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 8 135.42 0.01 2 3 6 3 156.77 0.54 3 3 7 4 146.51 1.44 4 4 7 3 157.68 0.98 5 4 8 4 144.12 2.63 6 4 118 114 21.33 0.12 7 5 8 3 153.77 2.04 8 5 9 4 146.09 0.83 9 5 116 111 23.71 0.76 10 5 118 113 21.48 0.14 11 6 9 3 153.85 0.01 12 6 10 4 147.81 1.03 13 7 10 3 152.58 0.64 14 7 11 4 149.33 1.79 15 8 11 3 151.22 1.31 16 8 12 4 146.96 1.46 17 8 13 5 146.96 1.46 18 8 54 46 68.59 0.46 19 8 108 100 35.44 0.56 20 8 117 109 35.80 0.39 21 8 118 110 35.44 0.56 22 8 119 111 35.44 0.56 23 8 120 112 35.40 0.55 24 9 12 3 156.43 1.11 25 9 13 4 143.53 3.17 26 9 33 24 116.76 1.34 27 9 51 42 87.71 0.58 28 10 33 23 116.75 1.34 29 10 34 24 116.84 1.38 30 10 35 25 116.84 1.38 31 11 35 24 116.84 1.38 32 11 41 30 116.81 1.39 33 11 44 33 115.04 1.06 34 11 46 35 114.86 1.11 35 12 44 32 116.28 1.14 36 12 45 33 115.03 1.06 37 12 46 34 114.86 1.11 38 12 47 35 114.84 1.11 39 12 120 108 36.16 0.27 40 13 33 20 119.14 0.58 41 13 47 34 114.92 1.12 42 13 49 36 114.81 1.12 43 13 50 37 114.59 1.08 44 13 51 38 105.73 0.59 45 13 54 41 94.03 2.50 46 14 17 3 160.37 0.56 47 14 25 11 119.17 0.58 48 14 29 15 119.16 0.58 49 14 33 19 119.15 0.57 50 14 46 32 116.30 1.14 51 14 47 33 115.43 0.89 52 14 48 34 114.88 1.12 53 15 48 33 114.92 1.12 54 15 49 34 114.91 1.11 55 15 50 35 114.69 1.09 56 17 48 31 118.59 0.43 57 18 48 30 118.91 0.56 58 18 80 62 118.92 0.57 59 19 48 29 119.12 0.57 60 19 80 61 118.97 0.57 61 19 101 82 119.14 0.57 62 20 25 5 119.28 0.58 63 20 48 28 119.17 0.56 64 20 82 62 119.17 0.58 65 20 99 79 119.22 0.60 66 20 101 81 119.17 0.58 67 22 25 3 143.30 0.61 68 22 99 77 142.76 0.01 69 23 99 76 146.66 1.94 70 24 27 3 336.50 0.10 71 24 28 4 336.60 0.18 72 25 29 4 336.50 0.10 73 25 46 21 172.73 3.18 74 25 48 23 160.04 1.46 75 25 82 57 167.38 0.50 76 25 99 74 185.12 1.80 77 26 30 4 336.48 0.10 78 26 82 56 237.15 1.22 79 26 97 71 217.36 0.69 80 26 98 72 217.41 0.65 81 26 99 73 198.34 0.85 82 27 96 69 229.86 0.55 83 27 97 70 228.06 1.44 84 29 46 17 230.36 0.51 85 30 35 5 330.30 3.08 86 30 36 6 327.43 4.51 87 30 41 11 230.77 0.47 88 30 44 14 230.62 0.49 89 30 46 16 230.49 0.45 90 30 97 67 230.00 0.62 91 31 36 5 330.29 3.08 92 33 46 13 230.44 0.47 93 35 41 6 230.83 0.48 94 35 44 9 230.73 0.45 95 35 46 11 230.71 0.46 96 36 40 4 331.72 1.01 97 36 95 59 331.76 0.98 98 36 97 61 328.43 1.65 99 40 86 46 230.71 0.49 100 42 85 43 230.69 0.48 101 42 86 44 230.72 0.48 102 43 84 41 230.64 0.48 103 43 85 42 230.65 0.48 104 44 84 40 230.59 0.48 105 45 81 36 230.66 0.48 106 45 82 37 230.63 0.48 107 45 83 38 230.59 0.48 108 45 120 75 37.25 0.41 109 46 81 35 230.63 0.48 110 46 82 36 230.59 0.48 111 46 84 38 230.55 0.48 112 47 54 7 336.17 0.24 113 47 79 32 230.66 0.48 114 47 80 33 230.63 0.48 115 47 81 34 230.58 0.48 116 47 106 59 167.56 1.59 117 47 120 73 37.50 0.49 118 48 80 32 230.60 0.48 119 48 81 33 230.58 0.48 120 48 82 34 