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 34 33 151.81 0.44 2 1 37 36 151.80 0.45 3 1 38 37 151.78 0.45 4 1 43 42 151.69 0.44 5 1 46 45 151.60 0.48 6 1 47 46 151.57 0.49 7 2 5 3 307.38 0.20 8 2 6 4 301.68 0.27 9 2 46 44 151.66 0.49 10 2 50 48 151.57 0.49 11 3 6 3 301.68 0.27 12 3 7 4 301.89 0.16 13 3 50 47 151.57 0.49 14 4 7 3 309.66 1.43 15 4 8 4 304.31 0.93 16 5 8 3 305.67 0.26 17 5 9 4 305.85 0.16 18 6 9 3 308.84 1.33 19 6 10 4 305.86 0.16 20 6 34 28 152.37 0.54 21 6 47 41 151.75 0.46 22 6 50 44 151.71 0.48 23 6 51 45 151.69 0.48 24 6 54 48 151.47 0.38 25 7 10 3 312.37 0.54 26 7 11 4 308.41 1.45 27 7 54 47 151.47 0.39 28 8 11 3 314.73 0.64 29 8 12 4 316.66 1.60 30 9 12 3 347.38 0.33 31 9 30 21 153.00 0.57 32 9 33 24 153.00 0.58 33 9 34 25 152.99 0.57 34 9 37 28 152.97 0.56 35 10 13 3 313.79 1.11 36 10 14 4 309.05 1.12 37 10 31 21 153.01 0.57 38 10 34 24 153.00 0.57 39 10 51 41 151.81 0.45 40 10 69 59 81.94 0.17 41 11 14 3 308.16 1.52 42 12 26 14 153.63 0.42 43 12 27 15 153.60 0.43 44 13 16 3 312.95 0.23 45 13 17 4 303.31 1.42 46 13 27 14 153.63 0.43 47 13 31 18 153.63 0.43 48 13 69 56 93.97 1.85 49 14 17 3 309.86 1.31 50 14 18 4 303.32 1.42 51 14 58 44 151.33 0.40 52 15 18 3 303.32 1.42 53 15 19 4 303.32 1.41 54 15 20 5 250.52 6.25 55 16 19 3 305.76 0.18 56 16 20 4 268.43 1.23 57 16 21 5 264.49 0.73 58 16 22 6 218.81 1.91 59 16 23 7 207.28 2.09 60 16 65 49 112.76 1.74 61 16 69 53 100.11 0.39 62 16 72 56 94.30 1.07 63 17 58 41 151.50 0.36 64 17 60 43 149.53 0.30 65 17 61 44 137.14 0.45 66 17 62 45 120.78 2.20 67 17 65 48 109.15 0.04 68 17 66 49 102.12 0.48 69 17 69 52 101.95 0.53 70 18 58 40 151.50 0.36 71 18 59 41 151.43 0.38 72 18 60 42 148.60 0.77 73 19 62 43 137.86 0.81 74 19 65 46 117.50 0.52 75 20 65 45 117.50 0.52 76 23 27 4 303.05 1.78 77 23 28 5 285.71 6.80 78 23 72 49 83.68 0.84 79 23 73 50 82.00 0.18 80 24 27 3 303.06 1.78 81 24 28 4 303.07 1.77 82 25 28 3 303.07 1.77 83 25 29 4 303.07 1.77 84 26 29 3 303.73 1.45 85 26 30 4 305.54 0.54 86 27 30 3 305.57 0.51 87 27 31 4 301.58 1.49 88 27 69 42 84.44 1.41 89 28 31 3 313.10 4.27 90 28 32 4 301.57 1.49 91 28 72 44 81.38 0.00 92 28 73 45 76.69 0.14 93 29 32 3 314.73 3.45 94 29 33 4 301.57 1.49 95 30 33 3 306.14 0.87 96 30 34 4 301.54 1.51 97 31 34 3 314.19 3.72 98 31 35 4 301.58 1.53 99 31 69 38 81.53 0.07 100 31 73 42 76.69 0.14 101 31 75 44 73.20 1.72 102 32 35 3 302.36 1.16 103 32 36 4 301.60 