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 12 72 60 45.47 2.52 2 12 75 63 45.53 2.48 3 13 16 3 376.43 2.87 4 13 72 59 48.46 2.94 5 16 21 5 376.32 0.59 6 16 62 46 85.06 0.42 7 17 20 3 389.42 2.67 8 17 21 4 376.85 0.85 9 18 21 3 379.31 2.08 10 18 22 4 376.86 0.85 11 18 72 54 82.45 1.04 12 18 75 57 82.49 1.02 13 18 76 58 82.44 1.04 14 18 79 61 82.52 1.02 15 18 81 63 82.49 1.02 16 19 22 3 392.23 1.26 17 19 23 4 389.23 2.29 18 19 81 62 82.53 1.03 19 20 23 3 389.23 2.29 20 20 24 4 389.23 2.29 21 21 24 3 392.63 0.59 22 21 25 4 388.17 2.82 23 21 56 35 92.99 0.51 24 21 57 36 93.03 0.53 25 21 62 41 93.16 0.56 26 21 72 51 92.97 0.50 27 22 25 3 392.62 0.59 28 22 26 4 388.17 2.82 29 22 76 54 92.56 0.57 30 22 81 59 92.55 0.57 31 22 111 89 92.55 0.57 32 22 112 90 92.56 0.57 33 22 113 91 92.50 0.54 34 23 26 3 388.01 2.89 35 23 27 4 387.17 3.31 36 24 27 3 389.91 2.50 37 24 30 6 231.00 22.28 38 24 31 7 92.91 0.47 39 24 56 32 93.12 0.55 40 25 31 6 92.91 0.47 41 25 32 7 92.91 0.47 42 25 53 28 93.00 0.51 43 25 56 31 93.12 0.55 44 25 57 32 95.70 0.72 45 25 76 51 95.59 0.71 46 25 111 86 92.86 0.45 47 26 113 87 92.82 0.46 48 27 30 3 361.07 1.78 49 27 31 4 159.16 15.36 50 30 56 26 123.01 0.51 51 31 56 25 123.00 0.50 52 32 48 16 122.99 0.53 53 32 53 21 122.98 0.52 54 32 56 24 123.01 0.50 55 32 111 79 112.14 1.29 56 33 48 15 123.03 0.53 57 34 46 12 123.10 0.56 58 34 47 13 123.06 0.54 59 34 48 14 123.02 0.54 60 35 46 11 123.20 0.55 61 35 47 12 123.08 0.54 62 36 44 8 152.77 13.85 63 37 43 6 197.52 2.08 64 37 44 7 180.41 0.07 65 37 47 10 123.85 0.64 66 37 49 12 124.03 0.66 67 37 108 71 124.00 0.67 68 38 41 3 407.51 0.66 69 38 42 4 305.42 7.01 70 38 43 5 245.78 26.21 71 38 121 83 103.56 5.08 72 39 42 3 379.87 4.78 73 39 44 5 328.55 8.48 74 39 108 69 124.01 0.65 75 41 120 79 103.78 5.03 76 41 121 80 103.66 5.03 77 41 123 82 103.56 5.08 78 42 119 77 103.81 5.03 79 42 120 78 103.67 5.03 80 42 121 79 103.65 5.04 81 43 118 75 104.21 4.81 82 43 119 76 103.78 5.02 83 43 121 78 103.64 5.04 84 44 47 3 393.42 0.92 85 44 85 41 139.57 2.72 86 44 116 72 104.70 4.94 87 44 118 74 103.77 5.01 88 45 116 71 104.67 4.94 89 45 117 72 104.59 4.92 90 45 119 74 104.31 4.86 91 46 110 64 146.98 1.04 92 46 114 68 104.70 4.94 93 46 115 69 104.67 4.94 94 47 108 61 162.51 0.01 95 47 109 62 161.50 0.44 96 48 53 5 372.07 2.02 97 48 82 34 162.97 0.20 98 48 108 60 162.97 0.20 99 48 109 61 161.58 0.43 100 48 110 62 161.58 0.43 101 48 111 63 161.58 0.43 102 49 52 3 389.52 1.02 103 49 53 4 385.72 0.88 104 49 105 56 171.63 1.43 105 49 107 58 169.15 2.07 106 49 108 59 163.09 0.20 107 50 53 3 394.03 3.33 108 50 54 4 385.67 0.86 109 50 101 51 172.06 1.25 110 50 104 54 172.50 1.24 111 50 107 57 170.82 1.29 112 50 109 59 169.15 2.07 113 51 54 3 387.88 0.24 114 51 55 4 385.73 0.83 115 51 103 52 172.75 1.26 116 51 104 53 172.75 1.27 117 51 105 54 172.58 1.20 118 52 55 3 391.06 0.26 119 52 56 4 385.74 0.83 120 53 56 3 387.79 1.84 121 53 57 4 385.76 0.82 122 53 73 20 172.63 1.13 123 53 