title: Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family.
abstract: 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 W(sequence) appeared to be accordant with high values of W(structure) 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 beta-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 beta-structure present in the final native structure of protein. The applicability of ClustalW procedure to structure comparison makes these two comparisons unified.
authors.affiliation: Department of Bioinformatics and Telemedicine, Collegium Medicum-Jagiellonian University, Kopernika 17, 31501 Cracow, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Brylinski
authors.forename: Leszek
authors.initials: L
authors.lastname: Konieczny
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kononowicz
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman
mesh_terms: D000818:Animals; D003198:Computer Simulation; D016384:Consensus Sequence; D017124:Conserved Sequence; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D015843:Serpins / Q000737:chemistry*
chemical_list: D015843:Serpins