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 1 99 98 29.71 0.77 2 2 9 7 32.47 0.06 3 2 94 92 31.70 0.14 4 2 95 93 29.98 0.68 5 2 96 94 29.86 0.70 6 2 100 98 29.96 0.70 7 3 9 6 32.20 0.08 8 3 10 7 31.92 0.00 9 3 94 91 32.02 0.02 10 3 95 92 31.73 0.07 11 3 97 94 31.89 0.01 12 4 7 3 171.40 0.14 13 4 8 4 41.13 1.15 14 4 9 5 35.33 0.51 15 4 10 6 32.01 0.01 16 4 92 88 32.09 0.01 17 4 93 89 32.11 0.01 18 5 8 3 41.97 1.05 19 5 10 5 34.47 0.94 20 5 77 72 43.66 0.12 21 5 78 73 36.93 1.21 22 5 91 86 32.16 0.04 23 5 92 87 32.16 0.04 24 10 92 82 81.40 0.06 25 10 95 85 82.79 0.29 26 10 97 87 88.58 0.81 27 11 97 86 88.61 0.81 28 12 47 35 81.54 0.10 29 12 52 40 81.53 0.10 30 12 80 68 81.62 0.09 31 13 47 34 81.54 0.10 32 14 97 83 88.61 0.81 33 14 122 108 166.32 0.60 34 15 19 4 182.28 0.92 35 15 45 30 74.81 1.12 36 15 92 77 82.94 0.40 37 15 95 80 84.85 0.20 38 15 97 82 87.39 1.40 39 15 101 86 82.33 0.21 40 16 45 29 80.95 0.01 41 16 46 30 81.12 0.01 42 16 47 31 81.23 0.04 43 16 122 106 166.35 0.59 44 17 44 27 81.78 0.20 45 17 45 28 81.79 0.19 46 17 122 105 166.36 0.59 47 18 43 25 81.89 0.14 48 18 44 26 81.86 0.21 49 18 122 104 166.36 0.59 50 19 42 23 82.39 0.12 51 19 43 24 82.34 0.12 52 19 45 26 82.56 0.12 53 19 97 78 167.22 0.50 54 19 99 80 167.23 0.54 55 19 100 81 166.36 0.59 56 19 101 82 166.32 0.60 57 19 120 101 166.33 0.59 58 19 121 102 166.36 0.59 59 19 122 103 166.85 0.35 60 20 42 22 82.47 0.14 61 20 120 100 166.91 0.38 62 20 121 101 167.34 0.48 63 20 122 102 167.58 0.56 64 20 123 103 167.49 0.51 65 20 124 104 167.47 0.51 66 20 156 136 64.88 0.84 67 21 40 19 82.47 0.14 68 21 41 20 82.45 0.14 69 21 42 21 82.48 0.14 70 21 120 99 167.43 0.48 71 21 151 130 82.83 0.26 72 21 156 135 67.23 0.09 73 22 119 97 168.15 0.67 74 22 120 98 168.07 0.64 75 22 121 99 168.03 0.61 76 22 123 101 168.06 0.60 77 22 124 102 167.96 0.58 78 22 125 103 167.59 0.54 79 22 126 104 167.59 0.53 80 22 131 109 167.41 0.49 81 22 150 128 85.01 0.68 82 22 151 129 83.16 0.10 83 22 152 130 82.48 0.14 84 22 156 134 67.95 0.28 85 23 118 95 168.28 0.73 86 23 119 96 168.16 0.67 87 23 131 108 167.50 0.48 88 23 134 111 159.94 0.45 89 23 148 125 91.54 0.53 90 23 149 126 86.81 0.78 91 23 150 127 85.11 0.62 92 24 32 8 119.19 17.00 93 24 117 93 168.42 0.80 94 24 118 94 168.29 0.73 95 24 148 124 93.40 0.40 96 24 149 125 91.45 0.48 97 24 151 127 86.71 0.82 98 25 32 7 165.05 0.24 99 25 116 91 168.47 0.80 100 25 117 92 168.44 0.80 101 25 134 109 167.62 0.42 102 25 138 113 150.80 0.43 103 25 143 118 140.63 0.83 104 25 147 122 103.45 0.29 105 25 148 123 93.41 0.40 106 26 29 3 173.36 2.14 107 26 32 6 167.74 0.47 108 26 115 89 168.47 0.81 109 26 116 90 168.47 0.81 110 26 143 117 141.33 0.98 111 26 147 121 122.95 0.68 112 27 142 115 146.58 0.06 113 27 143 116 141.49 0.99 114 27 144 117 141.44 1.02 115 27 147 120 138.06 0.46 116 28 114 86 168.50 0.81 117 29 33 4 285.05 0.35 118 29 146 117 141.50 1.01 