Monte Carlo simulation studies of the correlation between global size and helical structures in biopolymers

There are several secondary structures in biological macromolecules such as beta sheets, loops, and helices. The subject of the present paper is to adopt different methods of inducing certain quotas of helical regions in macromolecules and to examine how the quota of helices influences global proper...

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Veröffentlicht in:The Journal of chemical physics 2001-10, Vol.115 (13), p.6236-6242
Hauptverfasser: Zifferer, Gerhard, Hofstetter, Mark, Olaj, Oskar Friedrich
Format: Artikel
Sprache:eng
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Zusammenfassung:There are several secondary structures in biological macromolecules such as beta sheets, loops, and helices. The subject of the present paper is to adopt different methods of inducing certain quotas of helical regions in macromolecules and to examine how the quota of helices influences global properties such as the radius of gyration. Two different methods were used to produce the chains on a tetrahedral lattice; a static step-by-step method with deliberately chosen probabilities of bond vectors in order to favor helices, and a dynamic method with intrachain potentials which induced the formation of helices, the latter approach being a simple model of self organization. Comparison of the results of the different methods revealed correspondence in many points but—not unexpectedly—also some differences, because of the use of different effective potentials in the polymer formation processes.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.1398589