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 understanding the common character of globular proteins. We argue that a recent critique of the tube idea is not well founded.
Banavar
Jayanth R
JR
Department of Physics, 104 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Cieplak
Marek
M
Flammini
Alessandro
A
Hoang
Trinh X
TX
Kamien
Randall D
RD
Lezon
Timothy
T
Marenduzzo
Davide
D
Maritan
Amos
A
Seno
Flavio
F
Snir
Yehuda
Y
Trovato
Antonio
A
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D043942:Nanotubes / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D013237:Stereoisomerism
D011506:Proteins