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 85.03 0.33 2 3 6 3 114.15 1.27 3 3 7 4 102.21 4.70 4 4 7 3 110.52 0.59 5 4 8 4 109.58 1.02 6 4 118 114 24.25 0.74 7 5 8 3 118.10 3.21 8 5 9 4 109.58 1.02 9 5 116 111 25.33 1.27 10 5 117 112 24.34 0.78 11 5 118 113 24.32 0.78 12 6 9 3 117.14 3.13 13 6 10 4 102.02 2.98 14 7 10 3 108.70 0.85 15 7 11 4 108.53 0.23 16 8 11 3 116.83 1.60 17 8 12 4 108.49 0.25 18 8 13 5 100.08 3.95 19 8 54 46 62.47 10.97 20 8 108 100 34.91 0.49 21 8 117 109 34.96 0.51 22 8 118 110 34.91 0.49 23 8 119 111 34.32 0.78 24 8 120 112 34.09 0.67 25 9 12 3 120.05 1.74 26 9 13 4 98.83 4.55 27 9 33 24 123.24 3.23 28 9 51 42 87.04 1.23 29 10 33 23 122.88 3.40 30 10 34 24 123.47 3.10 31 10 35 25 123.48 3.10 32 11 35 24 123.48 3.10 33 11 41 30 123.46 3.08 34 11 44 33 111.39 0.16 35 11 46 35 106.26 0.01 36 12 44 32 122.10 3.56 37 12 45 33 109.27 0.38 38 12 46 34 106.26 0.01 39 12 47 35 106.25 0.01 40 12 120 108 35.93 0.80 41 13 33 20 204.78 0.49 42 13 47 34 108.16 0.94 43 13 49 36 106.20 0.01 44 13 50 37 106.19 0.07 45 13 51 38 105.77 0.03 46 13 54 41 96.49 0.35 47 14 33 19 204.90 0.46 48 14 46 32 122.53 3.33 49 14 47 33 111.64 0.03 50 14 48 34 106.28 0.02 51 15 48 33 110.45 0.21 52 15 49 34 107.28 0.46 53 15 50 35 106.25 0.04 54 17 48 31 127.87 0.86 55 18 48 30 128.63 0.58 56 18 80 62 132.50 0.67 57 19 48 29 132.82 0.60 58 19 80 61 133.03 0.83 59 19 101 82 134.66 0.12 60 20 48 28 134.68 0.12 61 20 82 62 134.78 0.17 62 20 99 79 174.21 0.16 63 20 101 81 134.66 0.12 64 22 99 77 183.12 0.49 65 23 99 76 180.55 0.79 66 25 29 4 305.44 0.29 67 25 46 21 204.63 0.45 68 25 48 23 202.97 1.02 69 25 82 57 306.62 0.19 70 25 99 74 183.05 0.54 71 26 29 3 146.19 0.58 72 26 30 4 272.31 2.31 73 26 82 56 225.88 3.35 74 26 97 71 184.15 0.72 75 26 99 73 174.38 1.15 76 27 96 69 184.27 0.48 77 27 97 70 183.37 0.47 78 29 32 3 204.88 0.46 79 29 33 4 204.89 0.46 80 29 46 17 132.99 0.68 81 30 34 4 204.90 0.46 82 30 35 5 204.55 0.44 83 30 36 6 204.62 0.47 84 30 41 11 204.34 0.38 85 30 44 14 167.05 1.07 86 30 46 16 140.24 2.69 87 30 84 54 219.84 3.73 88 30 97 67 180.46 0.74 89 31 34 3 204.91 0.46 90 31 36 5 204.71 0.47 91 33 46 13 172.25 5.53 92 34 37 3 205.09 0.48 93 35 39 4 205.11 0.47 94 35 41 6 205.03 0.48 95 35 44 9 204.95 0.49 96 35 46 11 204.94 0.49 97 36 39 3 205.10 0.47 98 36 40 4 205.04 0.47 99 36 92 56 252.09 9.65 100 36 95 59 205.00 0.47 101 36 97 61 204.98 0.48 102 40 86 46 205.12 0.46 103 42 85 43 205.03 0.48 104 42 86 44 205.05 0.48 105 43 84 41 204.93 0.48 106 43 85 42 204.96 0.48 107 44 83 39 204.94 0.48 108 44 84 40 204.91 0.48 109 45 81 36 204.99 0.48 110 45 82 37 204.93 0.48 111 45 83 38 204.87 0.47 112 45 120 75 36.60 0.83 113 46 81 35 204.94 0.48 114 46 82 36 204.90 0.48 115 46 84 38 204.86 0.47 116 47 54 7 179.50 1.97 117 47 79 32 205.00 0.48 118 47 80 33 204.95 0.48 119 47 81 34 204.86 0.48 120 47 106 59 142.50 2.60 121 47 120 73 37.51 1.08 122 48 80 32 204.90 0.47 123 48 81 33 204.86 0.48 124 48 82 34 204.86 0.48 125 49 53 4 306.74 0.37 126 49 54 5 299.81 3.71 127 49 79 30 204.91 0.47 128 49 80 31 204.88 0.48 129 50 53 3 306.89 0.30 130 50 54 4 306.75 0.38 131 51 55 4 306.74 0.38 132 52 56 4 306.90 0.17 133 53 57 4 306.91 0.17 134 53 79 26 204.46 0.48 135 54 57 3 306.94 0.18 136 54 79 25 199.62 0.57 137 54 117 63 69.85 0.43 138 55 116 61 70.69 0.43 139 55 117 62 70.17 0.60 140 57 73 16 204.65 0.44 141 57 74 17 204.56 0.48 142 57 75 18 190.91 0.45 143 57 79 22 180.18 0.61 144 58 73 15 204.52 0.46 145 58 115 57 72.75 0.21 146 58 116 58 72.74 0.21 147 58 117 59 72.68 0.22 148 60 73 13 204.77 0.49 149 60 74 14 204.68 0.47 150 60 75 15 204.65 0.47 151 60 76 16 194.21 0.77 152 61 73 12 204.79 0.48 153 61 74 13 204.68 0.47 154 61 76 15 204.66 0.47 155 62 70 8 223.31 1.00 156 62 72 10 204.90 0.48 157 62 73 11 204.85 0.46 158 63 72 9 204.94 0.48 159 63 73 10 204.90 0.47 160 63 74 11 204.89 0.47 161 63 107 44 205.06 0.52 162 64 72 8 240.38 1.79 163 65 109 44 204.49 0.47 164 65 121 56 70.37 0.30 165 66 121 55 70.40 0.29 166 66 122 56 70.40 0.29 167 71 109 38 204.66 0.47 168 71 110 39 204.65 0.47 169 71 111 40 204.56 0.49 170 71 115 44 123.88 3.40 171 72 107 35 204.82 0.46 172 72 108 36 204.66 0.47 173 72 109 37 204.49 0.47 174 72 121 49 70.33 0.32 175 73 107 34 204.75 0.47 176 73 108 35 204.65 0.47 177 73 110 37 202.83 0.35 178 73 115 42 96.48 0.65 179 74 105 31 204.87 0.47 180 74 106 32 204.75 0.47 181 74 107 33 204.19 0.32 182 74 124 50 38.54 1.38 183 75 79 4 193.19 5.40 184 75 105 30 204.71 0.45 185 75 106 31 204.65 0.47 186 76 105 29 204.69 0.46 187 77 105 28 203.34 0.49 188 78 103 25 204.64 0.47 189 78 104 26 189.72 1.45 190 78 105 27 183.38 0.47 191 79 103 24 194.25 0.98 192 79 104 25 186.25 0.28 193 79 106 27 177.00 0.66 194 80 101 21 204.75 0.46 195 80 102 22 201.75 0.18 196 80 103 23 183.65 0.70 197 81 101 20 194.25 0.98 198 81 102 21 186.24 0.28 199 81 104 23 178.25 0.09 200 81 106 25 137.37 1.96 201 81 123 42 37.48 1.14 202 82 99 17 204.69 0.45 203 82 100 18 190.43 1.12 204 82 101 19 183.22 0.51 205 83 98 15 204.75 0.47 206 83 99 16 192.47 0.10 207 83 100 17 184.09 0.79 208 84 97 13 204.66 0.46 209 84 98 14 186.38 0.23 210 85 97 12 204.75 0.48 211 85 98 13 204.43 0.47 212 86 96 10 204.90 0.47 213 86 97 11 204.77 0.48 214 87 96 9 204.99 0.47 215 87 97 10 204.93 0.48 216 87 98 11 204.88 0.47 217 90 95 5 209.80 1.84 218 90 96 6 205.16 0.47 219 104 123 19 37.80 1.21 220 104 124 20 36.90 0.84 221 105 123 18 37.65 1.10 222 105 124 19 37.49 1.11 223 106 120 14 68.67 0.12 224 106 122 16 40.39 0.60 225 106 123 17 38.09 1.34 226 107 120 13 69.14 0.20 227 107 121 14 64.38 0.70 228 107 122 15 41.43 0.10 229 107 124 17 40.36 0.60 230 108 117 9 72.19 0.45 231 108 119 11 70.05 0.46 232 108 120 12 69.19 0.22 233 108 121 13 68.67 0.12 234 109 117 8 72.60 0.26 235 109 118 9 72.50 0.29 236 109 119 10 70.34 0.33 237 110 115 5 74.34 0.55 238 110 116 6 72.98 0.32 239 110 117 7 72.70 0.22 240 110 118 8 72.67 0.21 241 111 115 4 75.56 0.04 242 111 116 5 74.35 0.55 243 111 118 7 72.75 0.21 244 112 115 3 113.67 8.51