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 21 24 3 349.52 0.94 2 21 25 4 335.09 6.05 3 22 25 3 347.57 0.18 4 28 32 4 329.50 0.43 5 28 33 5 324.67 1.20 6 28 36 8 310.87 0.07 7 29 32 3 331.54 0.99 8 29 33 4 331.52 0.58 9 30 33 3 334.38 0.86 10 30 34 4 334.20 0.77 11 31 34 3 339.69 1.75 12 31 35 4 334.22 0.77 13 32 35 3 334.23 0.77 14 32 36 4 334.20 0.77 15 33 36 3 336.00 1.66 16 33 37 4 332.21 1.76 17 34 37 3 335.84 0.65 18 34 38 4 335.12 0.29 19 35 38 3 344.64 0.42 20 35 39 4 339.23 2.33 21 36 39 3 344.69 0.40 22 36 40 4 339.23 2.33 23 37 40 3 344.69 0.40 24 37 41 4 339.22 2.33 25 38 41 3 340.81 1.54 26 38 42 4 338.51 2.68 27 39 42 3 341.47 1.19 28 39 43 4 338.49 2.68 29 39 88 49 78.15 1.01 30 39 107 68 67.17 3.40 31 39 110 71 56.43 1.97 32 40 43 3 341.33 1.79 33 40 44 4 331.30 0.23 34 41 44 3 336.19 0.26 35 42 48 6 285.49 8.25 36 42 86 44 82.04 0.12 37 42 88 46 82.04 0.12 38 43 49 6 268.35 6.83 39 43 52 9 255.72 1.27 40 43 88 45 83.73 0.71 41 43 110 67 66.41 2.98 42 45 48 3 337.91 0.89 43 45 49 4 328.83 0.59 44 46 49 3 342.54 1.43 45 46 50 4 333.13 0.90 46 47 50 3 336.49 0.78 47 47 51 4 336.56 0.82 48 47 79 32 185.74 0.37 49 48 51 3 337.17 0.51 50 48 52 4 336.56 0.82 51 48 82 34 185.74 0.36 52 48 83 35 185.72 0.36 53 48 86 38 185.64 0.32 54 49 52 3 337.18 0.52 55 49 53 4 336.56 0.82 56 50 53 3 338.68 1.35 57 50 54 4 337.08 0.56 58 50 69 19 186.35 0.23 59 51 54 3 346.67 2.64 60 51 55 4 339.76 0.85 61 51 65 14 186.36 0.22 62 51 69 18 186.40 0.21 63 51 76 25 186.05 0.29 64 51 79 28 185.97 0.29 65 51 83 32 185.78 0.35 66 52 55 3 339.62 0.93 67 52 56 4 338.02 1.72 68 52 83 31 185.78 0.35 69 52 88 36 185.38 0.30 70 52 89 37 185.31 0.30 71 52 102 50 173.38 3.02 72 53 56 3 339.62 0.93 73 53 57 4 340.15 1.19 74 53 111 58 77.62 1.85 75 54 57 3 348.82 0.71 76 54 58 4 339.62 0.93 77 54 60 6 313.07 1.59 78 54 65 11 192.81 3.37 79 54 68 14 186.63 0.29 80 54 69 15 186.59 0.29 81 55 58 3 338.04 1.72 82 55 59 4 325.90 2.98 83 55 60 5 314.66 2.39 84 55 65 10 202.38 1.39 85 55 80 25 186.07 0.28 86 55 89 34 185.37 0.30 87 55 100 45 184.44 0.33 88 55 101 46 181.42 0.10 89 55 102 47 175.93 1.75 90 56 102 46 180.34 0.45 91 56 108 52 90.44 1.41 92 56 111 55 92.89 0.17 93 59 92 33 185.30 0.32 94 59 99 40 184.58 0.35 95 59 100 41 184.52 0.35 96 59 101 42 184.06 0.31 97 60 64 4 332.94 1.81 98 60 65 5 332.93 1.80 99 60 99 39 184.56 0.35 100 60 100 40 184.45 0.33 101 61 64 3 340.97 4.19 102 61 65 4 334.20 1.18 103 61 97 36 184.69 0.35 104 61 98 37 184.66 0.34 105 61 99 38 184.59 0.32 106 62 65 3 341.05 4.15 107 62 66 4 334.21 1.18 108 62 73 11 186.79 0.27 109 62 76 14 186.73 0.24 110 62 77 15 186.71 0.25 111 62 