230.54 0.48 121 49 79 30 230.62 0.49 122 49 80 31 230.59 0.48 123 53 79 26 230.30 0.48 124 54 79 25 227.91 1.27 125 54 117 63 56.06 3.05 126 55 116 61 56.53 3.25 127 55 117 62 56.48 3.26 128 57 73 16 230.44 0.45 129 57 74 17 230.38 0.46 130 57 75 18 217.49 0.66 131 57 79 22 211.30 0.69 132 58 73 15 230.31 0.46 133 58 115 57 63.43 0.62 134 58 116 58 59.55 2.56 135 58 117 59 59.53 2.58 136 60 73 13 230.50 0.46 137 60 74 14 230.40 0.46 138 60 75 15 229.78 0.57 139 60 76 16 217.50 0.67 140 61 73 12 230.51 0.46 141 61 74 13 230.43 0.45 142 61 76 15 229.47 0.72 143 62 70 8 240.48 0.76 144 62 72 10 230.62 0.49 145 62 73 11 230.52 0.47 146 63 72 9 230.65 0.50 147 63 73 10 230.62 0.49 148 63 74 11 230.62 0.49 149 63 107 44 230.65 0.48 150 64 70 6 335.37 1.24 151 64 72 8 255.77 0.69 152 65 109 44 230.40 0.46 153 65 121 56 56.52 3.23 154 66 121 55 56.54 3.23 155 71 109 38 230.44 0.45 156 71 110 39 230.40 0.46 157 71 111 40 230.38 0.46 158 71 115 44 161.63 2.93 159 72 107 35 230.51 0.48 160 72 108 36 230.41 0.46 161 72 109 37 230.30 0.46 162 72 121 49 55.93 3.00 163 73 107 34 230.39 0.46 164 73 108 35 230.38 0.46 165 73 110 37 230.12 0.41 166 73 115 42 133.19 4.83 167 74 105 31 230.53 0.48 168 74 106 32 230.40 0.46 169 74 107 33 230.03 0.52 170 74 124 50 38.17 0.67 171 75 79 4 217.12 0.76 172 75 105 30 230.41 0.45 173 75 106 31 230.39 0.46 174 76 105 29 230.40 0.46 175 77 105 28 229.26 0.62 176 78 103 25 230.38 0.46 177 78 104 26 218.05 0.38 178 78 105 27 215.96 0.14 179 79 103 24 222.63 1.91 180 79 104 25 217.44 0.65 181 79 106 27 203.34 1.33 182 80 101 21 230.41 0.45 183 80 102 22 228.84 0.70 184 80 103 23 216.99 0.83 185 81 101 20 219.41 0.93 186 81 102 21 217.43 0.65 187 81 104 23 198.11 0.03 188 81 106 25 169.09 0.20 189 81 123 42 36.78 0.17 190 82 99 17 230.35 0.47 191 82 100 18 220.28 0.72 192 82 101 19 216.12 0.39 193 83 99 16 225.50 1.64 194 83 100 17 217.25 0.73 195 84 97 13 230.30 0.45 196 84 98 14 225.48 1.65 197 85 97 12 230.34 0.47 198 85 98 13 230.06 0.58 199 86 90 4 265.91 0.19 200 86 96 10 230.57 0.49 201 86 97 11 230.46 0.48 202 87 90 3 334.70 0.02 203 87 96 9 230.65 0.50 204 87 97 10 230.59 0.48 205 87 98 11 230.56 0.48 206 90 95 5 238.75 3.48 207 90 96 6 230.75 0.50 208 91 94 3 336.88 0.01 209 91 95 4 293.39 1.79 210 104 123 19 37.56 0.48 211 104 124 20 36.78 0.17 212 105 123 18 37.68 0.53 213 105 124 19 37.47 0.48 214 106 120 14 49.69 0.49 215 106 122 16 38.30 0.60 216 106 123 17 37.67 0.54 217 107 121 14 44.76 0.19 218 107 122 15 38.40 0.57 219 107 124 17 38.16 0.66 220 108 117 9 59.54 2.58 221 108 119 11 56.62 3.27 222 108 120 12 55.45 3.23 223 109 117 8 59.55 2.58 224 109 118 9 59.48 2.56 225 109 119 10 57.16 3.52 226 110 115 5 65.39 0.01 227 110 116 6 64.59 0.07 228 110 117 7 59.55 2.58 229 110 118 8 59.53 2.58 230 111 115 4 69.39 1.99 231 111 116 5 65.08 0.24 232 111 118 7 59.59 2.57 233 112 115 3 141.63 5.09