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 56 77 21 245.46 0.75 2 56 80 24 245.62 0.81 3 57 74 17 247.28 0.47 4 57 75 18 246.22 0.66 5 57 76 19 246.06 0.60 6 57 120 63 156.55 0.24 7 57 121 64 156.55 0.24 8 57 123 66 156.46 0.23 9 57 124 67 156.41 0.24 10 57 125 68 156.37 0.24 11 58 73 15 247.40 0.42 12 58 74 16 247.28 0.47 13 58 75 17 247.03 0.42 14 58 125 67 156.41 0.24 15 58 126 68 156.40 0.24 16 58 150 92 38.77 0.05 17 58 154 96 25.32 1.03 18 59 73 14 247.42 0.42 19 59 74 15 247.38 0.43 20 59 76 17 247.37 0.41 21 59 123 64 156.53 0.24 22 59 124 65 156.50 0.24 23 59 125 66 156.46 0.24 24 59 127 68 156.39 0.25 25 59 129 70 156.36 0.24 26 59 150 91 38.84 0.04 27 60 70 10 249.16 0.76 28 60 71 11 248.02 0.33 29 60 72 12 247.94 0.30 30 60 73 13 247.60 0.34 31 60 127 67 156.44 0.24 32 60 128 68 156.38 0.26 33 60 129 69 156.38 0.25 34 60 146 86 58.55 0.70 35 60 150 90 38.86 0.04 36 61 69 8 250.03 0.53 37 61 71 10 248.04 0.34 38 61 72 11 248.02 0.32 39 61 74 13 247.87 0.38 40 61 87 26 245.41 0.73 41 61 91 30 245.08 0.74 42 61 95 34 244.70 0.64 43 61 108 47 161.22 1.16 44 61 129 68 156.38 0.25 45 61 131 70 156.34 0.24 46 62 69 7 250.02 0.53 47 62 70 8 249.38 0.82 48 62 71 9 248.05 0.33 49 62 128 66 156.47 0.24 50 62 129 67 156.44 0.24 51 62 130 68 156.35 0.24 52 62 131 69 156.35 0.24 53 62 142 80 72.56 0.42 54 62 143 81 72.48 0.39 55 62 146 84 70.94 0.28 56 63 66 3 348.47 0.88 57 63 69 6 258.09 1.83 58 63 95 32 244.74 0.65 59 63 97 34 244.74 0.65 60 63 100 37 211.74 4.08 61 63 101 38 204.15 7.88 62 63 130 67 156.43 0.24 63 63 131 68 156.38 0.25 64 63 142 79 74.73 0.53 65 64 101 37 213.88 3.01 66 64 130 66 156.45 0.24 67 64 131 67 156.41 0.24 68 64 132 68 156.35 0.25 69 64 135 71 153.50 0.61 70 64 136 72 126.91 0.10 71 64 137 73 98.98 0.84 72 64 138 74 98.95 0.83 73 64 142 78 93.08 0.33 74 65 138 73 98.98 0.84 75 65 140 75 98.82 0.83 76 65 142 77 98.03 0.58 77 66 69 3 363.37 0.69 78 66 140 74 98.87 0.85 79 67 70 3 439.58 1.06 80 67 138 71 102.14 0.72 81 67 140 73 98.73 0.87 82 69 95 26 245.02 0.72 83 70 142 72 72.54 0.41 84 70 144 74 72.39 0.38 85 70 146 76 67.55 0.05 86 72 94 22 244.91 0.71 87 72 95 23 244.71 0.65 88 73 150 77 38.84 0.03 89 74 81 7 302.78 5.92 90 74 87 13 256.72 1.60 91 74 90 16 245.20 0.79 92 74 91 17 245.18 0.80 93 74 94 20 244.72 0.65 94 75 80 5 309.92 2.35 95 75 81 6 303.48 5.57 96 76 87 11 275.78 2.84 97 76 123 47 156.53 0.24 98 77 80 3 362.78 1.05 99 77 81 4 333.64 4.12 100 78 81 3 357.89 3.50 101 78 82 4 309.89 2.33 102 81 86 5 327.48 6.37 103 81 87 6 306.64 4.04 104 81 90 9 303.19 2.86 105 81 120 39 157.03 0.19 106 83 86 3 352.25 0.61 107 83 87 4 347.10 0.56 108 83 120 37 157.06 0.19 109 84 87 3 355.73 1.90 110 84 88 4 348.13 1.07 111 84 108 24 161.92 1.76 112 84 117 33 157.74 0.29 113 