80 18 186.50 0.35 112 62 100 38 184.52 0.29 113 63 66 3 348.52 1.30 114 63 67 4 334.21 1.18 115 63 73 10 186.84 0.24 116 64 67 3 345.40 2.87 117 64 68 4 333.56 0.85 118 65 68 3 346.44 1.47 119 65 69 4 346.44 1.48 120 65 76 11 186.74 0.24 121 65 80 15 186.66 0.23 122 65 100 35 184.44 0.33 123 66 69 3 346.45 1.47 124 66 70 4 328.08 0.35 125 66 71 5 237.96 1.56 126 66 72 6 227.50 4.86 127 66 73 7 208.55 4.61 128 66 76 10 186.75 0.24 129 67 70 3 339.31 5.04 130 71 75 4 338.92 1.72 131 71 76 5 321.45 0.52 132 72 75 3 342.08 0.14 133 72 76 4 332.35 1.56 134 73 76 3 346.76 1.12 135 73 77 4 332.29 1.54 136 74 77 3 334.08 0.70 137 74 78 4 334.02 0.68 138 75 78 3 334.03 0.68 139 75 79 4 336.70 2.02 140 76 79 3 344.88 2.08 141 76 80 4 336.16 1.65 142 77 80 3 345.91 1.67 143 77 81 4 341.01 0.78 144 78 81 3 349.38 0.07 145 78 82 4 345.88 1.68 146 79 82 3 350.15 0.32 147 79 83 4 341.35 0.62 148 80 83 3 341.35 0.62 149 80 84 4 337.43 1.33 150 80 89 9 205.93 2.90 151 80 100 20 184.32 0.38 152 81 84 3 341.35 0.62 153 81 85 4 336.51 1.79 154 82 85 3 333.38 3.36 155 82 86 4 330.91 4.59 156 83 86 3 337.12 1.48 157 83 87 4 330.89 4.58 158 83 88 5 282.66 3.27 159 83 89 6 241.95 17.05 160 84 87 3 338.58 0.73 161 84 89 5 282.63 3.29 162 84 91 7 241.78 17.14 163 84 100 16 184.49 0.32 164 87 103 16 173.54 2.99 165 88 102 14 178.34 0.61 166 88 103 15 173.47 3.02 167 88 107 19 156.21 5.38 168 89 100 11 184.51 0.33 169 89 101 12 183.98 0.33 170 89 102 13 178.34 0.61 171 89 103 14 175.98 1.78 172 90 100 10 184.53 0.33 173 90 101 11 184.43 0.34 174 90 103 13 179.34 0.11 175 91 98 7 184.71 0.31 176 91 99 8 184.62 0.33 177 91 100 9 184.53 0.33 178 91 101 10 184.52 0.33 179 92 98 6 187.77 1.22 180 92 99 7 184.68 0.31 181 93 97 4 251.48 3.99 182 93 98 5 187.78 1.23 183 94 97 3 337.41 0.58 184 94 99 5 266.79 11.63 185 102 107 5 318.51 2.90 186 102 108 6 250.72 7.63 187 103 107 4 332.95 0.33 188 104 107 3 347.64 0.72 189 104 108 4 343.29 1.39 190 105 108 3 343.35 1.36 191 105 109 4 328.31 5.36 192 106 109 3 337.89 4.39 193 106 110 4 328.32 5.36 194 107 110 3 342.56 2.05 195 107 111 4 330.17 1.73 196 108 111 3 336.34 1.35 197 108 112 4 321.61 1.56 198 109 112 3 339.97 3.35 199 109 113 4 321.49 1.48 200 110 113 3 335.00 0.27 201 110 114 4 318.99 0.17 202 111 114 3 335.00 0.27 203 111 115 4 334.99 0.28 204 112 115 3 343.54 1.57 205 112 116 4 328.89 2.79 206 113 116 3 339.51 2.52 207 113 117 4 326.51 1.59 208 114 117 3 341.00 1.78 209 114 118 4 340.99 1.78 210 115 118 3 343.78 0.38 211 115 119 4 332.59 2.43 212 116 119 3 340.05 1.30 213 116 120 4 332.59 2.43 214 117 120 3 340.05 1.31 215 117 121 4 339.00 3.83 216 118 121 3 347.62 0.41