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 50 53 3 316.57 1.04 2 50 54 4 306.49 0.05 3 51 54 3 316.74 1.12 4 51 55 4 303.22 0.81 5 52 55 3 315.36 0.65 6 52 56 4 308.31 3.35 7 53 56 3 315.37 0.65 8 53 57 4 308.31 3.35 9 54 57 3 314.55 0.24 10 54 58 4 308.31 3.35 11 55 58 3 311.14 1.94 12 55 59 4 311.14 1.93 13 56 59 3 318.30 1.65 14 56 60 4 312.31 1.35 15 57 60 3 317.51 1.27 16 57 61 4 309.11 0.24 17 58 61 3 313.12 0.44 18 58 62 4 311.08 0.58 19 59 62 3 319.73 2.88 20 59 63 4 310.93 0.66 21 60 63 3 331.41 2.96 22 60 64 4 307.12 2.54 23 61 64 3 331.41 2.96 24 61 65 4 309.96 0.98 25 62 65 3 314.88 3.44 26 62 66 4 303.81 0.89 27 63 66 3 306.75 0.58 28 63 67 4 299.10 1.46 29 64 67 3 317.61 1.66 30 64 68 4 303.00 0.56 31 64 129 65 66.22 0.21 32 64 132 68 63.62 0.14 33 64 133 69 63.76 0.07 34 65 68 3 311.24 1.53 35 65 69 4 308.86 0.35 36 66 69 3 316.86 1.31 37 66 70 4 308.86 0.35 38 67 70 3 321.62 2.14 39 67 71 4 309.19 0.52 40 67 132 65 66.19 0.19 41 68 71 3 309.21 0.52 42 68 72 4 309.20 0.53 43 68 128 60 67.03 0.60 44 68 129 61 67.22 0.51 45 68 132 64 66.22 0.21 46 69 72 3 320.64 0.03 47 69 73 4 309.19 0.53 48 70 73 3 312.66 2.25 49 70 74 4 315.67 2.64 50 71 74 3 320.58 0.19 51 71 75 4 320.56 0.20 52 71 128 57 72.34 1.88 53 71 131 60 72.48 1.76 54 71 132 61 72.17 1.90 55 72 75 3 318.99 0.60 56 72 76 4 315.31 1.24 57 72 121 49 77.03 1.12 58 72 124 52 76.16 1.11 59 72 125 53 75.31 1.52 60 72 128 56 72.54 1.78 61 73 76 3 325.80 2.42 62 73 77 4 318.02 0.12 63 73 121 48 81.68 1.20 64 74 77 3 329.52 1.23 65 74 78 4 318.98 0.59 66 75 78 3 318.33 0.29 67 75 79 4 318.75 0.49 68 75 124 49 76.53 0.98 69 75 127 52 76.56 0.99 70 75 128 53 76.45 1.00 71 76 79 3 329.35 2.13 72 76 120 44 83.11 1.61 73 76 121 45 82.96 1.67 74 76 124 48 76.69 1.05 75 77 80 3 330.69 1.47 76 78 83 5 318.60 0.34 77 79 83 4 316.05 0.10 78 79 84 5 316.04 0.10 79 79 120 41 96.48 1.90 80 79 124 45 91.86 1.43 81 80 83 3 328.94 0.89 82 80 84 4 324.53 1.31 83 81 84 3 323.89 0.99 84 81 85 4 316.07 0.08 85 81 113 32 107.31 0.24 86 81 116 35 107.03 0.31 87 81 117 36 106.99 0.30 88 81 120 39 103.34 1.46 89 82 85 3 319.06 1.42 90 82 86 4 316.04 0.10 91 83 86 3 316.63 0.47 92 83 87 4 311.17 0.69 93 84 87 3 311.76 1.02 94 84 88 4 306.75 1.28 95 84 106 22 120.20 1.00 96 84 116 32 107.28 0.19 97 84 120 36 104.38 1.23 98 85 88 3 319.81 5.25 99 85 89 4 306.38 1.46 100 85 102 17 124.17 0.29 101 85 106 21 120.20 1.00 102 85 107 22 121.42 0.42 103 86 89 3 306.26 0.70 