Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family

Michal Brylinski, Uniwersytet Jagielloński Collegium Medicum
Leszek Konieczny, Uniwersytet Jagielloński Collegium Medicum
Andrzej Kononowicz, Uniwersytet Jagielloński Collegium Medicum
Irena Roterman, Uniwersytet Jagielloński Collegium Medicum


The well-known procedure implemented in ClustalW oriented on the sequence comparison was applied to structure comparison. The consensus sequence as well as consensus structure has been defined for proteins belonging to serpine family. The structure of early stage intermediate was the object for similarity search. The high values of Wsequence appeared to be accordant with high values of Wstructure making possible structure comparison using common criteria for sequence and structure comparison. Since the early stage structural form has been created according to limited conformational sub-space which does not include the β-structure (this structure is mediated by C7eq structural form), is particularly important to see, that the C7eq structural form may be treated as the seed for β-structure present in the final native structure of protein. The applicability of ClustalW procedure to structure comparison makes these two comparisons unified. © 2007 Elsevier Ltd. All rights reserved.