Predicting alternate structure attainment and amyloidogenesis: a nonlinear signal analysis approach

Chain hydrophobicity values have been used in prediction of alternate structure attainment by a polypeptide. Nonlinear signal analysis on the hydrophobicity values gives important clues about the propensities of particular stretches of a protein to form local or nonlocal contacts. These contacts determine the folding behavior of a polypeptide and helps in predicting the final structure that can be attained. A nonlinear signal analysis called the recurrent quantification analysis has been carried out using the hydrophobicity values on a wide range of proteins obtained from human, plant, and fungal sources. Here, we show that such an analysis gives us an easy handle in determining sequences within the proteins that may be important in beta-sheet formation leading to amyloidosis.