Abstract
The aromatic di-alanine repeat is a novel 12-amino acid-long motif constituting alternate small and large hydrophobic residues that mediate the close packing of alpha-helices. A hidden Markov model profile was constructed from the motifs initially described in Soluble N-ethyl maleimide-sensitive factor attachment proteins (SNAP), a family of soluble proteins involved in intracellular membrane fusion. Scanning different sets of protein sequences showed unambiguously that this profile defines a structural motif independent of the tetratrico peptide repeat, another widespread alpha-helical motif. In addition to SNAP, aromatic di-alanine repeats are found in selective LIM homeodomain binding proteins (SLB) and in proteins from the Pyrococcus and Archaeoglobus prokaryotes.
Copyright 2001 Wiley-Liss, Inc.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Alanine / chemistry*
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Alanine / metabolism*
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Amino Acid Motifs
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Amino Acid Sequence
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Carrier Proteins / chemistry*
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Carrier Proteins / metabolism
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Computer Simulation
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Crystallography, X-Ray
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Databases, Factual
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Expressed Sequence Tags
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Markov Chains
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Membrane Proteins / chemistry*
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Membrane Proteins / metabolism
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Models, Molecular
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Protein Structure, Secondary
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Protein Structure, Tertiary
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Repetitive Sequences, Amino Acid*
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Saccharomyces cerevisiae Proteins*
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Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins
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Vesicular Transport Proteins*
Substances
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Carrier Proteins
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Membrane Proteins
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SEC17 protein, S cerevisiae
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Saccharomyces cerevisiae Proteins
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Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins
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Vesicular Transport Proteins
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Alanine