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 3 24 21 324.72 3.50 2 3 25 22 325.49 3.84 3 3 98 95 250.39 1.02 4 3 107 104 244.55 1.51 5 4 22 18 263.89 1.20 6 4 23 19 336.93 0.02 7 4 24 20 336.88 0.00 8 4 34 30 261.10 6.33 9 4 96 92 244.46 1.48 10 4 97 93 245.03 1.40 11 4 98 94 250.60 0.95 12 4 107 103 244.60 1.50 13 4 108 104 244.53 1.51 14 4 109 105 244.03 1.66 15 6 109 103 244.60 1.50 16 6 110 104 244.55 1.52 17 6 111 105 244.40 1.50 18 6 112 106 244.41 1.49 19 7 111 104 244.59 1.50 20 7 112 105 244.49 1.49 21 8 112 104 244.52 1.50 22 8 113 105 244.50 1.49 23 8 154 146 33.10 0.81 24 8 205 197 32.57 0.86 25 9 112 103 244.55 1.51 26 9 113 104 244.51 1.50 27 9 153 144 33.95 0.96 28 9 154 145 33.30 0.89 29 9 205 196 32.95 0.77 30 9 206 197 33.30 0.94 31 10 112 102 244.62 1.51 32 10 113 103 244.58 1.50 33 10 114 104 244.52 1.50 34 10 115 105 244.49 1.49 35 11 115 104 244.52 1.51 36 11 117 106 244.44 1.48 37 11 119 108 193.62 1.71 38 11 121 110 40.26 0.55 39 11 151 140 37.98 0.57 40 11 152 141 35.45 1.53 41 12 114 102 244.62 1.50 42 12 115 103 244.55 1.51 43 12 116 104 244.44 1.48 44 12 117 105 244.44 1.48 45 13 116 103 244.55 1.51 46 13 117 104 244.45 1.48 47 13 118 105 244.41 1.49 48 13 120 107 244.38 1.49 49 14 116 102 244.56 1.51 50 14 117 103 244.54 1.51 51 14 118 104 244.50 1.50 52 18 114 96 244.54 1.51 53 20 112 92 244.49 1.49 54 20 114 94 244.44 1.49 55 37 95 58 337.99 0.25 56 86 116 30 244.55 1.51 57 87 116 29 244.55 1.51 58 88 116 28 244.55 1.51 59 90 116 26 244.53 1.51 60 91 114 23 244.55 1.52 61 91 115 24 244.49 1.50 62 91 116 25 244.41 1.49 63 92 112 20 245.30 1.52 64 92 113 21 244.58 1.50 65 92 114 22 244.50 1.50 66 93 111 18 245.17 1.48 67 93 112 19 244.58 1.49 68 93 113 20 244.49 1.50 69 94 111 17 244.61 1.51 70 94 112 18 244.51 1.50 71 94 114 20 244.41 1.49 72 95 109 14 264.94 1.95 73 95 110 15 244.68 1.48 74 95 111 16 244.40 1.50 75 113 153 40 33.75 1.06 76 113 154 41 32.97 0.73 77 115 151 36 38.79 0.20 78 115 152 37 34.20 0.91 79 117 151 34 113.37 1.23 80 119 151 32 118.77 2.10 81 119 178 59 119.18 1.89 82 120 151 31 122.48 0.34 83 121 151 30 122.63 0.28 84 121 152 31 122.47 0.32 85 121 204 83 96.45 0.68 86 121 206 85 95.88 0.67 87 121 207 86 94.53 0.60 88 122 149 27 138.54 0.28 89 122 150 28 135.60 0.80 90 122 151 29 127.22 1.26 91 122 179 57 138.64 0.20 92 122 204 82 96.69 0.73 93 122 207 85 95.94 0.70 94 123 149 26 138.78 0.23 95 123 150 27 138.00 0.14 96 123 207 84 95.94 0.70 97 123 209 86 95.27 0.56 98 124 147 23 138.46 0.29 99 124 148 24 138.76 0.23 100 124 149 25 138.78 0.23 101 124 150 26 138.48 0.37 102 124 202 78 96.95 0.75 103 124 204 80 96.74 0.72 104 124 209 85 95.96 0.70 105 125 146 21 138.76 0.23 106 125 147 22 138.77 0.23 107 125 148 23 138.78 0.23 108 126 145 19 138.58 0.28 109 126 146 20 138.75 0.23 110 126 147 21 138.78 0.23 111 126 200 74 131.97 0.80 112 126 202 76 101.39 0.66 113 126 211 85 95.97 0.70 114 126 213 87 87.47 1.70 115 127 145 18 138.76 0.23 116 127 146 19 138.78 0.23 117 128 145 17 138.77 0.23 118 128 213 85 95.92 0.70 119 128 215 87 82.07 0.94 120 129 143 14 138.91 0.22 121 129 144 15 138.85 0.23 122 129 145 16 138.77 0.22 123 129 146 17 138.91 0.23 124 129 183 54 138.92 0.22 125 129 215 86 95.14 0.78 126 130 193 63 139.05 0.25 127 130 215 85 95.42 0.64 128 130 216 86 95.08 0.79 129 130 217 87 78.31 0.79 130 130 218 88 73.08 0.52 131 131 135 4 154.53 0.40 132 131 141 10 139.19 0.19 133 131 143 12 139.14 0.17 134 131 193 62 139.19 0.19 135 131 218 87 78.53 0.81 136 132 135 3 169.16 3.08 137 137 140 3 202.84 1.39 138 137 190 53 337.37 0.27 139 143 215 72 95.70 0.82 140 144 215 71 94.58 0.58 141 145 215 70 83.11 0.44 142 147 155 8 337.57 0.17 143 152 206 54 215.19 1.06 144 155 182 27 337.57 0.17 145 157 170 13 336.38 0.44 146 157 184 27 294.30 18.04 147 159 186 27 310.45 9.93 148 159 215 56 95.97 0.71 149 188 198 10 336.12 0.88 150 193 198 5 335.79 1.02 151 193 215 22 96.33 0.64 152 193 216 23 96.15 0.67 153 193 217 24 95.97 0.71 154 194 217 23 95.99 0.72 155 197 214 17 96.23 0.69 156 198 214 16 96.12 0.66 157 198 215 17 95.99 0.70 158 199 212 13 96.20 0.63 159 199 213 14 96.04 0.70 160 199 214 15 95.94 0.70 161 200 212 12 96.03 0.70 162 200 213 13 95.99 0.70 163 201 210 9 96.23 0.64 164 201 211 10 96.12 0.66 165 201 212 11 95.96 0.71 166 202 210 8 96.14 0.65 167 202 211 9 96.00 0.71 168 203 209 6 96.14 0.65 169 203 210 7 95.96 0.70 170 204 207 3 171.56 0.86 171 204 208 4 157.49 1.36 172 204 209 5 95.97 0.71 173 205 208 3 158.16 1.03