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 10 13 3 297.05 0.17 2 10 101 91 42.26 0.79 3 10 105 95 37.41 1.47 4 11 14 3 278.60 2.23 5 11 17 6 196.59 23.68 6 12 17 5 248.98 0.27 7 12 18 6 245.56 1.43 8 12 44 32 95.38 1.19 9 12 58 46 93.20 2.10 10 12 108 96 42.27 0.79 11 13 18 5 270.88 1.67 12 13 58 45 93.20 2.10 13 13 59 46 93.20 2.10 14 13 93 80 45.81 0.29 15 13 101 88 42.31 0.80 16 13 105 92 42.27 0.80 17 13 108 95 42.27 0.79 18 14 17 3 290.04 3.52 19 14 18 4 279.06 0.42 20 14 94 80 45.83 0.29 21 15 18 3 287.64 4.71 22 15 19 4 274.57 0.19 23 15 40 25 97.99 0.29 24 16 19 3 286.70 5.17 25 16 20 4 274.21 0.01 26 17 20 3 275.25 0.51 27 17 21 4 274.22 0.01 28 18 21 3 286.60 0.22 29 18 22 4 286.60 0.22 30 18 39 21 103.06 0.07 31 18 40 22 104.57 0.69 32 18 42 24 103.05 0.07 33 18 43 25 103.05 0.07 34 18 44 26 103.03 0.06 35 18 58 40 102.95 0.03 36 19 22 3 287.06 0.04 37 19 36 17 110.29 3.54 38 19 39 20 103.06 0.07 39 21 44 23 118.95 0.20 40 21 45 24 118.98 0.21 41 22 25 3 280.99 0.17 42 22 35 13 119.02 0.19 43 22 38 16 119.02 0.20 44 22 39 17 119.01 0.20 45 22 43 21 119.00 0.21 46 22 44 22 119.00 0.21 47 22 45 23 119.00 0.21 48 23 45 22 135.48 0.23 49 24 45 21 141.41 2.65 50 25 28 3 336.27 0.32 51 25 33 8 151.62 1.48 52 25 35 10 142.50 2.10 53 25 38 13 142.50 2.10 54 25 45 20 141.41 2.65 55 25 53 28 142.02 2.35 56 25 67 42 151.62 1.48 57 27 31 4 263.78 1.93 58 27 33 6 151.68 1.50 59 27 35 8 156.94 1.14 60 27 67 40 151.68 1.49 61 27 68 41 164.46 4.90 62 27 69 42 151.68 1.50 63 28 35 7 198.21 6.04 64 29 34 5 203.31 1.07 65 30 34 4 253.91 4.04 66 31 34 3 291.31 5.44 67 31 69 38 231.59 1.42 68 31 70 39 231.59 1.43 69 32 37 5 236.83 0.87 70 32 69 37 231.68 1.45 71 32 70 38 231.65 1.44 72 32 71 39 231.61 1.44 73 32 72 40 231.53 1.46 74 32 73 41 231.53 1.46 75 33 38 5 236.83 0.87 76 33 67 34 231.68 1.45 77 33 68 35 231.68 1.45 78 33 69 36 231.68 1.45 79 33 71 38 231.65 1.44 80 33 73 40 231.58 1.43 81 34 37 3 265.63 1.74 82 34 38 4 265.12 2.00 83 35 38 3 272.99 5.41 84 35 39 4 258.51 1.31 85 36 40 4 256.52 2.30 86 37 40 3 256.75 2.41 87 37 41 4 256.53 2.29 88 37 73 36 233.00 0.83 89 38 41 3 279.60 3.24 90 38 42 4 256.30 2.18 91 38 43 5 237.83 1.61 92 38 55 17 233.10 0.79 93 38 67 29 233.28 0.79 94 38 73 35 233.00 0.83 95 39 42 3 274.01 6.03 96 39 43 4 251.44 0.24 97 40 86 46 207.78 0.54 98 41 73 32 233.19 0.76 99 41 74 33 233.14 0.75 100 41 77 36 233.13 0.76 101 41 86 45 203.80 1.45 102 42 57 15 233.06 0.79 103 42 58 16 233.08 0.79 104 42 86 44 208.05 0.67 105 43 55 12 233.22 0.74 106 43 56 13 233.18 0.74 107 43 57 14 233.16 0.74 