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A test of proposed rules for helix capping: Implications for protein design
Author(s) -
Sagermann Martin,
Mårtensson LarsGöran,
Baase Walter A.,
Matthews Brian W.
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.39802
Subject(s) - structural motif , sequence motif , protein folding , protein structure , motif (music) , protein design , computational biology , peptide sequence , sequence (biology) , helix turn helix , alpha helix , biology , genetics , biochemistry , physics , dna , dna binding protein , gene , acoustics , transcription factor
Abstract α‐helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative α L motif. Rose and coworkers developed stereochemical rules to identify the locations of such motifs in proteins of unknown structure based only on their amino acid sequences. To check the effectiveness of these rules, they made specific predictions regarding the structural and thermodynamic consequences of certain mutations in T4 lysozyme. We have constructed these mutants and show here that they have neither the structure nor the stability that was predicted. The results show the complexity of the protein‐folding problem. Comparison of known protein structures may show that a characteristic sequence of amino acids (a sequence motif) corresponds to a conserved structural motif. In any particular protein, however, changes in other parts of the sequence may result in a different conformation. The structure is determined by sequence as a whole, not by parts considered in isolation.