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 2 7 5 146.64 3.13 2 2 10 8 134.80 0.24 3 3 6 3 149.76 1.81 4 3 7 4 149.58 1.70 5 4 7 3 155.40 1.22 6 4 8 4 149.59 1.69 7 4 118 114 22.23 0.14 8 5 8 3 150.94 1.39 9 5 9 4 149.63 1.67 10 5 116 111 26.16 0.67 11 5 118 113 23.89 0.26 12 6 9 3 151.90 2.79 13 6 10 4 155.38 1.21 14 7 10 3 157.65 0.09 15 7 11 4 155.34 1.24 16 8 11 3 157.91 0.22 17 8 12 4 142.22 0.87 18 8 54 46 37.37 1.08 19 8 108 100 33.76 0.93 20 8 117 109 34.01 0.86 21 8 118 110 33.23 0.80 22 8 119 111 33.09 0.73 23 8 120 112 33.09 0.73 24 9 12 3 155.81 1.01 25 9 13 4 134.31 0.78 26 9 33 24 116.36 1.14 27 9 51 42 78.69 0.65 28 10 33 23 116.35 1.14 29 10 34 24 116.39 1.16 30 10 35 25 116.37 1.15 31 11 35 24 116.36 1.15 32 11 41 30 116.33 1.16 33 11 44 33 112.06 0.01 34 11 46 35 111.98 0.02 35 12 45 33 112.04 0.01 36 12 46 34 111.98 0.02 37 12 47 35 111.98 0.03 38 13 33 20 117.14 1.01 39 13 47 34 112.00 0.03 40 13 49 36 111.98 0.03 41 13 50 37 111.96 0.01 42 13 51 38 107.05 1.57 43 13 54 41 96.56 3.12 44 14 17 3 169.26 0.49 45 14 25 11 117.17 1.01 46 14 29 15 117.17 1.01 47 14 33 19 117.17 1.01 48 14 46 32 116.14 1.21 49 14 47 33 113.03 0.27 50 14 48 34 112.00 0.04 51 15 49 34 112.06 0.01 52 15 50 35 111.97 0.01 53 17 48 31 116.79 0.96 54 18 48 30 116.94 1.02 55 18 80 62 116.99 0.99 56 19 48 29 117.03 0.98 57 19 80 61 117.00 0.98 58 19 101 82 117.14 1.00 59 20 25 5 117.34 1.02 60 20 48 28 117.22 1.01 61 20 82 62 117.20 1.02 62 20 99 79 117.26 1.04 63 20 101 81 117.17 1.02 64 22 25 3 150.58 1.76 65 22 99 77 149.93 1.59 66 23 99 76 150.10 1.50 67 25 46 21 183.39 1.00 68 25 48 23 165.78 1.11 69 25 82 57 172.53 0.41 70 25 99 74 185.00 0.70 71 26 82 56 238.21 3.27 72 26 97 71 214.93 1.05 73 26 98 72 214.87 1.06 74 26 99 73 200.65 0.48 75 27 96 69 227.62 1.03 76 27 97 70 223.00 0.31 77 29 46 17 228.14 1.06 78 30 35 5 336.12 0.10 79 30 36 6 335.25 0.54 80 30 41 11 228.50 1.12 81 30 44 14 228.44 1.09 82 30 46 16 228.25 1.06 83 30 97 67 228.08 1.06 84 33 46 13 228.24 1.06 85 35 41 6 245.81 7.52 86 35 44 9 228.61 1.07 87 35 46 11 228.56 1.05 88 36 40 4 333.70 1.48 89 36 95 59 327.93 1.85 90 36 97 61 322.69 4.20 91 40 86 46 228.53 1.08 92 42 85 43 228.52 1.09 93 42 86 44 228.54 1.08 94 43 84 41 228.46 1.09 95 43 85 42 228.48 1.08 96 44 83 39 228.46 1.09 97 44 84 40 228.39 1.08 98 45 81 36 228.50 1.08 99 45 82 37 228.46 1.09 100 45 83 38 228.38 1.08 101 45 120 75 35.19 1.33 102 46 81 35 228.44 1.08 103 46 82 36 228.41 1.09 104 46 84 38 228.34 1.08 105 47 54 7 334.28 0.77 106 47 79 32 228.51 1.07 107 47 80 33 228.46 1.09 108 47 81 34 228.36 1.08 109 47 106 59 217.22 23.49 110 47 120 73 36.09 1.48 111 48 80 32 228.39 1.08 112 48 81 33 228.36 1.08 113 48 82 34 228.36 1.08 114 49 79 30 228.41 1.07 115 49 80 31 228.38 1.08 116 53 79 26 228.10 1.11 