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 28 36 8 283.63 0.62 2 29 32 3 311.77 0.24 3 29 33 4 306.15 0.97 4 30 33 3 310.62 0.29 5 30 34 4 306.14 0.97 6 31 34 3 310.61 0.29 7 31 35 4 305.78 0.80 8 32 35 3 312.69 1.34 9 32 36 4 306.19 0.58 10 33 36 3 313.83 0.77 11 33 37 4 306.15 0.56 12 34 37 3 308.13 0.37 13 34 38 4 305.80 0.46 14 35 38 3 310.56 1.03 15 35 39 4 313.74 0.56 16 36 39 3 313.75 0.57 17 36 40 4 313.85 0.52 18 37 40 3 315.33 0.23 19 37 41 4 313.86 0.51 20 38 41 3 313.85 0.51 21 38 42 4 317.34 2.25 22 39 42 3 322.63 0.39 23 39 43 4 317.35 2.25 24 39 88 49 61.46 0.32 25 39 107 68 44.02 0.99 26 39 110 71 43.94 0.96 27 40 43 3 317.37 2.24 28 40 44 4 311.65 0.60 29 41 44 3 317.95 1.95 30 42 45 3 339.46 2.94 31 42 48 6 289.89 3.62 32 42 86 44 63.91 0.79 33 42 88 46 63.68 0.67 34 43 49 6 265.32 0.88 35 43 52 9 263.83 0.29 36 43 88 45 62.45 0.04 37 43 110 67 47.15 0.58 38 45 48 3 310.42 0.65 39 45 49 4 307.47 0.80 40 46 49 3 309.13 0.01 41 46 50 4 307.47 0.80 42 47 50 3 310.89 0.89 43 47 51 4 304.41 2.35 44 47 79 32 158.55 1.71 45 48 51 3 310.45 0.71 46 48 52 4 303.43 0.55 47 48 82 34 158.56 1.70 48 48 83 35 158.53 1.71 49 48 86 38 158.54 1.71 50 49 52 3 309.66 1.65 51 49 53 4 303.58 0.62 52 50 53 3 314.01 0.53 53 50 54 4 314.01 0.53 54 50 69 19 159.62 1.65 55 51 54 3 318.04 0.42 56 51 55 4 313.88 0.59 57 51 65 14 159.59 1.66 58 51 69 18 159.63 1.66 59 51 76 25 158.91 1.69 60 51 79 28 158.83 1.69 61 51 80 29 158.81 1.69 62 51 83 32 158.69 1.71 63 52 55 3 313.88 0.59 64 52 56 4 309.95 2.56 65 52 83 31 158.74 1.72 66 52 89 37 158.49 1.72 67 52 102 50 153.19 1.44 68 53 56 3 315.53 0.24 69 53 57 4 313.87 0.59 70 53 111 58 54.30 1.23 71 54 57 3 325.57 2.81 72 54 58 4 312.39 1.31 73 54 60 6 295.12 2.58 74 54 65 11 162.34 0.42 75 54 68 14 159.84 1.68 76 54 69 15 162.38 0.42 77 55 58 3 310.57 1.07 78 55 59 4 301.19 0.63 79 55 60 5 295.13 2.58 80 55 65 10 193.59 0.51 81 55 89 34 158.65 1.74 82 55 100 45 156.88 0.98 83 55 101 46 154.75 1.67 84 55 102 47 153.22 1.45 85 56 102 46 154.76 0.73 86 56 111 55 64.43 0.69 87 59 92 33 158.65 1.71 88 59 99 40 157.06 0.95 89 59 100 41 156.95 0.99 90 59 101 42 156.62 0.94 91 60 64 4 299.85 0.56 92 60 65 5 299.83 0.57 93 60 99 39 156.97 0.98 94 60 100 40 156.94 1.00 95 61 64 3 316.18 0.56 96 61 65 4 307.05 0.54 97 61 98 37 157.20 1.01 98 61 99 38 156.95 0.99 99 62 65 3 320.04 1.38 100 62 66 4 307.05 0.55 101 62 73 11 164.30 0.28 102 62 76 14 162.62 0.42 103 62 80 18 159.98 1.73 104 62 100 38 156.93 1.01 105 63 66 3 