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 26.27 0.66 2 5 118 113 26.22 0.69 3 8 54 46 70.06 0.42 4 8 108 100 41.38 6.84 5 8 117 109 26.44 0.64 6 8 118 110 26.37 0.68 7 8 119 111 26.34 0.68 8 8 120 112 26.23 0.69 9 9 13 4 147.50 1.42 10 9 33 24 94.00 1.92 11 9 51 42 79.20 0.25 12 10 33 23 93.00 1.43 13 10 34 24 93.98 1.92 14 10 35 25 93.98 1.92 15 11 35 24 93.97 1.92 16 11 41 30 93.95 1.92 17 11 44 33 92.91 2.06 18 11 46 35 88.62 1.39 19 12 44 32 93.60 1.89 20 12 45 33 88.67 1.41 21 12 46 34 88.61 1.39 22 12 47 35 88.56 1.35 23 12 120 108 26.16 0.70 24 13 33 20 97.01 1.43 25 13 47 34 88.58 1.35 26 13 49 36 88.52 1.38 27 13 50 37 88.41 1.42 28 13 51 38 84.11 0.49 29 13 54 41 81.71 1.09 30 14 17 3 131.00 0.60 31 14 25 11 96.81 1.49 32 14 29 15 96.84 1.49 33 14 33 19 97.04 1.44 34 14 46 32 93.65 1.89 35 14 47 33 93.30 1.75 36 14 48 34 88.57 1.35 37 15 49 34 88.51 1.42 38 15 50 35 88.45 1.41 39 15 51 36 88.45 1.41 40 17 48 31 95.78 1.24 41 18 48 30 96.21 1.44 42 18 80 62 96.20 1.44 43 19 48 29 96.67 1.48 44 19 101 82 96.83 1.52 45 20 25 5 97.49 1.52 46 20 48 28 96.88 1.51 47 20 82 62 96.88 1.51 48 20 99 79 101.48 0.57 49 20 101 81 97.07 1.61 50 22 25 3 122.00 1.02 51 22 99 77 125.44 0.47 52 23 99 76 128.39 1.01 53 25 46 21 199.34 0.07 54 25 48 23 199.19 0.07 55 25 99 74 187.36 0.28 56 26 97 71 199.24 0.06 57 26 98 72 199.16 0.07 58 26 99 73 189.11 0.27 59 27 96 69 199.23 0.04 60 27 97 70 199.17 0.07 61 29 46 17 199.40 0.07 62 30 35 5 303.91 0.52 63 30 36 6 303.91 0.52 64 30 41 11 199.72 0.01 65 30 44 14 199.62 0.01 66 30 46 16 199.53 0.01 67 30 97 67 199.19 0.06 68 31 36 5 303.89 0.53 69 33 46 13 199.56 0.01 70 35 41 6 299.17 2.24 71 35 44 9 199.77 0.03 72 35 46 11 199.64 0.01 73 40 86 46 199.74 0.03 74 42 85 43 199.68 0.02 75 42 86 44 199.71 0.02 76 43 84 41 199.62 0.03 77 43 85 42 199.65 0.02 78 44 83 39 199.62 0.03 79 44 84 40 199.50 0.06 80 45 81 36 199.59 0.02 81 45 82 37 199.41 0.07 82 45 83 38 199.43 0.07 83 45 120 75 26.48 0.63 84 46 81 35 199.44 0.07 85 46 82 36 199.40 0.07 86 46 84 38 199.46 0.07 87 47 79 32 199.62 0.02 88 47 80 33 199.45 0.06 89 47 81 34 199.34 0.07 90 47 106 59 270.00 7.26 91 47 120 73 27.27 0.31 92 48 80 32 199.37 0.06 93 48 81 33 199.34 0.07 94 48 82 34 199.34 0.07 95 49 79 30 199.40 0.07 96 49 80 31 199.37 0.06 97 53 79 26 199.12 0.04 98 54 79 25 197.91 0.16 99 54 117 63 43.90 0.27 100 55 117 62 45.41 1.12 101 57 73 16 199.12 0.04 102 57 74 17 199.10 0.05 103 57 75 18 195.03 0.23 104 57 79 22 174.58 0.29 105 58 73 15 199.10 0.05 106 58 115 57 100.87 2.20 107 