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 55 50 110.04 2.60 2 6 25 19 115.16 1.52 3 6 55 49 118.22 0.82 4 7 24 17 118.45 0.77 5 7 25 18 118.46 0.76 6 7 55 48 118.35 0.79 7 7 56 49 118.09 0.77 8 7 57 50 118.02 0.73 9 8 56 48 118.64 0.83 10 8 57 49 118.42 0.76 11 10 24 14 118.75 0.80 12 10 30 20 118.60 0.81 13 10 57 47 118.73 0.81 14 10 61 51 115.47 0.46 15 11 61 50 118.16 0.79 16 12 61 49 118.50 0.78 17 13 32 19 118.70 0.81 18 13 61 48 118.53 0.77 19 13 62 49 118.44 0.75 20 13 64 51 115.48 0.12 21 14 64 50 118.25 0.82 22 15 34 19 118.56 0.80 23 15 35 20 118.55 0.80 24 15 38 23 118.35 0.78 25 15 64 49 118.42 0.76 26 16 33 17 118.69 0.78 27 16 34 18 118.56 0.80 28 16 35 19 118.56 0.81 29 16 64 48 118.48 0.79 30 17 32 15 118.80 0.81 31 17 33 16 118.73 0.79 32 17 35 18 118.62 0.80 33 18 30 12 147.37 1.79 34 18 31 13 118.87 0.81 35 18 32 14 118.80 0.81 36 18 61 43 118.80 0.80 37 19 30 11 158.43 7.30 38 19 31 12 119.05 0.90 39 20 30 10 186.69 6.83 40 24 48 24 118.72 0.81 41 25 48 23 118.73 0.81 42 26 47 21 118.77 0.82 43 26 48 22 118.67 0.83 44 26 49 23 118.65 0.86 45 26 50 24 118.66 0.87 46 27 47 20 118.71 0.81 47 27 48 21 118.67 0.83 48 28 47 19 118.67 0.82 49 28 48 20 118.59 0.81 50 29 45 16 118.75 0.81 51 29 46 17 118.67 0.83 52 29 47 18 118.45 0.78 53 30 45 15 118.72 0.81 54 30 46 16 118.62 0.80 55 31 44 13 118.72 0.81 56 31 45 14 118.48 0.77 57 32 40 8 118.81 0.81 58 32 43 11 118.72 0.81 59 32 44 12 118.50 0.79 60 32 45 13 118.41 0.76 61 32 46 14 118.42 0.76 62 33 40 7 118.77 0.81 63 34 38 4 118.81 0.81 64 34 39 5 118.76 0.82 65 34 40 6 118.74 0.82 66 35 38 3 118.81 0.81 67 36 89 53 48.12 1.36 68 36 113 77 59.59 2.47 69 37 66 29 118.73 0.80 70 37 67 30 118.12 0.80 71 37 89 52 48.11 1.36 72 37 113 76 61.91 1.31 73 38 64 26 118.75 0.81 74 38 65 27 118.73 0.81 75 38 66 28 118.39 0.76 76 38 67 29 117.59 0.55 77 39 64 25 118.73 0.81 78 39 65 26 118.71 0.81 79 39 67 28 116.08 0.07 80 39 116 77 73.39 1.53 81 40 44 4 118.40 0.76 82 40 62 22 118.75 0.81 83 40 63 23 118.71 0.82 84 40 64 24 118.67 0.82 85 41 62 21 118.72 0.81 86 41 63 22 118.61 0.81 87 41 65 24 118.47 0.76 88 42 62 20 118.48 0.76 89 43 59 16 118.75 0.81 90 43 60 17 118.75 0.81 91 43 62 19 118.45 0.76 92 45 59 14 118.73 0.81 93 46 57 11 118.73 0.81 94 46 58 12 118.66 0.82 95 46 59 13 118.30 0.81 96 47 57 10 118.66 0.82 97 47 58 11 118.41 0.75 98 48 55 7 118.74 0.81 99 48 56 8 118.66 0.82 100 48 57 9 118.23 0.81 101 49 55 6 118.75 0.81 102 49 56 7 118.70 0.81 103 49 58 9 118.23 0.81 104 50 54 4 118.78 0.81 105 50 55 5 118.75 0.81 106 51 54 3 118.80 0.81 107 51 56 5 