320.04 1.37 106 63 67 4 309.26 0.79 107 63 73 10 173.52 2.38 108 64 67 3 315.00 2.35 109 64 68 4 307.44 1.70 110 65 68 3 312.19 1.61 111 65 69 4 309.24 0.79 112 65 76 11 163.19 0.26 113 65 80 15 163.06 0.20 114 66 69 3 320.75 0.51 115 66 70 4 305.73 2.54 116 66 71 5 235.47 17.32 117 66 72 6 203.31 1.25 118 66 73 7 189.77 1.84 119 66 76 10 163.19 0.26 120 67 70 3 311.97 3.88 121 69 76 7 261.56 2.67 122 71 75 4 301.09 1.45 123 71 76 5 297.83 0.18 124 72 75 3 309.36 0.62 125 72 76 4 307.34 0.40 126 73 76 3 316.68 2.79 127 73 77 4 309.71 0.79 128 74 77 3 314.99 1.45 129 74 78 4 309.72 0.79 130 75 78 3 316.79 2.73 131 75 79 4 309.73 0.80 132 76 79 3 311.39 0.04 133 76 80 4 309.70 0.81 134 77 80 3 312.50 0.41 135 77 81 4 309.62 0.85 136 78 81 3 316.78 2.73 137 78 82 4 310.81 1.41 138 79 82 3 322.58 1.12 139 79 83 4 310.81 1.41 140 80 83 3 310.81 1.41 141 80 84 4 310.80 1.41 142 80 89 9 167.68 2.65 143 80 100 20 157.10 0.94 144 81 84 3 317.64 3.52 145 81 85 4 311.89 0.86 146 82 85 3 311.89 0.86 147 82 86 4 307.45 1.78 148 83 86 3 311.32 0.58 149 83 87 4 307.45 1.77 150 83 88 5 239.64 3.70 151 83 89 6 194.66 7.08 152 84 87 3 312.78 2.17 153 84 89 5 220.50 5.84 154 84 91 7 198.88 4.95 155 84 100 16 157.30 0.96 156 87 103 16 155.12 0.90 157 88 102 14 155.93 1.27 158 88 103 15 155.72 1.21 159 88 107 19 140.17 0.02 160 89 100 11 157.50 0.86 161 89 101 12 157.33 0.85 162 89 102 13 155.90 1.28 163 89 103 14 155.09 0.89 164 90 100 10 157.53 0.86 165 90 101 11 157.44 0.86 166 90 103 13 155.89 1.28 167 91 98 7 157.74 0.83 168 91 99 8 157.60 0.89 169 91 100 9 157.53 0.86 170 91 101 10 157.53 0.86 171 92 98 6 157.77 0.82 172 92 99 7 157.62 0.89 173 92 101 9 157.62 0.88 174 93 97 4 247.80 0.45 175 93 98 5 157.80 0.82 176 94 97 3 306.14 3.56 177 94 99 5 196.84 13.54 178 102 107 5 293.83 3.96 179 102 108 6 257.41 14.22 180 103 107 4 304.80 1.46 181 104 107 3 321.47 0.85 182 104 108 4 310.28 1.28 183 105 108 3 315.46 3.86 184 105 109 4 306.44 0.64 185 106 109 3 321.11 4.44 186 106 110 4 305.35 1.19 187 107 110 3 321.63 4.17 188 107 111 4 310.48 1.40 189 108 111 3 314.25 0.48 190 108 112 4 310.45 1.42 191 109 112 3 319.50 1.12 192 109 113 4 308.46 0.30 193 110 113 3 310.57 1.36 194 110 114 4 308.48 0.31 195 111 114 3 312.63 2.37 196 111 115 4 305.69 1.12 197 112 115 3 309.31 0.69 198 112 116 4 305.17 1.39 199 113 116 3 312.39 2.23 200 113 117 4 305.69 1.12 201 114 117 3 309.14 2.23 202 114 118 4 305.70 1.11 203 115 118 3 313.40 1.26 204 115 119 4 298.69 2.39 205 116 119 3 299.19 2.14