58 116 58 49.68 0.49 108 58 117 59 48.51 1.07 109 60 73 13 199.28 0.07 110 60 74 14 199.24 0.06 111 60 75 15 198.74 0.17 112 60 76 16 195.03 0.24 113 61 73 12 199.28 0.07 114 61 74 13 199.28 0.07 115 61 76 15 199.21 0.04 116 62 70 8 204.01 1.94 117 62 71 9 199.59 0.04 118 62 72 10 199.47 0.06 119 62 73 11 199.30 0.07 120 63 72 9 199.51 0.05 121 63 73 10 199.47 0.06 122 63 74 11 199.47 0.06 123 63 107 44 199.57 0.01 124 64 72 8 226.28 0.14 125 65 109 44 199.10 0.05 126 65 121 56 46.58 0.84 127 66 121 55 46.84 0.96 128 66 122 56 46.59 0.83 129 71 109 38 199.24 0.06 130 71 110 39 199.21 0.06 131 71 111 40 199.13 0.04 132 71 115 44 134.78 1.44 133 72 107 35 199.29 0.07 134 72 108 36 199.24 0.06 135 72 109 37 199.06 0.06 136 72 121 49 45.37 0.30 137 73 107 34 199.24 0.06 138 73 108 35 199.20 0.06 139 73 110 37 198.66 0.14 140 73 115 42 113.59 0.62 141 74 105 31 199.32 0.08 142 74 106 32 199.25 0.06 143 74 107 33 199.10 0.06 144 74 124 50 29.73 0.48 145 75 79 4 191.69 3.75 146 75 105 30 199.24 0.06 147 75 106 31 199.22 0.06 148 76 105 29 199.24 0.06 149 77 105 28 198.46 0.05 150 78 103 25 199.22 0.06 151 78 104 26 194.99 0.21 152 78 105 27 183.35 0.08 153 79 103 24 197.06 0.53 154 79 104 25 192.02 1.19 155 79 106 27 166.28 1.25 156 80 101 21 199.24 0.06 157 80 102 22 198.66 0.16 158 80 103 23 183.52 0.16 159 81 101 20 197.42 0.34 160 81 102 21 187.42 0.24 161 81 104 23 169.28 0.32 162 81 106 25 141.47 1.16 163 81 123 42 26.64 0.54 164 82 99 17 199.22 0.06 165 82 100 18 198.46 0.06 166 82 101 19 181.75 0.88 167 83 98 15 199.41 0.07 168 83 99 16 199.22 0.06 169 83 100 17 198.75 0.12 170 84 97 13 199.38 0.07 171 84 98 14 199.21 0.06 172 85 97 12 199.42 0.07 173 85 98 13 199.35 0.04 174 86 96 10 199.59 0.03 175 86 97 11 199.46 0.06 176 87 96 9 199.62 0.03 177 87 97 10 199.54 0.04 178 87 98 11 199.50 0.05 179 90 95 5 287.51 5.32 180 90 96 6 199.82 0.04 181 104 123 19 27.64 0.17 182 104 124 20 26.64 0.54 183 105 123 18 28.91 0.80 184 105 124 19 27.49 0.11 185 106 120 14 43.95 0.02 186 106 122 16 30.51 0.57 187 106 123 17 29.50 0.50 188 107 120 13 43.96 0.02 189 107 121 14 42.22 0.14 190 107 122 15 30.59 0.17 191 107 124 17 29.79 0.46 192 108 117 9 48.51 1.07 193 108 119 11 46.45 0.91 194 108 120 12 43.96 0.02 195 108 121 13 43.81 0.04 196 109 117 8 48.56 1.10 197 109 118 9 48.50 1.07 198 109 119 10 47.29 1.25 199 110 115 5 109.14 0.38 200 110 116 6 77.41 12.75 201 110 117 7 48.57 1.10 202 110 118 8 48.55 1.09 203 111 115 4 113.57 0.29 204 111 116 5 109.01 0.31 205 111 118 7 49.67 0.58 206 112 115 3 123.67 0.58