A test of proposed rules for helix capping: Implications for protein designSagermann, M., Martensson, L.-G., Baase, W.A., Matthews, B.W.
(2002) Protein Sci. 11: 516-521
- PubMed: 11847274
- DOI: 10.1110/ps.39802
- Primary Citation of Related Structures:  1JOZ, 1LLH
- PubMed Abstract:
- Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution.
Weaver, L.H.,Matthews, B.W.
(1987) J.Mol.Biol. 193: 189
- The alpha-L Conformations at the Ends of Helices
(1980) Protein Folding --: 53
- Rules for alpha-helix termination by glycine.
Aurora, R.,Srinivasan, R.,Rose, G.D.
(1994) Science 264: 1126
alpha-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative alpha(L) motif. Rose and coworkers developed stereochemical rules ...
alpha-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative alpha(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.
Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA.