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 19 115 96 30.94 0.10 2 20 112 92 31.55 0.36 3 20 113 93 31.24 0.24 4 20 114 94 30.94 0.10 5 20 118 98 31.24 0.24 6 20 151 131 31.68 0.34 7 21 28 7 31.74 0.33 8 21 112 91 31.69 0.35 9 21 113 92 31.55 0.36 10 21 115 94 31.63 0.34 11 22 25 3 42.05 1.01 12 22 28 6 31.83 0.30 13 22 110 88 31.71 0.35 14 22 111 89 31.73 0.36 15 22 112 90 31.70 0.35 16 23 28 5 31.84 0.30 17 23 96 73 31.78 0.35 18 23 109 86 31.77 0.35 19 23 110 87 31.76 0.35 20 24 95 71 33.30 0.29 21 24 96 72 31.89 0.39 22 24 109 85 31.88 0.38 23 28 33 5 137.99 22.34 24 28 110 82 61.76 1.03 25 28 113 85 62.18 0.87 26 28 115 87 74.11 0.64 27 29 32 3 189.75 2.02 28 29 115 86 78.96 2.23 29 30 33 3 189.02 2.40 30 30 65 35 68.64 0.90 31 30 70 40 70.20 0.12 32 30 98 68 70.69 0.11 33 31 34 3 190.58 1.61 34 31 65 34 70.45 0.00 35 32 115 83 87.65 0.54 36 32 140 108 110.65 0.83 37 33 37 4 196.75 1.01 38 33 63 30 85.34 0.46 39 33 65 32 85.59 0.43 40 33 70 37 85.70 0.38 41 33 110 77 87.33 0.41 42 33 113 80 88.40 0.21 43 33 115 82 88.72 0.06 44 33 119 86 87.34 0.42 45 33 140 107 134.44 10.06 46 34 63 29 85.42 0.43 47 34 64 30 85.57 0.44 48 34 65 31 85.60 0.43 49 34 140 106 178.09 0.26 50 35 62 27 85.64 0.42 51 35 63 28 85.60 0.45 52 35 140 105 178.10 0.26 53 36 61 25 85.73 0.39 54 36 62 26 85.70 0.40 55 36 140 104 178.10 0.26 56 37 60 23 86.09 0.22 57 37 61 24 85.75 0.39 58 37 63 26 87.38 0.26 59 37 115 78 179.72 0.93 60 37 117 80 179.66 0.92 61 37 118 81 178.26 0.18 62 37 119 82 177.88 0.01 63 37 138 101 178.07 0.26 64 37 139 102 178.97 0.54 65 37 140 103 179.53 0.97 66 38 60 22 86.23 0.17 67 38 138 100 179.71 0.89 68 38 139 101 179.78 0.93 69 38 140 102 179.93 1.01 70 38 141 103 179.81 1.01 71 38 142 104 179.72 1.06 72 39 42 3 226.97 0.01 73 39 58 19 87.44 0.23 74 39 59 20 86.13 0.20 75 39 60 21 87.02 0.18 76 39 137 98 180.34 1.02 77 39 138 99 180.30 1.03 78 39 169 130 87.62 0.10 79 40 137 97 180.43 1.02 80 40 138 98 180.37 1.01 81 40 139 99 180.38 1.00 82 40 141 101 180.46 1.01 83 40 142 102 180.44 1.01 84 40 143 103 180.20 0.93 85 40 144 104 179.83 1.11 86 40 149 109 179.72 1.06 87 40 168 128 89.62 0.45 88 40 169 129 87.62 0.10 89 40 170 130 86.03 0.17 90 41 136 95 180.45 1.03 91 41 137 96 180.43 1.02 92 41 149 108 179.72 1.06 93 41 152 111 172.34 0.33 94 41 166 125 97.02 0.89 95 41 167 126 93.23 0.85 96 41 168 127 89.63 0.45 97 41 169 128 88.88 0.07 98 42 50 8 125.28 16.45 99 42 56 14 127.86 15.36 100 42 57 15 91.73 0.33 101 42 58 16 91.69 0.34 102 42 134 92 180.66 1.04 103 42 135 93 180.59 1.06 104 42 136 94 180.46 1.04 105 42 138 96 180.57 1.04 106 42 166 124 97.03 0.89 107 42 167 125 96.88 0.87 108 42 169 127 91.92 0.21 109 43 50 7 162.28 0.36 110 43 134 91 180.67 1.03 111 43 135 92 180.63 1.04 112 43 152 109 179.80 1.01 113 43 156 113 150.94 0.55 114 43 161 118 142.24 0.20 115 43 165 122 107.55 2.85 116 43 166 123 97.03 0.89 117 44 47 3 180.03 0.91 118 44 50 6 177.61 1.10 119 44 132 88 180.72 1.03 120 44 133 89 180.70 