1.54 104 32 73 41 76.69 0.14 105 32 74 42 76.66 0.16 106 32 75 43 73.20 1.72 107 33 36 3 307.18 3.58 108 33 37 4 301.60 1.54 109 34 37 3 302.59 2.08 110 34 38 4 299.39 2.65 111 34 47 13 165.98 3.02 112 35 38 3 303.97 0.36 113 35 75 40 69.07 0.34 114 35 76 41 68.89 0.25 115 35 77 42 66.11 1.12 116 36 39 3 319.75 0.33 117 37 43 6 278.06 3.91 118 38 43 5 253.52 2.71 119 38 44 6 242.36 8.28 120 38 47 9 219.99 0.30 121 39 43 4 297.95 1.67 122 39 44 5 290.99 1.81 123 40 43 3 302.72 0.71 124 40 44 4 297.96 1.66 125 41 44 3 302.14 1.28 126 41 45 4 291.88 1.38 127 41 91 50 14.95 0.11 128 42 45 3 309.36 2.33 129 42 46 4 291.86 1.36 130 43 46 3 300.82 2.73 131 43 47 4 296.69 1.08 132 44 47 3 297.53 0.67 133 44 48 4 296.64 1.10 134 44 90 46 15.91 0.35 135 44 91 47 15.21 0.02 136 45 48 3 299.22 1.02 137 45 49 4 296.54 1.15 138 45 87 42 23.32 0.65 139 45 90 45 16.22 0.35 140 45 91 46 15.21 0.02 141 46 49 3 302.17 0.46 142 46 50 4 296.47 1.18 143 47 50 3 308.19 0.14 144 47 51 4 303.60 2.39 145 48 51 3 312.94 1.82 146 48 52 4 295.86 0.90 147 48 85 37 32.26 0.01 148 48 87 39 23.68 0.82 149 48 90 42 19.28 0.61 150 49 52 3 306.76 0.58 151 49 53 4 297.96 0.16 152 49 87 38 23.66 0.83 153 50 53 3 307.14 0.60 154 50 54 4 301.56 0.88 155 51 54 3 305.83 1.26 156 51 55 4 301.55 0.89 157 52 55 3 315.14 2.81 158 52 56 4 303.38 0.01 159 52 83 31 33.51 0.07 160 52 84 32 33.55 0.10 161 52 85 33 32.82 0.17 162 52 87 35 31.65 0.31 163 53 56 3 319.70 0.53 164 53 57 4 303.38 0.01 165 54 57 3 306.86 1.24 166 54 58 4 303.37 0.01 167 55 58 3 303.02 1.34 168 55 61 6 202.08 4.36 169 58 61 3 302.62 5.01 170 62 65 3 303.75 2.50 171 62 66 4 296.64 0.54 172 63 66 3 298.80 0.54 173 63 67 4 297.87 0.42 174 63 81 18 55.70 0.01 175 63 82 19 54.00 0.84 176 64 67 3 302.49 1.57 177 64 68 4 302.49 1.58 178 65 68 3 305.66 0.01 179 65 69 4 305.90 0.12 180 66 69 3 316.85 1.67 181 66 70 4 318.77 0.70 182 66 81 15 55.72 0.01 183 67 70 3 336.48 2.85 184 67 81 14 55.72 0.01 185 69 72 3 307.52 0.90 186 69 73 4 279.37 0.38 187 70 73 3 296.73 3.01 188 70 74 4 270.19 4.21 189 70 75 5 198.26 3.29 190 70 77 7 165.71 2.06 191 70 81 11 63.38 0.32 192 71 74 3 287.44 1.63 193 77 81 4 323.97 0.07 194 79 85 6 183.65 3.42 195 79 90 11 32.72 0.96 196 79 91 12 34.83 0.10 197 80 85 5 195.63 5.41 198 82 85 3 294.13 1.85 199 85 90 5 313.69 0.46 200 86 89 3 315.76 0.48 201 86 90 4 313.69 0.46 202 87 90 3 320.09 3.65 203 88 91 3 445.14 3.85