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 8 12 4 305.63 1.29 2 9 12 3 320.99 0.30 3 9 13 4 305.60 1.30 4 10 13 3 311.68 4.34 5 10 14 4 305.60 1.30 6 10 67 57 65.97 0.36 7 11 14 3 314.56 4.95 8 11 15 4 314.56 4.94 9 12 15 3 321.63 1.41 10 12 16 4 314.55 4.95 11 13 16 3 309.73 2.54 12 13 17 4 309.73 2.54 13 13 62 49 85.02 1.28 14 13 67 54 82.33 0.07 15 14 17 3 319.05 0.18 16 14 18 4 309.71 2.54 17 14 71 57 80.64 0.77 18 14 75 61 89.33 1.74 19 15 18 3 320.64 0.63 20 15 19 4 305.27 2.42 21 16 19 3 316.44 2.73 22 16 20 4 310.54 0.21 23 16 61 45 96.03 0.08 24 17 20 3 311.95 0.48 25 17 21 4 311.94 0.48 26 17 58 41 96.08 0.10 27 17 62 45 96.02 0.07 28 17 67 50 96.01 0.07 29 17 68 51 95.91 0.04 30 17 71 54 96.00 0.07 31 18 21 3 315.50 1.29 32 18 22 4 308.94 1.04 33 18 71 53 96.34 0.23 34 18 72 54 95.95 0.07 35 18 75 57 96.41 0.21 36 18 76 58 96.36 0.24 37 19 22 3 308.94 1.04 38 19 23 4 308.95 1.05 39 20 23 3 317.67 0.19 40 20 24 4 314.56 1.75 41 20 57 37 98.00 0.23 42 20 58 38 97.87 0.30 43 20 61 41 98.01 0.23 44 21 24 3 322.50 2.60 45 21 25 4 306.82 2.12 46 21 52 31 97.70 0.23 47 21 58 37 98.00 0.24 48 21 68 47 97.80 0.19 49 21 80 59 97.62 0.10 50 21 89 68 88.61 0.21 51 22 25 3 307.83 1.61 52 22 26 4 268.67 5.83 53 22 76 54 97.66 0.12 54 23 28 5 243.96 1.48 55 23 29 6 228.06 3.25 56 23 57 34 98.39 0.12 57 24 29 5 228.06 3.25 58 24 30 6 228.06 3.25 59 24 33 9 221.36 2.48 60 24 35 11 221.12 2.38 61 24 36 12 210.60 2.77 62 24 52 28 98.02 0.13 63 24 57 33 98.48 0.10 64 24 58 34 98.47 0.10 65 25 29 4 262.85 3.90 66 25 30 5 245.36 0.49 67 25 36 11 210.84 2.68 68 25 79 54 97.81 0.08 69 25 80 55 97.78 0.07 70 25 89 64 94.39 1.79 71 25 90 65 88.59 0.20 72 25 91 66 87.95 0.09 73 27 30 3 317.42 0.29 74 27 31 4 305.76 0.23 75 27 91 64 88.42 0.22 76 27 97 70 34.82 0.99 77 27 98 71 32.79 0.03 78 27 100 73 27.36 0.81 79 28 31 3 319.86 1.51 80 28 100 72 27.34 0.80 81 29 32 3 315.50 0.55 82 29 33 4 285.76 2.66 83 29 35 6 285.78 2.65 84 30 33 3 309.92 2.24 85 30 37 7 271.81 4.29 86 30 91 61 88.41 0.22 87 30 97 67 42.93 2.19 88 31 97 66 43.01 2.21 89 31 99 68 32.79 0.03 90 33 36 3 315.81 1.15 91 33 37 4 306.28 3.62 92 34 37 3 316.48 0.81 93 34 38 4 315.80 1.15 94 35 38 3 316.48 0.81 95 35 39 4 312.65 0.42 96 35 55 20 112.16 4.03 97 36 39 3 313.34 0.76 98 36 40 4 312.63 0.42 99 36 47 11 109.70 5.55 100 36 52 16 107.79 1.88 101 37 40 3 315.08 0.78 102 37 41 4 306.42 2.68 103 38 41 3 313.62 0.90 104 38 42 4 295.80 