Study Of The Relationship Between Sequence And Structure In The Beta-propeller Fold Proteins

It is widely accepted that the tertiary structure of the protein is determined by its amino acid sequence after Afinsin's experiments. However, it is still not very clear that to what extent and how does this accepted mechanism operate in proteins. It is known from sequence alignment that if two proteins have more than 30% identical amino acids, they likely have similar tertiary structures. The same rule may hold for the subsequence alignment in a protein sequence, i.e., as long as two subsequences have certain number of identical amino acids, they likely have similar local tertiary structures. So our work is to find the hidden information in the sequence which determines the symmetry of structure. We choose beta-propeller fold proteins as our study object. Our work can be summarized as below:Firstly, we use our method analysis the propeller fold proteins. In order to eliminate the influence of random noise, we use p as 0.05, which are considered significant. We found some similar subsequences but it is not very clear.Secondly, we furthered used Pearson correlation analysis based similar sub matrices. This method can give not only the symmetry of sequence but also the clear boundary between them. We compared with RADAR and TRUST. The results showed that our method is useful in finding the symmetry of sequences. Our result may help to solve the sequence-structure relationship of proteins and would provide further evidences to the duplication mechanism of protein evolution.Thirdly, as we transformed the protein sequence into NP patterns according the propensity of forming strand during the course of alignment, we discussed the random property of NP sequence. We also computed the key residues of structure through all-atom interaction energy.