characterize the phase of a long chain. Essentially, the only known attribute is the radius of gyration. The way how it changes when the degree of polymerization becomes different, and how it evolves when the ambient temperature and solvent properties change, is commonly used to disclose the phase. But in any finite length chain there are corrections to scaling that complicate the detailed analysis of the phase structure. Here we introduce a quantity that we call the folding angle to identify and scrutinize the phase structure, as a complement to the radius of gyration. We argue for a mean-field level relationship between the folding angle and the scaling exponent in the radius of gyration. We then estimate the value of the folding angle in the case of crystallographic a-helical protein structures in the Protein Data Bank. We also show how the experimental value of the folding angle can be obtained computationally, using a semiclassical Born-Oppenheimer description of alpha-helical chiral chains. (C) 2014 AIP Publishing LLC.

Place, publisher, year, edition, pages
2014. Vol. 140, no 9, 095103- p.
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-224469DOI: 10.1063/1.4865933ISI: 000334067400040OAI: oai:DiVA.org:uu-224469DiVA: diva2:717426
Available from: 2014-05-15 Created: 2014-05-13 Last updated: 2017-12-05Bibliographically approved

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Niemi, Antti J.

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