Comprehensive folding variations for protein folding

Abstract

The revelation of protein folding is a challenging subject in both discovery and description. Except for acquirement of accurate 3D structure in protein stable state, another big hurdle is how to discover structural flexibility for protein innate character. Even if a huge number of flexible conformations are known, difficulty is how to represent these conformations. A novel approach, protein structure fingerprint, has been developed to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. The backbone of five amino acid residues was identified as a universal folden, and then a set of Protein Folding Shape Code (PFSC) was derived for completely covering folding space in alphabetic description. Sequentially, a database was created to collect all possible folding shapes of local folding variations for all permutation of five amino acids. Successively, Protein Folding Variation Matrix (PFVM) assembled all possible local folding variations along sequence for a protein, which possesses several prominent features. First, it showed the fluctuation with certain folding patterns along sequence which revealed how the protein folding was related the order of amino acids in sequence. Second, all folding variations for an entire protein can be simultaneously apprehended at a glance within PFVM. Third, all conformations can be determined by local folding variations from PFVM, so total number of conformations is no longer ambiguous for any protein.Finally, the most possible folding conformation and its 3D structure can be acquired according PFVM for protein structure prediction. Therefore, the protein structure fingerprint approach provides a significant means for investigation of protein folding problem.

Impact of alternating amino acid sequences on beta-amyloid-induced neurotoxicity and neuroinflammation in Alzheimer's disease

“…In our study, we used an algorithm approach named the protein folding-shape code (PFSC) method, which integrates geometric, morphological, and topological features to provide a comprehensive description of folding shape patterns [ 17 , 18 ]. According to the PFSC method and Protein Folding Variation Matrix (PFVM), we analyzed 42 amino acids of Aβ with certain folding patterns along the sequence, the specific number and arrangement of which played an important role in the polymerization of Aβ.…”