104 86 90 4 301.00 1.21 105 87 90 3 306.08 0.62 106 87 91 4 301.00 1.21 107 88 91 3 318.69 0.27 108 88 92 4 294.33 2.12 109 88 102 14 130.76 0.96 110 88 106 18 126.22 1.31 111 89 93 4 309.72 3.10 112 89 99 10 142.87 0.83 113 89 102 13 131.67 0.27 114 91 94 3 335.62 0.53 115 91 95 4 323.01 1.11 116 92 95 3 319.95 0.42 117 92 96 4 317.37 0.88 118 92 97 5 226.71 4.21 119 92 102 10 200.05 5.79 120 93 96 3 320.53 0.80 121 93 97 4 280.83 4.38 122 93 99 6 222.24 6.44 123 93 102 9 214.74 1.53 124 97 101 4 308.69 1.32 125 97 102 5 308.68 1.35 126 98 101 3 313.71 1.13 127 98 102 4 311.17 0.14 128 99 102 3 320.54 2.06 129 99 103 4 311.17 0.14 130 100 103 3 311.17 0.14 131 100 104 4 311.17 0.14 132 101 104 3 318.61 1.75 133 101 105 4 311.17 0.14 134 102 105 3 318.87 3.79 135 102 106 4 308.47 1.41 136 103 106 3 312.36 0.13 137 103 107 4 285.18 5.41 138 103 108 5 270.28 1.31 139 104 108 4 258.88 1.89 140 104 109 5 211.09 9.17 141 105 109 4 202.27 7.17 142 105 112 7 202.24 7.19 143 105 113 8 202.24 7.19 144 106 112 6 239.43 16.36 145 106 113 7 202.22 7.17 146 106 116 10 202.19 7.16 147 107 113 6 286.24 5.17 148 108 113 5 306.07 0.21 149 109 112 3 323.27 1.59 150 109 113 4 306.08 0.21 151 110 113 3 318.66 0.51 152 110 114 4 306.08 0.21 153 111 114 3 317.28 0.19 154 111 115 4 306.02 0.17 155 112 115 3 314.27 1.69 156 112 116 4 305.94 0.17 157 113 116 3 317.28 0.18 158 113 117 4 305.56 0.01 159 114 117 3 315.14 4.80 160 114 118 4 305.51 0.00 161 115 118 3 310.31 2.38 162 115 119 4 312.27 3.38 163 116 119 3 313.55 2.75 164 116 120 4 312.27 3.39 165 117 120 3 317.57 0.73 166 117 121 4 310.19 4.42 167 118 121 3 315.52 1.76 168 118 122 4 309.40 4.82 169 119 122 3 314.82 0.64 170 119 123 4 303.28 0.96 171 120 123 3 315.65 1.82 172 120 124 4 304.52 3.26 173 121 124 3 323.87 2.29 174 121 125 4 303.46 3.55 175 122 125 3 315.67 1.81 176 122 126 4 304.64 3.02 177 123 126 3 306.15 2.67 178 123 127 4 305.04 3.23 179 124 127 3 306.15 2.67 180 124 128 4 305.75 2.48 181 125 128 3 306.27 2.62 182 125 129 4 305.99 2.56 183 126 129 3 317.46 0.54 184 126 130 4 311.20 0.04 185 127 130 3 312.10 0.41 186 127 131 4 308.12 3.62 187 128 131 3 313.32 1.03 188 128 132 4 308.12 3.63 189 129 132 3 317.49 0.03 190 129 133 4 308.05 3.66 191 130 133 3 316.81 0.72 192 130 134 4 311.08 2.15 193 131 134 3 319.25 0.50 194 131 135 4 315.25 2.50 195 132 135 3 324.28 1.11 196 132 136 4 316.81 0.72 197 133 136 3 331.73 1.64 198 133 137 4 326.09 1.18 199 134 137 3 337.25 1.12