BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 4 7 3 271.31 1.98 2 4 8 4 265.63 0.82 3 5 8 3 271.63 3.81 4 5 9 4 265.12 0.56 5 6 9 3 271.12 0.50 6 6 10 4 265.06 0.54 7 6 53 47 70.84 5.11 8 6 77 71 39.43 0.46 9 6 78 72 38.05 0.23 10 6 81 75 30.64 0.29 11 7 10 3 279.00 0.38 12 7 11 4 268.70 0.71 13 7 74 67 42.19 1.08 14 8 11 3 277.41 0.41 15 8 12 4 268.18 1.02 16 9 12 3 268.17 1.02 17 9 13 4 264.83 0.38 18 10 13 3 277.70 0.90 19 10 14 4 272.55 3.48 20 10 49 39 79.15 9.11 21 10 53 43 80.16 9.61 22 10 73 63 54.48 0.65 23 10 74 64 54.47 0.65 24 10 77 67 54.41 0.64 25 11 14 3 272.62 3.44 26 11 15 4 277.61 0.95 27 11 23 12 125.55 1.26 28 11 24 13 125.52 1.27 29 11 27 16 121.48 0.44 30 11 70 59 54.54 0.66 31 11 74 63 54.48 0.65 32 12 15 3 281.32 0.91 33 12 16 4 265.97 0.07 34 13 16 3 272.41 0.36 35 13 17 4 269.06 1.61 36 13 45 32 81.01 9.38 37 13 48 35 81.12 9.45 38 14 17 3 277.93 2.79 39 14 18 4 269.06 1.61 40 14 23 9 148.97 8.32 41 14 31 17 118.61 0.10 42 14 45 31 81.17 9.44 43 14 73 59 54.56 0.64 44 15 18 3 281.91 0.81 45 15 19 4 266.16 0.16 46 15 20 5 256.81 0.32 47 15 23 8 130.36 1.12 48 15 24 9 130.18 1.06 49 16 19 3 268.23 1.19 50 17 37 20 118.20 0.07 51 17 41 24 82.01 8.99 52 17 42 25 82.02 9.00 53 17 45 28 81.96 9.05 54 18 23 5 226.75 3.12 55 18 31 13 118.76 0.06 56 18 36 18 118.27 0.04 57 20 36 16 118.87 0.03 58 21 24 3 281.75 0.42 59 22 25 3 280.56 0.18 60 22 26 4 269.76 3.61 61 22 29 7 148.17 0.10 62 22 36 14 123.95 0.29 63 23 26 3 275.75 0.61 64 23 29 6 158.80 1.15 65 23 31 8 152.34 8.13 66 23 70 47 95.84 1.93 67 26 29 3 278.24 1.01 68 26 70 44 97.08 1.76 69 27 70 43 97.08 1.76 70 27 71 44 97.06 1.75 71 27 74 47 97.08 1.76 72 28 69 41 97.16 1.72 73 28 70 42 97.16 1.73 74 29 34 5 187.37 0.23 75 29 36 7 176.71 4.11 76 29 70 41 99.58 0.57 77 30 33 3 267.87 1.94 78 30 34 4 211.06 6.32 79 30 68 38 101.23 0.47 80 30 69 39 101.14 0.43 81 31 36 5 172.88 6.03 82 31 37 6 172.84 6.04 83 31 67 36 101.61 0.64 84 31 68 37 101.54 0.61 85 31 69 38 101.53 0.61 86 31 70 39 101.45 0.57 87 31 73 42 101.53 0.61 88 32 35 3 262.24 4.50 89 32 37 5 172.88 6.03 90 32 38 6 172.88 6.04 91 32 39 7 172.88 6.04 92 32 64 32 101.73 0.68 93 32 67 35 101.66 0.67 94 32 68 36 101.64 0.67 95 37 41 4 269.25 1.04 96 37 42 5 271.25 0.36 97 39 42 3 283.06 2.62 98 39 43 4 277.05 0.38 99 40 43 3 283.06 2.63 100 40 44 4 275.33 0.48 101 41 44 3 283.06 2.63 102 41 45 4 275.31 0.48 103 42 45 3 275.31 0.50 104 42 46 4 272.36 0.95 105 42 62 20 102.77 0.75 106 42 67 25 101.81 0.65 107 43 46 3 288.03 2.43 108 43 47 4 275.72 0.81 109 44 47 3 288.03 2.43 110 44 48 4 275.72 0.81 111 45 48 3 283.49 4.70 112 45 49 4 273.43 0.36 113 45 73 28 101.93 0.58 114 46 49 3 273.43 0.36 115 46 50 4 273.43 0.35 116 46 55 9 215.73 4.13 117 46 57 11 156.88 1.44 118 46 58 12 153.58 2.71 119 46 59 13 138.02 0.43 120 47 50 3 276.96 0.20 121 47 51 4 273.43 0.36 122 48 51 3 273.44 0.36 123 48 52 4 273.43 0.35 124 48 53 5 273.12 0.20 125 49 53 4 265.22 3.75 126 49 54 5 244.74 2.19 127 49 55 6 219.69 5.99 128 49 67 18 103.28 0.72 129 49 77 28 76.98 11.85 130 50 54 4 219.66 5.98 131 50 55 5 219.62 6.00 132 50 56 6 219.62 6.00 133 51 54 3 241.66 4.85 134 53 77 24 77.02 11.88 135 53 81 28 74.42 13.13 136 55 80 25 76.20 12.21 137 57 67 10 146.93 0.81 138 58 62 4 246.12 3.00 139 58 67 9 176.13 3.52 140 59 62 3 281.86 2.14 141 62 67 5 270.51 1.82 142 63 66 3 275.45 1.89 143 63 67 4 272.93 0.62 144 64 67 3 273.05 3.09 145 64 68 4 270.51 1.82 146 65 68 3 273.95 0.12 147 65 69 4 270.52 1.83 148 65 72 7 239.80 1.38 149 66 72 6 218.64 9.08 150 66 73 7 218.97 8.90 151 66 76 10 204.48 4.65 152 67 73 6 219.33 8.71 153 67 76 9 204.28 4.53 154 69 72 3 278.63 2.19 155 69 73 4 273.49 0.22 156 70 73 3 273.67 0.31 157 70 74 4 273.44 0.24 158 71 74 3 274.88 0.30 159 71 75 4 273.44 0.24 160 72 75 3 278.60 2.33 161 72 76 4 274.71 0.39 162 73 76 3 274.71 0.40 163 73 77 4 274.70 0.40 164 74 77 3 278.85 1.68 165 74 78 4 271.18 1.32 166 75 78 3 275.38 3.41 167 75 79 4 268.01 0.72 168 76 79 3 270.74 1.83 169 76 80 4 262.88 3.20 170 77 80 3 273.12 1.10 171 77 81 4 262.86 3.19