Continuum Secondary Structure Captures Protein Flexibility

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...

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Bibliographic Details
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
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Description
Summary: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.
ISSN:0969-2126
1878-4186
DOI:10.1016/S0969-2126(02)00700-1