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Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing
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10.1063/1.4816633
/content/aip/journal/jcp/139/12/10.1063/1.4816633
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4816633
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Cartoon illustration of energetic components included in the modified heteropolymer freezing Hamiltonian. The model is valid only for maximally compact polymer configurations, and monomers are coarse-grained to remove fine chemical detail. Left: the Hamiltonian contains the standard monomer-monomer contact energies, ε. Right: the modified Hamiltonian now includes a bending energy penalty term, where each component penalty, ε, is proportional to the persistence length of a given chain link.

Image of FIG. 2.
FIG. 2.

Phase diagram for unmodified model for heteropolymer freezing, derived from Eqs. (13) and (14) . Sequence design introduces three distinct phases into the model: a random phase (with relevant conformations); a glassy, misfolded phase (with relevant conformations); and a target, folded phase (also with relevant conformations).

Image of FIG. 3.
FIG. 3.

Phase diagram for secondary structure-modified version of our heteropolymer freezing model (derived from Eqs. (11)–(14) ), overlaid on the phase diagram for the unmodified system. Inclusion of persistence length-based secondary structure causes both the freezing temperature, , and the folding temperature, , to increase, introducing freezing and folding “gaps” in the modified model. The larger extent of the folding gap suggests an evolutionary reason for risking misfolding at higher temperatures.

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/content/aip/journal/jcp/139/12/10.1063/1.4816633
2013-07-31
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4816633
10.1063/1.4816633
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