Folding in a semi-flexible lattice model for Crambin

Using the Replica-Exchange Wang-Landau sampling method, we investigated and compared three different coarse-grained lattice protein models for the small, hydrophobic protein Crambin. We show that slight extensions of the HP lattice protein model, including the stiffness of bonds can lead to a signif...

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Published inJournal of physics. Conference series Vol. 686; no. 1; pp. 12001 - 12007
Main Authors Shi, Guangjie, Farris, Alfred C.K., Wüst, Thomas, Landau, David P.
Format Journal Article
LanguageEnglish
Published Bristol IOP Publishing 01.01.2016
Subjects
Physics
Proteins
Stiffness
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Abstract Using the Replica-Exchange Wang-Landau sampling method, we investigated and compared three different coarse-grained lattice protein models for the small, hydrophobic protein Crambin. We show that slight extensions of the HP lattice protein model, including the stiffness of bonds can lead to a significant decrease in ground-state degeneracies (up to 5 orders of magnitudes). Moreover, the ground-state structures begin to bear resemblance to native structures observed in real Crambin.
AbstractList Using the Replica-Exchange Wang-Landau sampling method, we investigated and compared three different coarse-grained lattice protein models for the small, hydrophobic protein Crambin. We show that slight extensions of the HP lattice protein model, including the stiffness of bonds can lead to a significant decrease in ground-state degeneracies (up to 5 orders of magnitudes). Moreover, the ground-state structures begin to bear resemblance to native structures observed in real Crambin.
Author Shi, Guangjie
Wüst, Thomas
Landau, David P.
Farris, Alfred C.K.
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