Predicted effects of MRP1 nsSNPs examined in this study according to various in silico prediction methods
| nsSNP | SIFT/SIFTBLink Probability Scoresa | PolyPhen2 Classificationb (Score) | I-Mutant Suite “Stability”c (DDG in kcal mol−1) | Grantham Value Difference (D)d | Blosum50e | PAM250f |
|---|---|---|---|---|---|---|
| (Threshold) | (<0.05) | (>1.000) | (<−0.5; >0.5) | (>50) | (<0) | (<0) |
| C43S | 0.51/0.08 | possibly damaging (0.819) | decrease (−0.74) | 112 | −1 | 0 |
| S92F | 0.11/0.05 | possibly damaging (0.303) | neutral (−0.05) | 155 | −3 | −3 |
| NBD1-R633Q | 0.66/0.57 | benign (0.001) | decrease (−1.16) | 43 | 1 | 1 |
| NBD1-G671V | 0.00/0.02 | probably damaging (1.000) | decrease (−0.57) | 109 | −4 | −1 |
| NBD1-R723Q | 0.49/0.39 | benign(0.002) | decrease (−0.71) | 43 | 1 | 1 |
| A989T | 0.53/0.12 | benign (0.000) | decrease (−0.73) | 58 | 0 | 1 |
| C1047S | 0.07/0.64 | benign (0.001) | decrease (−0.67) | 112 | −1 | 0 |
↵a SIFT (Sorting Intolerant From Tolerant) was used by manually entering a sequence alignment comprising only human homologs of MRP1, and SIFT-BLink probability scores were obtained using 100 aligned computer-selected sequences (threshold for nontolerated substitution set at <0.05).
↵b PolyPhen2 (polymorphism phenotyping version 2) predicts the possible impact of an amino acid substitution on the structure and function of a human protein using “straightforward physical and comparative considerations.”
↵c I-mutant suite is a predictor of the effects of single-point protein mutation and gives DDG values corresponding to DG (new protein) – DG (wild-type) (kcal mol−1), where DDG < −0.5 indicates a large decrease in stability, DDG > 0.5 a large increase in stability, and −0.5 ≤ DDG ≤ 0.5 a neutral effect on stability (Capriotti et al., 2005). See http://gpcr.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi.
↵d Grantham value differences examine/reflect the difference in the physicochemical properties of the amino acid substitution, based on composition, polarity, and molecular volume. A higher Grantham score is indicative of a greater difference in chemical properties between two amino acids and can indicate a stronger (deleterious) effect on protein structure and function, with the average of the Grantham values set at 50 (Grantham, 1974).
↵e Blosum (BLOcks SUbstitution Matrix) is a substitution matrix used for sequence alignment of proteins and then for scoring alignments between evolutionarily divergent protein sequences. A positive score is given to the more likely substitutions (Henikoff and Henikoff, 1992).
↵f The PAM (Point Accepted Mutation) matrix is calculated by observing the differences in closely related proteins. PAM gives the probability of a substitution of one amino acid for another (Dayhoff et al., 1978).