1.05 121 44 134 90 180.69 1.04 122 44 161 117 142.37 0.18 123 44 165 121 128.84 0.29 124 45 132 87 180.94 1.11 125 45 133 88 180.82 1.07 126 45 161 116 142.38 0.18 127 45 165 120 133.13 0.97 128 46 49 3 183.53 0.09 129 46 130 84 181.33 1.05 130 46 132 86 181.01 1.09 131 47 50 3 186.54 1.54 132 47 51 4 181.47 1.00 133 47 164 117 142.47 0.21 134 47 165 118 137.24 0.66 135 47 167 120 135.40 0.63 136 48 51 3 184.91 2.71 137 48 54 6 181.41 1.02 138 49 54 5 181.42 1.02 139 49 55 6 181.42 1.02 140 49 56 7 181.34 1.04 141 49 57 8 181.31 1.06 142 49 103 54 181.42 1.02 143 49 132 83 181.42 1.03 144 50 56 6 181.31 1.06 145 50 57 7 181.30 1.07 146 50 134 84 181.31 1.06 147 50 165 115 142.94 0.21 148 50 167 117 141.73 0.11 149 51 54 3 181.49 0.98 150 51 57 6 181.31 1.06 151 51 167 116 142.44 0.18 152 52 57 5 181.50 0.99 153 53 57 4 183.02 0.88 154 53 78 25 103.23 1.29 155 54 57 3 191.34 2.49 156 55 58 3 228.91 3.89 157 55 102 47 182.59 1.09 158 55 103 48 182.56 1.07 159 56 102 46 182.71 1.03 160 56 103 47 182.95 0.98 161 56 106 50 182.62 1.04 162 56 123 67 182.50 1.07 163 56 125 69 182.62 1.04 164 56 132 76 182.55 1.06 165 56 134 78 181.88 1.09 166 57 167 110 142.72 0.27 167 57 169 112 141.97 0.32 168 58 74 16 133.22 1.01 169 58 76 18 131.53 0.61 170 58 85 27 133.16 0.99 171 58 87 29 142.08 0.34 172 58 102 44 183.22 0.88 173 59 74 15 135.40 1.56 174 59 75 16 133.11 0.97 175 59 77 18 133.07 0.96 176 59 169 110 142.43 0.24 177 59 172 113 139.05 1.20 178 59 174 115 132.57 1.16 179 60 63 3 305.06 1.21 180 60 72 12 144.72 1.42 181 60 73 13 142.06 0.32 182 60 74 14 141.27 0.05 183 60 138 78 182.16 1.21 184 61 73 12 142.16 0.34 185 61 74 13 141.50 0.04 186 61 75 14 141.47 0.06 187 62 72 10 145.39 1.47 188 62 73 11 142.47 0.18 189 63 70 7 153.88 1.08 190 63 71 8 150.08 0.20 191 63 72 9 146.38 0.97 192 63 119 56 182.96 1.02 193 64 70 6 153.89 1.07 194 64 71 7 150.22 0.17 195 64 73 9 149.58 0.05 196 65 70 5 154.10 0.97 197 66 69 3 181.99 0.92 198 66 71 5 163.81 0.13 199 67 91 24 256.86 1.34 200 68 90 22 256.83 1.34 201 68 91 23 256.86 1.34 202 69 88 19 256.49 1.45 203 69 89 20 256.83 1.34 204 69 90 21 256.85 1.34 205 69 98 29 256.87 1.33 206 70 88 18 256.83 1.34 207 70 89 19 256.84 1.34 208 70 98 28 256.89 1.33 209 70 108 38 256.92 1.33 210 71 87 16 256.83 1.34 211 71 88 17 256.83 1.34 212 72 86 14 256.83 1.34 213 72 87 15 256.84 1.34 214 72 89 17 256.88 1.33 215 72 108 36 259.11 1.22 216 73 84 11 256.81 1.33 217 73 85 12 256.83 1.34 218 73 86 13 256.84 1.34 219 74 84 10 256.83 1.34 220 74 85 11 256.84 1.34 221 74 87 13 256.89 1.33 222 75 82 7 240.12 1.80 223 75 83 8 256.83 1.34 224 75 84 9 256.84 1.34 225 76 82 6 256.83 1.34 226 76 83 7 256.85 1.34 227 76 85 9 256.88 1.34 228 77 80 3 256.87 1.33 229 77 81 4 256.86 1.34 230 77 82 5 256.84 1.34 231 77 174 97 256.81 1.35 232 77 175 98 256.83 1.34 233 78 81 3 256.86 1.34 234 80 175 95 256.83 1.33 235 80 176 96 256.83 1.33 236 80 177 97 252.62 0.74 237 81 175 94 256.85 1.33 238 143 170 27 346.73 0.39