PMC:4331676 / 25929-27487 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4331676","sourcedb":"PMC","sourceid":"4331676","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4331676","text":"Additionally, we take protein 1AKH [PDB:1AKH] chain A as an example to show the availability of PSSM-DT based protein representation on DNA-binding protein identification. 1AKH is known as the MATa1/MATα2 homeodomain heterodimer and its chain A is the yeast mating type transcription factors (MATa1). MATa1 proteins are members of the homeodomain superfamily of DNA-binding proteins and contact the DNA with its homeodomain. It always folds into a compact three-helix domain containing a helix-turn-helix DNA-binding motif. Figure 2C lists the distributions of descriptors for the top four most discriminative pairs on the sequence of MATa1 protein. From this figure we can see that there are 5 occurrences of the proposed descriptors in the DNA-binding region and no occurrence in the non DNA-binding regions. There are totally 5 descriptors occurred in the DNA-binding region, including pair(R, R) with lg of 1, pair(R, R) with lg of 3, pair(P, R) with lg of 2, pair(P, R) with lg of 3 and pair(A, R) with lg of 1. This is further confirmed by the three dimensional structure shown in Figure 2D. As indicated by the figure, there is no descriptor for the four top most discriminative amino acid pairs that occur in the non DNA-binding regions, and all the five occurrences are within the one DNA-binding region. Furthermore, the figure showed that the pair(R, R) with lg of 1and pair(P, R) with lg of 3 are very closed to the three dimensional structure of DNA, indicating that these two descriptors are very discriminative for DNA and protein interaction.","tracks":[]}