119 29 147 118 139.36 0.96 120 29 149 120 139.25 0.91 121 30 36 6 169.15 0.67 122 31 36 5 169.13 0.66 123 31 37 6 169.13 0.66 124 31 38 7 169.09 0.66 125 31 39 8 169.10 0.65 126 31 85 54 169.12 0.66 127 31 114 83 169.06 0.72 128 32 38 6 169.10 0.67 129 32 39 7 169.02 0.62 130 32 116 84 169.16 0.73 131 32 147 115 141.53 1.02 132 32 149 117 140.71 0.85 133 33 36 3 169.21 0.69 134 33 39 6 169.06 0.63 135 33 149 116 140.74 0.85 136 34 39 5 169.12 0.65 137 35 59 24 138.67 0.84 138 35 61 26 137.34 0.82 139 36 39 3 175.19 1.89 140 36 58 22 138.83 0.87 141 37 40 3 220.38 4.06 142 37 58 21 138.84 0.88 143 37 84 47 169.81 0.43 144 37 85 48 169.78 0.43 145 38 84 46 169.90 0.40 146 38 88 50 170.09 0.54 147 38 105 67 169.75 0.69 148 38 107 69 170.06 0.57 149 38 114 76 170.22 0.66 150 38 116 78 169.65 0.71 151 39 58 19 138.85 0.88 152 39 149 110 141.55 1.03 153 39 151 112 140.51 1.28 154 39 154 115 139.31 0.99 155 40 56 16 139.97 1.07 156 40 57 17 139.83 1.05 157 40 58 18 139.47 1.19 158 40 120 80 169.89 0.62 159 40 151 111 141.29 1.14 160 41 56 15 140.00 1.07 161 41 57 16 139.86 1.03 162 41 58 17 139.87 1.03 163 41 59 18 139.87 1.03 164 41 151 110 141.50 1.05 165 41 155 114 139.53 0.87 166 41 156 115 105.66 1.54 167 41 157 116 99.12 1.73 168 42 45 3 326.90 1.81 169 42 54 12 143.12 0.28 170 42 55 13 141.31 1.15 171 42 56 14 140.84 0.97 172 42 120 78 169.73 0.70 173 43 55 12 141.52 1.07 174 43 56 13 141.22 1.10 175 43 57 14 141.24 1.11 176 43 66 23 141.30 1.15 177 44 53 9 150.31 0.48 178 44 54 10 145.60 0.11 179 44 55 11 141.56 1.05 180 45 52 7 151.62 0.04 181 45 53 8 148.06 0.64 182 45 54 9 146.81 0.06 183 45 103 58 171.15 0.96 184 46 52 6 152.32 0.26 185 46 53 7 150.34 0.48 186 46 68 22 150.82 0.23 187 47 51 4 168.06 0.06 188 47 52 5 152.31 0.26 189 48 51 3 168.13 0.09 190 48 53 5 160.25 2.32 191 48 70 22 167.25 0.35 192 50 72 22 239.68 1.01 193 50 73 23 239.68 1.01 194 51 70 19 239.52 0.99 195 51 71 20 239.66 1.01 196 51 72 21 239.68 1.01 197 51 80 29 239.69 1.01 198 52 70 18 239.67 1.01 199 52 71 19 239.68 1.01 200 52 80 28 239.69 1.01 201 52 90 38 239.69 1.01 202 53 68 15 239.66 1.01 203 53 69 16 239.67 1.01 204 53 70 17 239.68 1.01 205 54 68 14 239.66 1.01 206 54 69 15 239.67 1.01 207 54 71 17 239.72 1.01 208 54 90 36 265.64 5.18 209 54 103 49 262.45 6.72 210 55 66 11 239.66 1.01 211 55 67 12 239.66 1.01 212 55 68 13 239.66 1.01 213 56 66 10 239.66 1.01 214 56 67 11 239.66 1.01 215 56 69 13 239.72 1.02 216 57 64 7 237.27 1.56 217 57 65 8 239.66 1.01 218 57 66 9 239.66 1.01 219 57 157 100 137.61 15.53 220 58 64 6 239.66 1.01 221 58 65 7 239.66 1.01 222 58 67 9 239.72 1.01 223 59 62 3 239.69 1.01 224 59 63 4 239.67 1.01 225 59 64 5 239.66 1.01 226 59 155 96 239.67 1.00 227 59 157 98 239.66 1.01 228 60 63 3 239.69 1.01 229 60 65 5 239.70 1.01 230 124 152 28 322.49 5.00 231 124 156 32 322.48 5.01 232 124 158 34 322.38 5.06 233 125 152 27 322.49 5.00