82 29 172.46 1.14 124 53 101 48 173.20 1.42 125 54 57 3 392.17 0.34 126 54 58 4 381.76 1.40 127 54 66 12 173.64 1.32 128 54 69 15 173.27 1.34 129 54 70 16 173.29 1.36 130 54 73 19 173.02 1.32 131 54 101 47 173.28 1.38 132 54 103 49 173.09 1.42 133 55 58 3 384.98 0.46 134 55 59 4 381.75 1.40 135 55 66 11 176.31 0.01 136 56 59 3 387.31 1.16 137 56 60 4 380.44 2.04 138 57 60 3 385.85 1.91 139 57 61 4 378.30 1.03 140 57 62 5 324.10 1.51 141 57 63 6 315.20 2.17 142 57 69 12 173.66 1.31 143 57 72 15 173.66 1.30 144 57 73 16 173.61 1.30 145 58 61 3 376.22 0.01 146 58 63 5 312.51 0.82 147 58 65 7 273.37 4.25 148 58 66 8 228.44 23.04 149 63 68 5 347.44 4.04 150 63 69 6 302.86 1.54 151 63 72 9 291.08 3.79 152 64 68 4 395.59 5.38 153 65 68 3 395.60 5.38 154 65 69 4 395.61 5.38 155 66 69 3 395.62 5.38 156 66 70 4 395.62 5.37 157 67 70 3 396.14 5.11 158 67 71 4 395.63 5.37 159 68 71 3 406.06 0.15 160 69 72 3 388.22 1.67 161 69 73 4 378.24 1.56 162 70 73 3 381.86 0.85 163 70 74 4 375.07 3.14 164 70 99 29 265.11 3.08 165 70 101 31 264.89 3.16 166 70 103 33 264.10 2.83 167 71 74 3 376.62 3.52 168 71 75 4 376.41 3.62 169 72 75 3 387.28 1.61 170 72 76 4 376.57 3.54 171 73 76 3 388.34 1.63 172 73 77 4 376.57 3.53 173 73 82 9 306.92 2.16 174 73 101 28 265.07 3.10 175 74 77 3 388.39 3.06 176 74 78 4 383.16 1.20 177 74 99 25 265.22 3.13 178 74 100 26 265.12 3.08 179 74 101 27 265.00 3.12 180 75 78 3 383.17 1.20 181 75 79 4 371.74 1.28 182 76 80 4 361.24 3.85 183 76 81 5 312.56 4.95 184 76 82 6 306.95 2.15 185 77 80 3 372.61 1.40 186 77 82 5 306.94 2.15 187 77 83 6 306.94 2.15 188 77 84 7 306.92 2.16 189 77 93 16 265.64 3.25 190 77 100 23 265.61 3.23 191 77 101 24 265.49 3.21 192 77 109 32 264.95 3.01 193 78 100 22 265.62 3.23 194 80 83 3 421.66 1.68 195 80 112 32 259.52 0.65 196 81 111 30 264.12 2.91 197 81 112 31 259.56 0.64 198 82 101 19 265.75 3.17 199 82 109 27 264.95 3.02 200 82 110 28 264.64 3.10 201 82 111 29 259.14 0.46 202 83 109 26 265.07 3.06 203 83 110 27 264.70 3.10 204 83 112 29 262.19 1.98 205 84 89 5 312.23 10.37 206 84 90 6 304.36 9.52 207 84 93 9 304.35 9.52 208 84 108 24 265.33 2.98 209 84 109 25 265.19 3.00 210 84 110 26 265.21 3.00 211 85 108 23 265.35 2.98 212 85 109 24 265.32 2.98 213 85 110 25 265.32 2.98 214 86 89 3 396.32 1.65 215 86 90 4 377.08 1.40 216 87 90 3 383.69 1.28 217 87 91 4 378.14 2.33 218 88 91 3 396.26 1.55 219 88 92 4 386.29 0.68 220 88 102 14 266.16 3.12 221 88 104 16 265.91 3.09 222 88 106 18 265.61 3.04 223 88 107 19 265.56 3.02 224 89 92 3 385.43 1.10 225 89 93 4 385.43 1.10 226 89 102 13 265.91 3.10 227 89 107 18 265.55 3.02 228 89 109 20 265.45 2.98 229 90 93 3 389.42 0.88 230 90 94 4 385.44 1.11 231 91 94 3 386.69 0.49 232 91 95 4 385.36 1.15 233 92 95 3 385.36 1.16 234 92 100 8 266.23 3.11 235 92 102 10 266.26 3.08 236 93 100 7 266.19 3.12 237 101 109 8 266.24 2.57 238 102 107 5 292.80 0.14 239 102 109 7 282.30 5.40 240 104 107 3 360.00 5.77 241 110 116 6 243.84 14.57 242 111 114 3 379.53 3.78