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 8 134.02 0.26 2 3 6 3 149.90 1.75 3 3 7 4 147.63 1.41 4 4 7 3 150.80 1.05 5 4 8 4 148.87 2.02 6 4 118 114 24.41 0.33 7 5 8 3 149.89 1.85 8 5 9 4 149.55 2.00 9 5 116 111 24.58 0.34 10 5 117 112 24.57 0.34 11 5 118 113 24.57 0.34 12 6 9 3 151.71 2.89 13 6 10 4 149.20 1.83 14 7 10 3 157.64 0.09 15 7 11 4 148.69 2.08 16 8 11 3 157.65 0.09 17 8 12 4 148.68 2.09 18 8 13 5 144.55 0.03 19 8 54 46 64.18 6.55 20 8 108 100 34.74 1.04 21 8 117 109 34.74 1.04 22 8 118 110 34.52 0.94 23 8 119 111 34.50 0.93 24 8 120 112 34.48 0.93 25 9 12 3 151.53 1.15 26 9 13 4 140.81 0.26 27 9 33 24 117.29 1.60 28 9 51 42 90.47 0.07 29 10 33 23 117.28 1.60 30 10 34 24 118.07 2.00 31 10 35 25 118.06 2.00 32 11 35 24 118.06 2.00 33 11 41 30 119.26 2.62 34 11 44 33 115.80 1.22 35 11 46 35 113.52 0.73 36 12 41 29 119.37 2.66 37 12 44 32 115.81 1.22 38 12 45 33 114.16 0.43 39 12 46 34 113.50 0.73 40 12 47 35 113.50 0.73 41 12 120 108 35.94 0.79 42 13 33 20 120.13 2.38 43 13 49 36 113.52 0.72 44 13 50 37 113.45 0.72 45 13 51 38 111.80 0.83 46 13 54 41 100.92 1.89 47 14 17 3 169.81 0.77 48 14 25 11 117.95 1.28 49 14 29 15 119.22 1.91 50 14 33 19 120.14 2.37 51 14 46 32 117.09 1.53 52 14 47 33 115.06 0.85 53 14 48 34 113.53 0.73 54 15 49 34 113.75 0.61 55 15 50 35 113.43 0.70 56 15 51 36 113.43 0.70 57 17 25 8 120.20 2.35 58 17 48 31 118.09 1.46 59 18 48 30 119.12 1.95 60 18 80 62 119.11 1.95 61 19 48 29 119.86 2.30 62 19 80 61 119.14 1.95 63 19 101 82 119.95 2.35 64 20 25 5 120.26 2.35 65 20 48 28 120.06 2.35 66 20 82 62 120.06 2.35 67 20 99 79 120.05 2.35 68 20 101 81 119.98 2.33 69 22 25 3 164.60 1.12 70 22 99 77 155.66 1.28 71 23 99 76 151.06 1.02 72 24 99 75 173.40 0.83 73 25 46 21 186.03 3.52 74 25 48 23 164.93 0.97 75 25 82 57 173.41 0.84 76 25 99 74 194.33 0.70 77 26 82 56 236.37 1.93 78 26 97 71 217.02 0.03 79 26 98 72 216.08 0.45 80 26 99 73 203.94 1.79 81 27 95 68 230.08 1.06 82 27 96 69 229.91 1.14 83 27 97 70 227.40 0.98 84 29 46 17 229.94 0.97 85 30 36 6 336.90 1.63 86 30 41 11 230.33 1.08 87 30 44 14 230.28 1.06 88 30 46 16 230.15 1.02 89 30 97 67 230.06 1.11 90 33 46 13 229.98 0.96 91 35 40 5 338.00 0.41 92 35 41 6 312.28 10.84 93 35 44 9 230.34 1.07 94 35 46 11 230.34 1.07 95 36 40 4 337.67 0.58 96 36 95 59 337.93 0.70 97 36 97 61 337.66 0.58 98 40 86 46 230.41 1.07 99 42 85 43 230.31 1.09 100 42 86 44 230.33 1.09 101 43 84 41 230.28 1.07 102 43 85 42 230.29 1.07 103 44 83 39 230.28 1.07 104 44 84 40 230.22 1.08 105 45 81 36 230.33 1.08 106 45 82 37 230.27 1.07 107 45 83 38 230.18 1.09 108 45 120 75 38.06 0.14 109 46 81 35 230.27 1.07 110 46 82 36 230.25 1.08 111 46 84 38 230.16 1.10 112 47 79 32 230.32 1.08 113 47 80 33 230.28 1.08 114 47 81 34 230.19 1.07 115 47 106 59 289.59 2.77 116 47 120 73 38.43 0.32 117 48 80 32 230.25 1.07 118 48 81 33 230.21 1.09 119 48 82 34 230.19 1.08 120 49 79 30 230.25 1.08 121 49 80 31 230.24 1.08 122 53 79 26 229.95 1.09 123 54 79 25 227.58 1.04 124 54 117 63 67.28 0.73 125 55 116 61 68.28 1.13 126 55 117 62 67.28 0.73 127 57 73 16 229.98 1.08 128 57 74 17 229.98 1.08 129 57 75 18 221.27 2.04 130 57 79 22 212.28 0.10 131 58 73 15 229.96 1.09 132 58 115 57 69.55 0.94 133 58 116 58 69.39 0.97 134 58 117 59 69.39 0.97 135 60 73 13 230.19 1.08 136 60 74 14 230.14 1.10 137 60 75 15 228.68 0.51 138 60 76 16 222.57 1.40 139 61 73 12 230.22 1.08 140 61 74 13 230.16 1.09 141 61 76 15 230.08 1.10 142 62 70 8 247.39 2.58 143 62 72 10 230.28 1.07 144 62 73 11 230.23 1.09 145 63 72 9 230.32 1.09 146 63 73 10 230.25 1.08 147 63 74 11 230.24 1.08 148 63 107 44 230.31 1.09 149 64 72 8 257.88 0.38 150 65 109 44 230.00 1.12 151 65 121 56 67.39 0.81 152 66 121 55 67.48 0.77 153 71 109 38 230.12 1.09 154 71 110 39 230.09 1.09 155 71 111 40 230.02 1.07 156 71 115 44 162.55 0.58 157 72 107 35 230.20 1.08 158 72 108 36 230.12 1.09 159 72 109 37 229.88 1.07 160 72 121 49 67.36 0.82 161 73 107 34 230.15 1.09 162 73 108 35 230.11 1.09 163 73 110 37 228.63 0.53 164 73 115 42 103.55 8.14 165 74 105 31 230.22 1.08 166 74 106 32 230.15 1.09 167 74 107 33 229.63 0.97 168 74 124 50 41.63 1.76 169 75 79 4 215.81 0.58 170 75 105 30 230.13 1.08 171 75 106 31 230.12 1.09 172 76 105 29 230.13 1.09 173 77 105 28 228.95 1.37 174 78 103 25 230.10 1.09 175 78 104 26 217.40 0.12 176 78 105 27 215.94 0.52 177 79 103 24 222.57 1.40 178 79 104 25 217.08 0.04 179 79 106 27 209.01 1.09 180 80 101 21 230.15 1.09 181 80 102 22 229.41 1.06 182 80 103 23 215.94 0.51 183 81 101 20 220.75 1.42 184 81 102 21 216.09 0.45 185 81 104 23 212.28 1.07 186 81 106 25 169.78 0.40 187 82 99 17 230.12 1.09 188 82 100 18 219.07 0.79 189 82 101 19 215.89 0.54 190 83 98 15 230.15 1.09 191 83 99 16 220.57 1.51 192 83 100 17 215.93 0.53 193 84 97 13 230.07 1.11 194 84 98 14 217.31 0.14 195 85 97 12 230.11 1.09 196 85 98 13 229.56 1.06 197 86 90 4 267.29 6.87 198 86 96 10 230.24 1.08 199 86 97 11 230.12 1.11 200 87 90 3 338.08 0.34 201 87 96 9 230.27 1.09 202 87 98 11 230.13 1.11 203 90 95 5 230.34 1.10 204 90 96 6 230.32 1.09 205 104 123 19 41.48 1.83 206 104 124 20 37.68 0.67 207 105 123 18 41.63 1.76 208 105 124 19 38.41 0.30 209 106 120 14 67.07 0.70 210 106 122 16 43.02 1.65 211 106 123 17 38.41 0.30 212 107 120 13 67.20 0.77 213 107 121 14 64.64 0.36 214 107 122 15 45.24 0.53 215 107 124 17 42.59 1.44 216 108 117 9 69.36 0.98 217 108 119 11 67.40 0.79 218 108 120 12 67.21 0.76 219 108 121 13 66.79 0.76 220 109 117 8 69.39 0.97 221 109 118 9 69.38 0.98 222 109 119 10 68.42 1.26 223 110 115 5 70.35 1.28 224 110 116 6 69.73 1.05 225 110 117 7 69.40 0.97 226 110 118 8 69.39 0.97 227 111 115 4 103.42 8.07 228 111 116 5 70.36 1.29 229 111 118 7 69.42 0.99 230 112 115 3 156.85 2.34