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 5 117 112 27.02 0.08 2 5 118 113 27.00 0.09 3 8 54 46 69.20 0.14 4 8 108 100 27.06 0.09 5 8 117 109 27.47 0.22 6 8 118 110 27.06 0.09 7 8 119 111 27.03 0.08 8 8 120 112 27.00 0.09 9 9 13 4 154.15 2.75 10 9 33 24 96.92 0.33 11 9 51 42 69.22 0.15 12 10 33 23 95.31 0.92 13 10 34 24 96.75 0.24 14 10 35 25 96.75 0.24 15 11 35 24 96.76 0.24 16 11 41 30 96.81 0.16 17 11 44 33 93.28 0.76 18 11 46 35 89.78 0.32 19 12 44 32 95.67 0.12 20 12 45 33 89.82 0.35 21 12 46 34 89.77 0.32 22 12 47 35 89.77 0.33 23 12 120 108 26.71 0.21 24 13 33 20 98.02 0.24 25 13 47 34 89.83 0.34 26 13 49 36 89.76 0.33 27 13 50 37 89.49 0.36 28 13 51 38 82.17 0.84 29 13 54 41 74.19 2.33 30 14 17 3 141.90 1.14 31 14 25 11 98.02 0.27 32 14 29 15 98.00 0.26 33 14 33 19 98.09 0.21 34 14 46 32 96.53 0.28 35 14 47 33 94.06 0.30 36 14 48 34 89.84 0.33 37 15 48 33 89.86 0.33 38 15 49 34 89.84 0.33 39 15 50 35 89.66 0.28 40 17 48 31 97.00 0.35 41 18 48 30 97.54 0.07 42 18 80 62 97.55 0.09 43 19 48 29 97.92 0.22 44 19 80 61 97.86 0.23 45 19 101 82 98.06 0.25 46 20 25 5 98.53 0.39 47 20 48 28 98.07 0.24 48 20 82 62 98.08 0.24 49 20 99 79 100.23 1.25 50 20 101 81 98.06 0.26 51 22 25 3 125.69 2.76 52 22 99 77 128.99 0.23 53 23 99 76 128.99 0.23 54 25 46 21 198.76 0.81 55 25 48 23 198.44 0.83 56 25 99 74 187.19 0.50 57 26 97 71 198.42 0.84 58 26 98 72 198.41 0.84 59 26 99 73 190.41 0.97 60 27 95 68 198.80 0.83 61 27 96 69 198.54 0.83 62 27 97 70 198.47 0.87 63 29 46 17 198.91 0.80 64 30 35 5 304.17 0.08 65 30 36 6 304.11 0.12 66 30 41 11 199.43 0.86 67 30 44 14 199.16 0.80 68 30 46 16 198.94 0.79 69 30 97 67 198.55 0.78 70 31 36 5 304.10 0.11 71 33 46 13 199.16 0.80 72 35 41 6 282.79 9.75 73 35 44 9 199.37 0.83 74 35 46 11 199.27 0.83 75 36 40 4 303.00 0.35 76 36 95 59 302.52 0.12 77 36 97 61 298.87 1.71 78 40 86 46 199.47 0.85 79 42 85 43 199.24 0.82 80 42 86 44 199.28 0.81 81 43 84 41 199.16 0.79 82 43 85 42 199.16 0.79 83 44 83 39 199.16 0.79 84 44 84 40 199.06 0.78 85 45 81 36 199.12 0.81 86 45 82 37 198.96 0.80 87 45 83 38 199.02 0.78 88 45 120 75 27.69 0.25 89 46 81 35 198.97 0.80 90 46 82 36 198.90 0.80 91 46 84 38 199.00 0.80 92 47 54 7 304.44 0.10 93 47 79 32 199.12 0.81 94 47 80 33 198.98 0.79 95 47 81 34 198.77 0.80 96 47 106 59 228.17 7.44 97 47 120 73 27.69 0.25 98 48 80 32 198.91 0.80 99 48 81 33 198.77 0.81 100 48 82 34 198.77 0.81 101 49 79 30 198.93 0.80 102 49 80 31 198.81 0.82 103 53 79 26 198.41 0.83 104 54 79 25 196.37 0.10 105 54 117 63 45.48 0.06 106 55 116 61 51.76 0.41 107 55 117 62 48.17 1.35 108 57 73 16 198.47 0.84 109 57 74 17 198.44 0.83 110 57 75 18 190.52 0.91 111 57 79 22 