108 43 67 24 233.55 0.78 109 43 73 30 233.28 0.76 110 43 77 34 233.21 0.76 111 44 55 11 233.25 0.75 112 44 56 12 233.23 0.75 113 44 58 14 233.21 0.75 114 45 52 7 233.69 0.77 115 45 53 8 233.54 0.76 116 45 54 9 233.49 0.75 117 46 54 8 233.53 0.76 118 46 56 10 233.38 0.70 119 47 51 4 236.76 2.25 120 47 52 5 233.69 0.77 121 47 54 7 233.53 0.76 122 48 51 3 249.25 1.81 123 48 52 4 237.66 1.81 124 49 52 3 298.73 0.49 125 51 54 3 277.31 0.21 126 53 65 12 327.19 0.32 127 53 66 13 344.38 8.27 128 53 67 14 344.36 8.28 129 54 63 9 326.86 0.18 130 54 64 10 344.39 8.26 131 54 65 11 344.38 8.27 132 55 63 8 344.43 8.25 133 55 64 9 366.37 18.94 134 55 67 12 431.45 5.57 135 56 61 5 326.22 0.14 136 56 62 6 327.25 0.35 137 56 63 7 344.73 8.11 138 57 60 3 324.20 0.48 139 57 61 4 327.22 0.36 140 57 77 20 424.31 2.17 141 57 84 27 324.19 0.48 142 58 86 28 300.76 1.66 143 58 108 50 42.54 0.90 144 59 85 26 326.55 0.24 145 59 86 27 295.30 0.10 146 59 104 45 43.12 0.96 147 59 107 48 42.66 0.96 148 59 108 49 42.54 0.90 149 59 111 52 42.49 0.89 150 61 108 47 42.61 0.92 151 61 111 50 42.49 0.89 152 61 112 51 42.48 0.89 153 61 115 54 40.78 1.02 154 74 87 13 443.39 0.55 155 78 87 9 443.41 0.55 156 84 87 3 292.01 0.48 157 84 88 4 291.97 0.46 158 85 88 3 293.24 1.09 159 85 89 4 291.58 0.64 160 85 104 19 43.40 0.94 161 85 107 22 43.05 0.99 162 86 89 3 294.57 0.87 163 86 93 7 129.58 31.34 164 89 93 4 292.26 0.89 165 89 96 7 100.85 2.37 166 89 104 15 44.80 0.24 167 91 95 4 260.41 2.50 168 91 96 5 254.06 0.28 169 92 95 3 277.81 1.55 170 92 96 4 272.29 0.18 171 93 96 3 269.12 1.41 172 96 100 4 267.80 5.19 173 96 104 8 242.91 2.52 174 97 100 3 274.49 2.05 175 97 101 4 279.51 0.62 176 98 101 3 279.68 0.55 177 98 102 4 267.84 5.20 178 99 102 3 283.36 1.04 179 99 103 4 279.50 0.63 180 100 103 3 279.51 0.64 181 100 104 4 278.93 0.35 182 101 104 3 279.00 0.32 183 101 105 4 279.32 0.15 184 102 105 3 279.35 0.14 185 102 106 4 288.27 2.10 186 103 106 3 292.38 0.04 187 103 107 4 288.29 2.09 188 104 107 3 289.37 1.55 189 104 108 4 288.28 2.09 190 105 108 3 288.28 2.09 191 105 109 4 288.26 2.08 192 106 109 3 293.14 0.35 193 106 110 4 276.91 3.75 194 107 110 3 279.37 4.99 195 107 111 4 269.51 3.26 196 108 111 3 273.91 2.25 197 108 112 4 268.11 5.15 198 109 112 3 285.03 2.81 199 109 113 4 278.94 0.24 200 110 113 3 288.19 2.15 201 110 114 4 278.94 0.23 202 111 114 3 278.94 0.23 203 111 115 4 278.94 0.23 204 112 115 3 281.19 1.34 205 112 116 4 278.94 0.23 206 113 116 3 280.15 0.83 207 113 117 4 267.62 5.44 208 114 117 3 266.24 4.83 209 114 118 4 263.11 3.27 210 115 118 3 259.74 4.96