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 2 10 8 85.94 0.12 2 3 6 3 94.51 0.33 3 3 7 4 91.84 0.48 4 4 7 3 94.75 0.96 5 4 8 4 92.44 0.79 6 4 118 114 23.75 0.88 7 5 8 3 111.16 6.68 8 5 9 4 110.98 8.49 9 5 116 111 25.32 1.27 10 5 117 112 24.20 0.71 11 5 118 113 24.18 0.71 12 6 9 3 126.20 0.89 13 6 10 4 114.58 6.69 14 7 10 3 119.43 4.28 15 7 11 4 114.58 6.68 16 8 11 3 126.14 0.92 17 8 12 4 95.22 3.00 18 8 13 5 95.22 3.00 19 8 54 46 71.94 6.24 20 8 108 100 34.33 0.78 21 8 117 109 34.91 0.49 22 8 118 110 34.90 0.50 23 8 119 111 33.55 0.41 24 8 120 112 33.53 0.40 25 9 12 3 125.20 1.58 26 9 13 4 90.70 0.74 27 9 33 24 123.42 2.00 28 9 51 42 86.95 1.28 29 10 33 23 123.42 2.00 30 10 34 24 123.48 2.02 31 10 35 25 123.48 2.02 32 11 35 24 123.48 2.03 33 11 44 33 112.44 0.07 34 11 46 35 112.41 0.07 35 12 41 29 132.54 0.77 36 12 44 32 114.30 0.91 37 12 45 33 112.43 0.06 38 12 46 34 112.40 0.07 39 12 47 35 112.41 0.07 40 12 120 108 35.71 0.90 41 13 33 20 206.33 1.32 42 13 47 34 112.42 0.07 43 13 49 36 112.41 0.07 44 13 50 37 112.40 0.07 45 13 51 38 109.39 0.94 46 13 54 41 100.66 2.83 47 14 33 19 206.36 1.33 48 14 46 32 121.64 1.78 49 14 47 33 112.61 0.12 50 14 48 34 112.42 0.07 51 15 48 33 112.44 0.07 52 15 49 34 112.42 0.07 53 15 50 35 112.40 0.07 54 17 48 31 124.01 1.14 55 18 48 30 124.09 1.10 56 18 80 62 124.05 1.12 57 19 48 29 124.44 1.26 58 19 80 61 124.09 1.10 59 19 101 82 127.95 0.51 60 20 48 28 127.86 0.09 61 20 82 62 132.43 2.65 62 20 99 79 178.22 1.29 63 20 101 81 128.75 0.84 64 22 99 77 183.31 0.23 65 23 99 76 182.84 0.20 66 25 29 4 305.47 0.02 67 25 46 21 206.17 1.38 68 25 48 23 205.17 1.10 69 25 82 57 306.06 0.22 70 25 99 74 182.94 0.26 71 26 29 3 143.55 0.41 72 26 30 4 279.79 1.58 73 26 82 56 220.05 1.69 74 26 97 71 186.03 0.46 75 26 98 72 184.05 0.34 76 26 99 73 175.06 1.38 77 27 96 69 186.26 0.35 78 27 97 70 184.01 0.32 79 29 32 3 206.34 1.35 80 29 33 4 206.36 1.33 81 29 46 17 128.31 1.01 82 30 34 4 206.35 1.33 83 30 35 5 205.99 1.49 84 30 36 6 206.21 1.34 85 30 41 11 206.03 1.43 86 30 44 14 168.95 0.33 87 30 46 16 138.66 1.52 88 30 84 54 222.77 0.86 89 30 97 67 183.30 0.02 90 31 34 3 206.36 1.33 91 31 36 5 206.22 1.33 92 33 46 13 204.44 0.88 93 34 37 3 206.52 1.31 94 35 39 4 206.59 1.33 95 35 41 6 206.52 1.33 96 35 44 9 206.45 1.35 97 35 46 11 206.43 1.34 98 36 39 3 206.56 1.31 99 36 40 4 206.53 1.32 100 36 92 56 251.91 1.72 101 36 95 59 206.49 1.33 102 36 97 61 206.46 1.34 103 40 86 46 206.59 1.33 104 42 85 43 206.50 1.33 105 42 86 44 206.52 1.33 106 43 84 41 206.43 1.34 107 43 85 42 206.44 1.34 108 44 83 39 206.44 1.34 109 44 84 40 206.37 1.35 110 45 81 36 206.47 1.34 111 45 82 37 206.43 1.34 112 45 83 38 206.34 1.34 113 45 120 75 36.08 0.86 114 46 81 35 206.43 1.34 115 46 82 36 206.39 1.35 116 46 84 38 206.33 1.34 117 47 54 7 195.08 8.82 118 47 79 32 206.48 1.34 119 47 80 33 206.43 1.34 120 47 81 34 206.34 1.35 121 47 106 59 142.52 2.10 122 47 120 73 36.60 0.68 123 48 80 32 206.40 1.34 124 48 81 33 206.33 1.34 125 48 82 34 206.33 1.34 126 49 53 4 306.00 0.62 127 