Table 1. A-site Binding Analysisa.
Position 2 | Position 1 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Positive | Polar | Negative | Aromati | Non-Polar | ||||||||||||
R | K | H | N | C | S | T | D | W | Y | F | βA | V | L | P | ||
N/A | 105 | 125 | 39 | 54 | 76 | 52 | 15 | 14 | 62 | 33 | 33 | 51 | 36 | 35 | 40 | |
Positive | R | 0 | - | 97 | 0 | 107 | 1 | 12 | 2 | 99 | 0 | 0 | 0 | 0 | 0 | 0 |
Polar | H | 107 | - | 33 | 8 | 94 | 17 | 41 | 7 | 74 | 57 | 61 | 67 | 35 | 65 | 41 |
N | 11 | - | 53 | 13 | 80 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | |
C | 103 | - | 21 | 1 | 39 | 9 | 37 | 0 | 85 | 29 | 0 | 46 | 67 | 0 | 22 | |
S | 70 | 112 | 77 | 2 | 78 | 41 | 9 | 0 | 111 | 7 | 40 | 28 | 44 | 36 | 42 | |
T | 84 | 94 | 53 | 48 | 45 | 44 | 38 | 3 | 93 | 58 | 48 | 49 | 47 | 41 | 42 | |
Negative | D | 26 | - | 17 | 0 | 59 | 2 | 3 | 0 | 49 | 9 | 6 | 9 | 6 | 4 | 1 |
Aromatic | W | 120 | - | 68 | 73 | 4 | 42 | 78 | 29 | 44 | 99 | 35 | 39 | 63 | 113 | 47 |
Y | 92 | 16 | 64 | 19 | 111 | 31 | 60 | 0 | 122 | 12 | 44 | 28 | 54 | 48 | 27 | |
F | 56 | - | 9 | 32 | 83 | 2 | 26 | 0 | 67 | 35 | 41 | 21 | 28 | 23 | 34 | |
Non-Polar | βA | 0 | - | 0 | 29 | 61 | 0 | 0 | 0 | 102 | 0 | 37 | 7 | 30 | 6 | 0 |
V | 89 | 81 | 65 | 70 | 132 | 50 | 37 | 16 | 66 | 61 | 50 | 46 | 48 | 35 | 45 | |
L | 69 | - | 58 | 14 | 29 | 49 | 41 | 0 | 116 | 24 | 26 | 47 | 16 | 40 | 44 | |
P | 90 | - | 75 | 37 | 40 | 36 | 27 | 12 | 96 | 34 | 19 | 37 | 46 | 38 | 39 | |
Color coding * = | +2 | +1 | 0 | -1 | -2 | Zwitter |
The compounds were analyzed based on the charge on individual amino acids.
The numbers are the percentage displacement of F-neo from an A-site/F-neo complex by peptidic neomycin as shown in Figure 1C for each DPA numbered compound as a function of each amino acid(s) conjugated. The third row gives the one-letter code of the amino acid on the conjugate position 1 (firstly conjugated to neomycin). The second column gives the one-letter code of the amino acid on conjugate position 2 (secondly conjugated to neomycin). Results are color coded as total charges of the amino acids on peptidic neomycin.
Total charges of the amino acids on peptidic neomycin under physiological pH. Zwitter indicates that the peptidic neomycin contains an amino acid with a positively charged side chain and an amino acid with a negatively charged side chain.