TAILIEUCHUNG - Báo cáo khoa học: Protein aggregation and amyloid fibril formation prediction software from primary sequence: towards controlling the formation of bacterial inclusion bodies

Proteins might aggregate into ordered or amorphous structures, utilizing relatively short sequence stretches, usually organized in b-sheet-like assem-blies. Here, we attempt to list all available software, developed during the last decade or so, for the prediction of such aggregation-prone stretches from protein primary structure, without distinguishing whether these algo | ịFEBS Journal MINIREVIEW Protein aggregation and amyloid fibril formation prediction software from primary sequence towards controlling the formation of bacterial inclusion bodies Stavros J. Hamodrakas Department of CellBiology and Biophysics Faculty of Biology University of Athens Greece Keywords aggregation-prone amino acid stretches amyloid-fibril forming regions amyloidoses functionalamyloids prediction software Correspondence S. J. Hamodrakas Department of Cell Biology and Biophysics Faculty of Biology University of Athens Panepistimiopolis Athens 157 01 Greece Fax 30 210 727 4254 Tel 30 210 727 4931 E-mail shamodr@ Website http Received 28 January 2011 revised 18 April 2011 accepted 3 May 2011 Proteins might aggregate into ordered or amorphous structures utilizing relatively short sequence stretches usually organized in b-sheet-like assemblies. Here we attempt to list all available software developed during the last decade or so for the prediction of such aggregation-prone stretches from protein primary structure without distinguishing whether these algorithms predict amino acid sequences destined to be involved in ordered fibrillar amyloids or amorphous aggregates. The results of application of four of these programs on 23 proteins related to amyloidoses are compared. Because protein aggregation during protein production in bacterial cell factories has been shown to resemble amyloid formation the algorithms might become useful tools to improve the solubility of recombinant proteins and for screening therapeutic approaches against amyloidoses under conditions that mimic physiologically relevant environments. One such example is given. doi Background and aims Normally soluble proteins or peptides convert under certain conditions into ordered fibrillar aggregates known as amyloid deposits. The fibrils which constitute these amyloid deposits are known as amyloid fibrils and the amyloid fibrils or

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