1.51 105 39 42 3 306.22 3.54 106 39 47 8 120.84 0.01 107 39 48 9 120.84 0.01 108 39 51 12 112.55 4.40 109 40 45 5 120.23 0.20 110 40 47 7 126.14 2.63 111 43 46 3 338.92 0.51 112 44 90 46 108.31 1.93 113 45 90 45 108.08 1.82 114 46 81 35 109.62 1.40 115 46 82 36 109.64 1.40 116 46 83 37 109.66 1.40 117 46 88 42 109.67 1.39 118 46 89 43 109.34 1.53 119 46 90 44 108.34 1.95 120 47 51 4 313.42 1.24 121 47 88 41 109.73 1.36 122 47 89 42 109.39 1.52 123 47 90 43 109.34 1.54 124 48 51 3 322.42 0.71 125 48 87 39 110.52 1.53 126 48 88 40 110.37 1.46 127 49 52 3 309.18 3.36 128 49 53 4 301.53 0.20 129 49 65 16 148.99 1.59 130 49 68 19 148.96 1.60 131 49 69 20 148.90 1.59 132 49 72 23 148.83 1.57 133 49 86 37 110.80 1.58 134 49 87 38 110.55 1.54 135 49 88 39 110.48 1.51 136 49 89 40 110.44 1.49 137 50 53 3 304.22 0.12 138 50 54 4 302.93 0.52 139 50 65 15 151.63 0.29 140 51 54 3 309.39 1.72 141 51 55 4 302.93 0.52 142 52 55 3 313.78 0.05 143 52 58 6 234.03 2.04 144 52 59 7 234.03 2.04 145 52 89 37 110.54 1.54 146 53 58 5 258.76 10.32 147 53 59 6 233.88 2.04 148 53 63 10 180.68 0.55 149 53 65 12 168.53 5.53 150 53 68 15 168.44 5.50 151 54 59 5 258.81 10.35 152 55 58 3 324.38 0.70 153 55 59 4 279.44 0.05 154 56 59 3 306.43 2.19 155 56 60 4 279.44 0.06 156 58 61 3 311.30 3.06 157 58 62 4 311.29 3.06 158 58 63 5 233.69 2.23 159 58 68 10 209.51 5.38 160 59 63 4 230.08 4.04 161 62 67 5 256.75 1.46 162 62 68 6 246.53 3.65 163 64 67 3 292.52 2.81 164 64 68 4 296.03 3.62 165 65 68 3 307.38 0.81 166 65 69 4 303.80 0.26 167 66 69 3 312.36 1.68 168 66 70 4 305.02 0.94 169 67 70 3 311.26 2.99 170 67 71 4 305.03 0.94 171 68 71 3 318.92 0.83 172 68 72 4 305.00 0.95 173 69 72 3 318.23 1.18 174 69 73 4 295.91 5.33 175 69 86 17 111.48 1.90 176 69 87 18 111.47 1.90 177 70 73 3 309.56 1.46 178 70 74 4 305.70 0.45 179 71 74 3 316.88 0.83 180 71 75 4 294.76 4.73 181 72 75 3 300.88 3.33 182 72 77 5 255.33 4.91 183 72 82 10 141.80 0.42 184 72 89 17 112.21 2.08 185 73 77 4 265.87 0.38 186 73 86 13 112.23 2.06 187 74 77 3 317.96 1.31 188 76 79 3 323.61 2.40 189 77 82 5 211.42 8.56 190 80 89 9 115.75 1.66 191 80 90 10 114.13 2.12 192 80 91 11 113.31 1.73 193 80 92 12 113.24 1.76 194 81 90 9 114.14 2.11 195 81 92 11 113.28 1.74 196 82 86 4 283.21 13.31 197 82 88 6 154.18 3.08 198 83 86 3 309.55 0.15 199 83 88 5 184.71 1.28 200 85 88 3 363.91 1.76 201 91 95 4 318.77 1.22 202 91 96 5 294.77 4.20 203 91 97 6 260.43 2.67 204 92 95 3 304.16 2.33