engleski

Novel structural attributes based on the average distances of hydrophobic amino acids improve models for predicting protein folding rates

Protein folding is a very important problem in life sciences that has been studied experimentally, but also through modelling (theoretical and simulation analyses).[1] It is assumed that all the information that determines the protein folding process and the protein folding rate is contained in the primary structure of the proteins (i.e. in the sequence of the amino acids). Modelling the protein folding constants kf (s-1), which are equal to 1 / (time required for protein folding), is a size-dependent problem, which means that ln (kf) depends on the length of the protein sequence. Here we have defined and calculated new descriptors (features) that take into account mutual arrangements of hydrophobic amino acids in the primary structure such as the average distance between amino acids. These attributes were found to have better agreement (correlation) with protein folding rates in three protein sets than protein length, relative contact order distance or other parameters calculated from the protein's primary sequence or its three-dimensional structure.

protein folding rate, prediction, model, protein secondary structure, sequence-based attributes

Basic grant of MZO/RBI to Bono Lučić