Geometry of proteins: hydrogen bonding, sterics and marginally compact tubes
Jayanth R. Banavar, Marek Cieplak, Alessandro Flammini, Trinh X. Hoang, Randall D. Kamien, Timothy Lezon, Davide Marenduzzo, Amos Maritan, Flavio Seno, Yehuda Snir, Antonio Trovato
Abstract
The functionality of proteins is related to 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.
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