173.97 0.32 112 58 73 15 198.45 0.83 113 58 115 57 80.20 13.21 114 58 116 58 53.33 0.05 115 58 117 59 53.26 0.02 116 60 73 13 198.68 0.85 117 60 74 14 198.49 0.84 118 60 75 15 197.96 0.69 119 60 76 16 191.03 1.15 120 61 73 12 198.69 0.84 121 61 74 13 198.50 0.85 122 61 76 15 197.97 0.68 123 62 70 8 202.38 0.71 124 62 71 9 199.12 0.80 125 62 72 10 199.01 0.76 126 62 73 11 198.70 0.84 127 63 72 9 199.07 0.77 128 63 73 10 199.02 0.76 129 63 74 11 198.93 0.79 130 63 107 44 198.94 0.82 131 64 70 6 303.53 0.62 132 64 72 8 214.79 1.50 133 65 109 44 198.45 0.83 134 65 121 56 46.77 0.64 135 66 121 55 50.72 0.81 136 71 109 38 198.47 0.84 137 71 110 39 198.44 0.84 138 71 111 40 198.44 0.84 139 71 115 44 138.61 1.81 140 72 107 35 198.68 0.85 141 72 108 36 198.47 0.84 142 72 109 37 198.41 0.84 143 72 121 49 45.52 0.02 144 73 107 34 198.58 0.89 145 73 108 35 198.47 0.84 146 73 110 37 198.31 0.84 147 73 115 42 116.92 0.51 148 74 105 31 198.75 0.88 149 74 106 32 198.58 0.89 150 74 107 33 198.31 0.85 151 74 124 50 31.94 0.48 152 75 79 4 190.25 3.52 153 75 105 30 198.49 0.85 154 75 106 31 198.47 0.84 155 76 105 29 198.49 0.85 156 77 105 28 198.22 0.81 157 78 103 25 198.47 0.84 158 78 104 26 190.94 1.00 159 78 105 27 182.23 0.48 160 79 103 24 196.87 0.93 161 79 104 25 188.45 0.07 162 79 106 27 166.52 0.14 163 80 101 21 198.50 0.85 164 80 102 22 197.99 0.69 165 80 103 23 184.04 0.43 166 81 101 20 197.59 0.58 167 81 102 21 188.35 0.04 168 81 104 23 167.40 1.24 169 81 106 25 138.80 0.84 170 81 123 42 27.59 0.28 171 82 99 17 198.44 0.83 172 82 100 18 197.57 0.57 173 82 101 19 177.32 1.47 174 83 98 15 198.91 0.79 175 83 99 16 198.46 0.83 176 83 100 17 198.08 0.73 177 84 97 13 198.84 0.83 178 84 98 14 198.48 0.86 179 85 97 12 198.96 0.80 180 85 98 13 198.61 0.80 181 86 90 4 302.08 1.14 182 86 96 10 199.12 0.80 183 86 97 11 198.99 0.81 184 87 96 9 199.21 0.83 185 87 97 10 199.13 0.81 186 87 98 11 199.07 0.78 187 90 95 5 301.81 0.99 188 90 96 6 205.68 0.73 189 104 123 19 28.39 0.62 190 104 124 20 27.61 0.28 191 105 123 18 28.49 0.67 192 105 124 19 27.77 0.36 193 106 120 14 44.27 0.03 194 106 122 16 32.38 0.28 195 106 123 17 28.28 0.57 196 107 120 13 45.05 0.05 197 107 121 14 44.04 0.08 198 107 122 15 36.23 0.09 199 107 123 16 32.37 0.28 200 107 124 17 32.36 0.28 201 108 117 9 53.33 0.06 202 108 119 11 49.97 0.72 203 108 120 12 45.13 0.00 204 108 121 13 44.49 0.13 205 109 117 8 53.45 0.11 206 109 118 9 53.34 0.06 207 109 119 10 51.83 0.43 208 110 115 5 108.42 0.47 209 110 116 6 55.44 0.85 210 110 117 7 53.45 0.11 211 110 118 8 53.34 0.06 212 111 115 4 118.13 0.41 213 111 116 5 108.25 0.54 214 111 118 7 53.46 0.10 215 112 115 3 128.24 0.33