Geometry of proteins: hydrogen bonding, sterics, and marginally compact tubes

The functionality of proteins is governed by their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for...

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Published inPhysical review. E, Statistical, nonlinear, and soft matter physics Vol. 73; no. 3 Pt 1; p. 031921
Main Authors Banavar, Jayanth R, Cieplak, Marek, Flammini, Alessandro, Hoang, Trinh X, Kamien, Randall D, Lezon, Timothy, Marenduzzo, Davide, Maritan, Amos, Seno, Flavio, Snir, Yehuda, Trovato, Antonio
Format Journal Article
LanguageEnglish
Published United States 01.03.2006
Subjects
Computer Simulation
Hydrogen Bonding
Models, Chemical
Models, Molecular
Nanotubes - chemistry
Nanotubes - ultrastructure
Protein Conformation
Proteins - chemistry
Proteins - ultrastructure
Stereoisomerism
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Summary:The functionality of proteins is governed by their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube barely subject to compaction provides a unified framework for understanding the common character of globular proteins. We argue that a recent critique of the tube idea is not well founded.
ISSN:1539-3755
DOI:10.1103/PhysRevE.73.031921