118.77 0.82 108 67 88 21 86.61 0.43 109 67 113 46 87.30 0.79 110 67 116 49 87.35 0.77 111 67 117 50 87.28 0.75 112 67 118 51 87.22 0.78 113 68 86 18 85.66 0.03 114 68 87 19 84.52 0.60 115 68 88 20 86.62 0.43 116 68 118 50 87.28 0.75 117 69 87 18 87.30 0.77 118 69 118 49 87.28 0.75 119 69 119 50 87.28 0.75 120 69 120 51 87.28 0.75 121 70 118 48 87.75 0.73 122 70 119 49 87.70 0.71 123 70 120 50 87.61 0.72 124 72 83 11 188.97 10.12 125 72 87 15 87.89 0.74 126 72 93 21 87.55 0.83 127 72 95 23 87.35 0.79 128 72 120 48 87.75 0.73 129 73 95 22 87.70 0.75 130 73 124 51 87.20 0.74 131 75 95 20 87.75 0.74 132 75 96 21 87.70 0.76 133 75 124 49 87.61 0.72 134 75 125 50 87.39 0.76 135 75 127 52 82.45 0.88 136 76 127 51 87.34 0.76 137 77 97 20 87.44 0.78 138 77 98 21 87.38 0.76 139 77 101 24 87.23 0.73 140 77 127 50 87.39 0.76 141 78 96 18 87.72 0.77 142 78 97 19 87.42 0.78 143 78 98 20 87.53 0.83 144 78 127 49 87.42 0.77 145 79 95 16 87.78 0.80 146 79 96 17 87.72 0.77 147 80 94 14 87.88 0.78 148 80 95 15 87.80 0.79 149 81 94 13 87.90 0.77 150 81 95 14 87.88 0.78 151 81 96 15 87.86 0.77 152 87 111 24 87.84 0.74 153 88 111 23 87.85 0.73 154 89 111 22 87.87 0.74 155 89 112 23 87.89 0.73 156 89 113 24 87.89 0.74 157 90 110 20 87.88 0.74 158 90 111 21 87.77 0.72 159 91 110 19 87.84 0.73 160 91 111 20 87.36 0.77 161 92 109 17 87.83 0.74 162 92 110 18 87.30 0.76 163 93 108 15 87.84 0.73 164 93 109 16 87.67 0.73 165 94 107 13 87.84 0.73 166 94 108 14 87.33 0.77 167 95 103 8 90.11 0.35 168 95 107 12 87.72 0.69 169 95 109 14 87.39 0.76 170 96 103 7 87.89 0.73 171 97 101 4 87.91 0.73 172 97 102 5 87.89 0.73 173 97 103 6 87.86 0.73 174 98 101 3 87.91 0.73 175 100 129 29 87.77 0.74 176 101 127 26 87.88 0.73 177 101 128 27 87.80 0.73 178 101 129 28 87.47 0.79 179 102 127 25 87.86 0.73 180 102 128 26 87.77 0.73 181 102 129 27 87.64 0.71 182 103 107 4 87.20 0.72 183 103 125 22 87.88 0.73 184 103 126 23 87.83 0.74 185 103 127 24 87.69 0.69 186 104 125 21 87.83 0.74 187 104 126 22 87.75 0.72 188 104 128 24 87.37 0.76 189 105 125 20 87.68 0.69 190 106 109 3 122.92 0.75 191 106 123 17 87.86 0.73 192 106 124 18 87.78 0.74 193 106 125 19 87.34 0.75 194 109 120 11 87.84 0.74 195 109 121 12 87.74 0.74 196 109 122 13 87.36 0.76 197 109 123 14 87.34 0.77 198 109 124 15 87.14 0.72 199 110 120 10 87.66 0.70 200 110 121 11 87.38 0.76 201 111 118 7 87.80 0.73 202 111 119 8 87.70 0.71 203 111 120 9 87.32 0.76 204 112 118 6 87.82 0.72 205 112 119 7 87.72 0.71 206 112 121 9 87.33 0.75 207 113 117 4 87.90 0.74 208 113 118 5 87.83 0.72 209 114 117 3 87.92 0.73 210 114 119 5 87.86 0.74