84 118 34 157.25 0.14 114 84 119 35 157.13 0.17 115 84 120 36 157.06 0.19 116 85 88 3 355.28 2.12 117 85 89 4 347.10 0.56 118 86 89 3 352.93 3.12 119 86 90 4 348.11 1.08 120 87 90 3 348.50 0.90 121 87 91 4 344.36 0.77 122 87 108 21 161.91 1.76 123 87 120 33 157.06 0.19 124 87 123 36 156.85 0.20 125 88 91 3 346.51 0.31 126 88 92 4 343.44 0.31 127 88 105 17 162.47 1.65 128 88 108 20 162.18 1.63 129 89 92 3 349.89 1.37 130 89 93 4 343.44 0.31 131 90 93 3 349.89 1.37 132 90 94 4 342.30 0.18 133 91 94 3 352.19 3.15 134 91 95 4 341.87 0.38 135 91 105 14 162.50 1.67 136 91 108 17 162.21 1.61 137 91 131 40 156.37 0.24 138 92 95 3 350.39 2.41 139 92 96 4 341.02 0.45 140 92 104 12 168.22 4.44 141 92 105 13 162.51 1.67 142 95 131 36 156.41 0.23 143 96 100 4 310.36 1.78 144 96 101 5 279.29 0.72 145 96 104 8 178.27 4.53 146 96 105 9 178.26 4.54 147 97 100 3 344.58 3.21 148 97 102 5 283.79 2.42 149 98 102 4 305.78 1.23 150 99 102 3 354.91 0.16 151 101 104 3 355.23 1.86 152 101 105 4 338.38 1.93 153 101 131 30 156.47 0.24 154 101 132 31 156.44 0.24 155 101 133 32 156.33 0.24 156 103 133 30 156.41 0.23 157 103 134 31 156.40 0.23 158 104 133 29 156.39 0.23 159 105 131 26 156.43 0.24 160 105 132 27 156.41 0.23 161 106 132 26 156.41 0.24 162 106 133 27 156.31 0.24 163 106 134 28 156.37 0.22 164 107 116 9 168.56 0.52 165 107 131 24 156.43 0.24 166 107 132 25 156.38 0.23 167 108 116 8 173.65 3.06 168 108 117 9 168.09 0.74 169 108 123 15 157.15 0.20 170 108 129 21 156.50 0.24 171 108 130 22 156.45 0.23 172 108 131 23 156.38 0.22 173 109 113 4 319.55 3.02 174 109 115 6 274.54 4.11 175 109 116 7 178.37 0.70 176 109 129 20 156.52 0.24 177 109 130 21 156.44 0.23 178 109 132 23 156.41 0.23 179 109 137 28 98.88 0.85 180 110 113 3 345.25 2.90 181 110 114 4 330.09 2.25 182 110 115 5 284.47 1.94 183 110 117 7 224.30 15.60 184 110 129 19 156.52 0.24 185 111 128 17 156.54 0.24 186 111 130 19 156.52 0.24 187 111 137 26 100.64 1.58 188 111 142 31 72.80 0.35 189 111 143 32 72.58 0.44 190 112 137 25 105.88 1.03 191 113 137 24 98.93 0.87 192 115 122 7 309.21 3.62 193 117 122 5 313.89 1.28 194 117 123 6 309.19 3.63 195 117 129 12 156.50 0.24 196 118 122 4 345.26 0.99 197 119 122 3 355.06 1.52 198 120 123 3 351.93 0.07 199 123 129 6 305.10 5.55 200 124 127 3 352.76 2.00 201 124 129 5 337.75 1.56 202 125 151 26 35.99 0.98 203 126 150 24 38.80 0.06 204 126 151 25 33.87 0.07 205 127 150 23 41.13 1.19 206 128 143 15 72.31 0.37 207 130 137 7 132.73 17.74 208 130 142 12 72.58 0.44 209 137 142 5 384.03 1.55 210 138 142 4 397.78 0.68 211 141 144 3 353.96 0.79 212 143 146 3 353.45 4.59 213 146 150 4 374.80 1.15 214 147 150 3 391.11 1.73 215 148 151 3 374.80 1.15 216 148 152 4 353.82 0.49 217 149 152 3 352.75 1.03 218 149 153 4 352.70 1.01 219 150 154 4 349.45 2.64