Role of context in the relationship between form and function: structural plasticity of some PROSITE patterns

True positive hits of PROSITE sequence pattern are expected to have a characteristic three-dimensional structure. The combined sequence–structure attributes of PROSITE patterns can be used for function prediction of an uncharacterized protein with known primary and 3D structure, a situation that mig...

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Bibliographic Details
Published in:Biochemical and biophysical research communications 2003-06, Vol.305 (4), p.1078-1084
Main Authors: Mondal, Sukanta, Jaishankar, S.P, Ramakumar, S
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Amino Acid Sequence
Databases, Protein
Genomics
Local conformational change
Models, Molecular
Molecular Sequence Data
Molecular Structure
PROSITE pattern
Protein Conformation
Protein function
Proteins - chemistry
Proteins - physiology
Sequence Analysis, Protein
Structural genomics
Structure
Structure-Activity Relationship
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Summary:True positive hits of PROSITE sequence pattern are expected to have a characteristic three-dimensional structure. The combined sequence–structure attributes of PROSITE patterns can be used for function prediction of an uncharacterized protein with known primary and 3D structure, a situation that might arise in structural genomics projects. We have found specific examples of true hits of PROSITE patterns displaying structural plasticity by assuming significantly different local conformation, depending upon the context. Our work highlights the importance of taking into account all the known distinct conformations of PROSITE patterns, while creating a sensitive 3D template for the pattern, for use in functional annotation.
ISSN:0006-291X
1090-2104
DOI:10.1016/S0006-291X(03)00882-9