The preference of the in situ crosstalk among tyrosine….docVIP

Supplemental materials Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues Zhicheng Pan1,?, Zexian Liu1,?, Han Cheng1, Tianshun Gao1, Shahid Ullah1, Jian Ren2, and Yu Xue1,* 1Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China 3State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China *To whom correspondence may be addressed. Yu Xue, Tel: +86-27 Fax: +86-27 E-mail: xueyu@hust.edu.cn.Supplemental experimental procedures The algorithm of GPS-TSP For the prediction of sulfation sites, we used the self-developed GPS 2.2 algorithm (1), which contains two computational parts including a scoring strategy and performance improvement. The basic hypothesis of the scoring strategy is that similarly short peptides would exhibit similar 3D structures and biochemical properties (1, 2). First, we defined sulfation site peptide SSP(m, n) as a tyrosine amino acid flanked by m residues upstream and n residues downstream. Then we used the amino acid substitution matrix BLOSUM62 to estimate the similarity between two SSP(m, n) peptides A and B as: Score(A[i], B[i]) denotes the substitution score of the two amino acids of A[i] and B[i] in the BLOSUM62 at the position i. If S(A, B) 0, we redefined it as S(A, B) = 0. A given SSP(m, n) is then compared with each of the experimentally verified sulfated peptides in a pairwise manner to calculate the similarity scores. The average value of the similarity scores is regarded as the final score. The performance improvement procedure comprises three steps, including motif length selection, weight training and matrix mutation. 1) Motif length selection. To optimize the length of the sequence window for prediction, the combinations of SSP(m, n) (m = 1, …, 30; n = 1, …, 30) were ex