49 54 5 293.39 3.64 128 49 79 30 206.40 1.34 129 49 80 31 206.37 1.35 130 50 53 3 306.89 0.18 131 51 55 4 306.12 0.56 132 52 55 3 306.88 0.19 133 52 56 4 306.75 0.24 134 53 56 3 306.76 0.24 135 53 57 4 306.74 0.24 136 53 79 26 206.10 1.35 137 54 57 3 306.86 0.17 138 54 79 25 197.82 0.33 139 54 117 63 59.01 4.92 140 55 117 62 59.01 4.92 141 57 73 16 206.12 1.44 142 57 74 17 206.06 1.41 143 57 75 18 191.93 0.34 144 57 79 22 180.54 0.76 145 58 73 15 206.05 1.41 146 58 115 57 65.53 3.45 147 58 116 58 65.50 3.43 148 58 117 59 65.26 3.53 149 60 73 13 206.31 1.35 150 60 74 14 206.27 1.34 151 60 75 15 205.30 1.26 152 60 76 16 191.91 0.35 153 61 73 12 206.32 1.35 154 61 74 13 206.27 1.34 155 61 76 15 205.92 1.27 156 62 70 8 217.22 4.04 157 62 72 10 206.41 1.35 158 62 73 11 206.32 1.35 159 63 72 9 206.43 1.35 160 63 73 10 206.41 1.35 161 63 74 11 206.41 1.35 162 63 107 44 206.51 1.33 163 64 72 8 235.95 0.27 164 65 109 44 206.11 1.38 165 65 121 56 61.62 4.92 166 66 121 55 63.11 4.33 167 66 122 56 62.97 4.26 168 71 109 38 206.19 1.38 169 71 110 39 206.12 1.36 170 71 111 40 206.06 1.38 171 71 115 44 120.56 2.57 172 72 107 35 206.28 1.36 173 72 108 36 206.20 1.38 174 72 109 37 205.99 1.39 175 72 121 49 61.14 4.71 176 73 107 34 206.23 1.39 177 73 108 35 206.18 1.39 178 73 110 37 205.62 1.42 179 73 115 42 87.61 2.00 180 74 105 31 206.31 1.35 181 74 106 32 206.25 1.37 182 74 107 33 205.43 1.11 183 74 124 50 37.78 1.15 184 75 79 4 183.99 0.32 185 75 105 30 206.27 1.37 186 75 106 31 206.18 1.39 187 76 105 29 206.22 1.39 188 77 105 28 204.75 1.32 189 78 103 25 206.17 1.39 190 78 104 26 190.34 1.14 191 78 105 27 185.72 0.53 192 79 103 24 196.38 0.23 193 79 104 25 187.07 0.49 194 79 106 27 178.34 0.26 195 80 101 21 206.27 1.37 196 80 102 22 204.11 0.73 197 80 103 23 184.49 0.59 198 81 101 20 192.47 0.10 199 81 102 21 186.46 0.18 200 81 104 23 180.38 0.70 201 81 106 25 141.22 2.91 202 81 123 42 36.45 0.75 203 82 99 17 206.24 1.38 204 82 100 18 190.36 1.15 205 82 101 19 183.90 0.33 206 83 98 15 206.29 1.36 207 83 99 16 192.97 0.34 208 83 100 17 184.03 0.34 209 84 97 13 206.17 1.38 210 84 98 14 187.75 0.14 211 85 97 12 206.27 1.38 212 85 98 13 205.97 1.31 213 86 96 10 206.38 1.34 214 86 97 11 206.30 1.36 215 87 96 9 206.43 1.35 216 87 97 10 206.38 1.34 217 87 98 11 206.37 1.34 218 90 95 5 215.06 2.89 219 90 96 6 206.61 1.33 220 91 95 4 306.88 0.07 221 104 123 19 36.62 0.68 222 104 124 20 36.49 0.72 223 105 123 18 36.62 0.67 224 105 124 19 36.58 0.69 225 106 120 14 59.22 4.75 226 106 122 16 39.65 0.24 227 106 123 17 36.59 0.68 228 107 120 13 59.23 4.76 229 107 121 14 54.30 4.25 230 107 122 15 40.73 0.24 231 107 124 17 38.50 0.79 232 108 117 9 65.46 3.41 233 108 119 11 61.80 4.15 234 108 120 12 59.58 4.62 235 108 121 13 58.67 4.75 236 109 117 8 65.50 3.42 237 109 118 9 65.19 3.54 238 109 119 10 63.31 4.25 239 110 115 5 74.12 0.42 240 110 116 6 65.77 3.56 241 110 117 7 65.49 3.43 242 110 118 8 65.26 3.54 243 111 115 4 86.93 1.67 244 111 116 5 70.94 1.17 245 111 118 7 65.53 3.44 246 112 115 3 96.45 0.20