Abstract
Motivation The β-sheet is an element of protein secondary structure, and intra- and inter-molecular β-sheet interactions play pivotal roles in biological regulatory processes including scaffolding, transporting, and oligomerization. In nature, β-sheet formation is tightly regulated, because dysregulated β-stacking often leads to severe diseases such as Alzheimer’s, Parkinson’s, systemic amyloidosis and diabetes. Thus, the identification of intrinsic β-sheet forming propensities could provide valuable insight into protein design for the development of novel therapeutics. However, structure-based design methods may not be generally applicable to such amyloidogenic peptides mainly due to high structural plasticity and complexity. Therefore, an alternative design strategy based on complementary sequence information is of great significance.
Results We developed B-SIDER (β-Sheet Interaction DEsign for Reciprocity), a database search method for the design of complementary β-strands. The method makes use of the structural database information and generates a query-specific score matrix. The discriminatory power of the B-SIDER score function was tested on representative amyloidogenic peptide substructures against a sequence-based score matrix (PASTA2.0) and two popular ab initio protein design score functions (Rosetta and FoldX). B-SIDER was able to distinguish wild-type amyloidogenic β-strands as favored interactions in a more consistent manner than the other methods. B-SIDER is then prospectively applied to the design of complementary β-strands for the splitGFP scaffold. Three variants were identified to have stronger interactions than its original sequence selected by directed evolution, emitting higher fluorescence intensities. Our results support that B-SIDER can be applicable to the design of other β-strands, assisting in the development of therapeutics against disease-related amyloidogenic peptides.
Availability B-SIDER is freely available at http://bel.kaist.ac.kr/research/B-SIDER.