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Geometric and physical considerations for realistic protein models.
Isaac A Hubner1, Eugene I Shakhnovich
1Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.
Summary
Protein secondary structure, like helices, requires both excluded volume and hydrogen bonding for formation. Geometric packing alone is insufficient for accurate biomacromolecular models.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Protein secondary structures (helices, sheets, loops) are defined by backbone geometry and hydrogen bonding.
- Recent 'tube' models propose secondary structure arises from optimal packing of cylinders.
Purpose of the Study:
- To investigate the sufficiency of geometric packing for protein secondary structure formation.
- To determine the essential factors for accurate modeling of protein secondary structures.
Main Methods:
- Atomically detailed simulations were employed.
- Analysis focused on excluded volume and hydrogen bonding interactions.
Main Results:
- Geometric packing alone is insufficient to define protein secondary structure.
- Both excluded volume and hydrogen bonding are necessary for helix formation.
Conclusions:
- Realistic biomacromolecular models must explicitly include excluded volume and hydrogen bonding.
- Current 'tube' models are inadequate for fully explaining protein secondary structure formation.