Beta-sandwich – beta-barrel transformation may serve as a model of a conversion of 'normal' soluble proteins into amyloid aggregates
by Praveen K. Chandrasekharan, Alexander E. Kister, James C. Phillips
International Journal of Medical Engineering and Informatics (IJMEI), Vol. 1, No. 4, 2009

Abstract: Many data suggest that specific sequence characteristics affect the ability to form amyloid fibrils. To pinpoint that structural variation in amino acids are responsible for transforming normal soluble proteins to insoluble amyloid aggregates, we propose that this process is similar to the interconversion of two types of beta proteins – sandwich proteins (SP) and barrel proteins (BP). We determine and compare conserved residues, which are common to SP and BP, which we call structural determinants of SP and BP. Common methods of sequence alignment for identification of conserved residues cannot be applied here because analysed sequences are very diverse. To uncover structural determinants, a new method of structural-based sequence alignment was applied, which allows comparing sequences with very low sequence similarity, but similar 3D structures. For analysis and comparison of structural determinants of BP and SP, a recently suggested scale of hydrophobicity was used. It allowed us to reveal delicate sequence features, which distinguish SP and BP and are likely responsible for amyloid aggregation.

Online publication date: Fri, 26-Jun-2009

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