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

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 1):031921. doi: 10.1103/PhysRevE.73.031921. Epub 2006 Mar 22.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Simulation
  • Hydrogen Bonding
  • Models, Chemical*
  • Models, Molecular*
  • Nanotubes / chemistry*
  • Nanotubes / ultrastructure*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Stereoisomerism


  • Proteins