117 54 79 25 226.87 1.64 118 54 117 63 63.74 0.68 119 55 116 61 64.33 0.66 120 55 117 62 64.01 0.81 121 57 73 16 228.12 1.13 122 57 74 17 228.11 1.12 123 57 75 18 216.47 0.64 124 57 79 22 211.27 0.41 125 58 73 15 228.05 1.14 126 58 115 57 65.90 0.24 127 58 116 58 65.73 0.20 128 58 117 59 65.72 0.18 129 60 73 13 228.29 1.09 130 60 74 14 228.13 1.12 131 60 75 15 227.68 1.01 132 60 76 16 219.40 0.72 133 61 73 12 228.34 1.07 134 61 74 13 228.13 1.12 135 61 76 15 227.72 1.11 136 62 70 8 243.78 0.15 137 62 72 10 228.44 1.08 138 62 73 11 228.37 1.07 139 63 72 9 228.46 1.07 140 63 73 10 228.44 1.07 141 63 74 11 228.44 1.07 142 63 107 44 228.49 1.09 143 64 72 8 249.80 2.02 144 65 109 44 228.05 1.14 145 65 121 56 64.12 0.58 146 66 121 55 65.06 0.12 147 66 122 56 64.38 0.46 148 71 109 38 228.09 1.12 149 71 110 39 228.06 1.14 150 71 111 40 228.05 1.14 151 71 115 44 163.25 0.24 152 72 107 35 228.27 1.09 153 72 108 36 228.09 1.12 154 72 109 37 228.03 1.14 155 72 121 49 63.95 0.64 156 73 107 34 228.16 1.10 157 73 108 35 228.09 1.11 158 73 110 37 227.91 1.12 159 73 115 42 110.20 11.50 160 74 105 31 228.33 1.07 161 74 106 32 228.16 1.10 162 74 107 33 227.75 0.96 163 74 124 50 37.73 0.84 164 75 79 4 223.77 3.43 165 75 105 30 228.16 1.10 166 75 106 31 228.13 1.09 167 76 105 29 228.16 1.09 168 77 105 28 226.19 0.43 169 78 103 25 228.11 1.11 170 78 104 26 218.31 0.57 171 78 105 27 214.82 1.04 172 79 103 24 220.48 0.38 173 79 104 25 216.09 0.46 174 79 106 27 210.12 0.53 175 80 101 21 228.22 1.07 176 80 102 22 226.95 0.78 177 80 103 23 214.77 1.09 178 81 101 20 217.32 0.13 179 81 102 21 214.87 1.06 180 81 104 23 207.84 0.61 181 81 106 25 166.83 1.38 182 82 99 17 228.16 1.09 183 82 100 18 217.02 0.03 184 82 101 19 214.69 1.15 185 83 98 15 228.21 1.07 186 83 99 16 218.24 0.61 187 83 100 17 214.87 1.05 188 84 97 13 228.15 1.08 189 84 98 14 217.38 0.17 190 85 97 12 228.15 1.09 191 85 98 13 228.02 1.12 192 86 90 4 264.60 9.70 193 86 96 10 228.40 1.10 194 86 97 11 228.21 1.07 195 87 90 3 335.69 0.86 196 87 96 9 228.46 1.08 197 87 97 10 228.41 1.10 198 87 98 11 228.35 1.08 199 90 95 5 239.22 4.26 200 90 96 6 228.55 1.07 201 91 95 4 323.51 3.60 202 104 123 19 36.18 1.50 203 104 124 20 35.56 1.72 204 105 123 18 36.55 1.30 205 105 124 19 35.81 1.60 206 106 120 14 49.18 1.99 207 106 122 16 38.77 0.52 208 106 123 17 36.59 1.21 209 107 121 14 48.80 1.89 210 107 122 15 39.73 0.09 211 107 123 16 38.59 0.42 212 107 124 17 37.74 0.84 213 108 117 9 65.53 0.09 214 108 120 12 57.25 2.04 215 108 121 13 49.14 1.97 216 109 117 8 65.61 0.12 217 109 118 9 65.55 0.10 218 109 119 10 64.26 0.60 219 110 115 5 66.00 0.23 220 110 116 6 65.81 0.15 221 110 117 7 65.61 0.12 222 110 118 8 65.60 0.12 223 111 115 4 110.23 11.48 224 111 116 5 66.01 0.23 225 111 118 7 65.89 0.21 226 112 115 3 149.23 0.56