Continuum Secondary Structure Captures Protein Flexibility

• Published in: Structure (London) 2002-02, Vol.10 (2), p.175-184
• Main Authors: Andersen, Claus A.F., Palmer, Arthur G., Brunak, Søren, Rost, Burkhard
• Format: Article
• Language: English
• Subjects: Computer Systems; evaluation; Hydrogen Bonding; Internet; Models, Molecular; Motion; NMR spectroscopy; Nuclear Magnetic Resonance, Biomolecular; Pliability; protein function; protein motion; protein secondary structure assignment; protein structure prediction; Protein Structure, Secondary; Proteins - chemistry; Proteins - metabolism; Software; structure comparison; Structure-Activity Relationship; Thermodynamics
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/S0969-2126(02)00700-1

The DSSP program assigns protein secondary structure to one of eight states. This discrete assignment cannot describe the continuum of thermal fluctuations. Hence, a continuous assignment is proposed. Technically, the continuum results from averaging over ten discrete DSSP assignments with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully reflected the structural variations observed between all NMR models in the ensemble. The structural variations between NMR models were verified to correlate with thermal motion; these variations were captured by the continuous assignments. Because the continuous assignment reproduces the structural variation between many NMR models from one single model, functionally important variation can be extracted from a single X-ray structure. Thus, continuous assignments of secondary structure may affect future protein structure analysis, comparison, and prediction.