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 33 69 36 21.70 0.60 2 33 70 37 21.70 0.60 3 34 70 36 26.55 1.62 4 36 41 5 196.75 3.06 5 36 69 33 123.69 0.78 6 36 70 34 111.08 1.36 7 37 69 32 123.70 0.78 8 37 70 33 122.47 1.34 9 37 79 42 123.64 0.80 10 38 68 30 123.77 0.79 11 38 69 31 123.70 0.78 12 38 70 32 123.70 0.78 13 38 71 33 123.70 0.78 14 38 79 41 123.67 0.79 15 38 136 98 123.70 0.78 16 38 137 99 123.70 0.78 17 38 138 100 123.69 0.78 18 39 67 28 123.73 0.78 19 39 68 29 123.79 0.80 20 39 136 97 123.70 0.78 21 40 65 25 123.95 0.78 22 40 66 26 123.94 0.78 23 40 67 27 123.83 0.80 24 40 133 93 123.84 0.83 25 40 134 94 123.90 0.80 26 40 135 95 123.83 0.82 27 40 136 96 123.73 0.78 28 41 65 24 123.96 0.78 29 41 66 25 123.95 0.78 30 41 68 27 123.97 0.77 31 42 65 23 123.96 0.79 32 42 66 24 124.01 0.76 33 43 63 20 124.06 0.76 34 43 64 21 124.04 0.76 35 43 65 22 124.03 0.76 36 43 66 23 124.03 0.76 37 44 61 17 124.23 0.72 38 44 62 18 124.16 0.72 39 44 63 19 124.06 0.77 40 45 50 5 150.93 0.29 41 45 61 16 124.23 0.72 42 45 62 17 124.20 0.73 43 45 64 19 124.12 0.73 44 46 49 3 151.16 0.18 45 46 50 4 151.15 0.18 46 46 60 14 124.28 0.73 47 46 61 15 124.23 0.72 48 47 50 3 151.91 0.52 49 47 51 4 151.15 0.18 50 47 52 5 141.80 2.84 51 47 56 9 124.62 0.68 52 47 59 12 124.48 0.68 53 47 60 13 124.31 0.74 54 47 61 14 124.28 0.73 55 47 62 15 124.28 0.73 56 48 51 3 151.15 0.18 57 48 53 5 141.38 2.64 58 48 60 12 124.34 0.74 59 52 55 3 153.85 1.53 60 52 56 4 147.91 0.96 61 53 56 3 152.15 1.16 62 54 117 63 216.38 7.54 63 55 116 61 148.19 1.09 64 55 117 62 148.57 0.91 65 55 128 73 188.52 0.11 66 56 59 3 269.80 0.09 67 56 114 58 143.89 3.08 68 56 115 59 147.97 1.11 69 56 116 60 148.02 1.09 70 57 115 58 143.87 3.08 71 57 117 60 148.56 0.92 72 58 114 56 136.62 1.25 73 58 115 57 139.20 1.29 74 59 113 54 134.90 0.40 75 59 114 55 134.91 0.40 76 62 112 50 124.49 0.67 77 67 104 37 123.92 0.79 78 67 105 38 123.94 0.78 79 67 106 39 123.97 0.78 80 68 104 36 123.94 0.78 81 69 104 35 123.86 0.81 82 70 79 9 143.00 3.71 83 70 101 31 124.00 0.77 84 71 75 4 202.49 0.40 85 71 79 8 142.94 3.71 86 71 89 18 124.51 0.69 87 71 101 30 123.95 0.78 88 71 102 31 123.88 0.81 89 71 103 32 123.81 0.81 90 71 104 33 123.73 0.78 91 72 89 17 124.52 0.69 92 72 101 29 123.96 0.79 93 73 89 16 124.53 0.68 94 73 90 17 124.51 0.69 95 73 93 20 124.25 0.74 96 75 79 4 176.90 4.00 97 75 81 6 142.89 3.70 98 75 85 10 128.63 2.42 99 75 86 11 124.81 0.71 100 75 89 14 124.56 0.69 101 75 138 63 165.18 1.01 102 76 79 3 253.59 7.96 103 77 80 3 251.48 8.84 104 79 137 58 142.94 3.71 105 79 138 59 142.92 3.71 106 80 107 27 123.96 0.78 107 80 136 56 142.94 3.71 108 80 137 57 142.91 3.71 109 81 85 4 178.00 2.60 110 81 86 5 174.50 1.59 111 81 138 57 142.53 3.54 112 82 85 3 219.69 2.45 113 82 86 4 218.75 1.98 114 82 138 56 142.53 3.54 115 83 86 3 219.69 2.45 116 83 87 4 213.54 4.58 117 84 87 3 233.72 4.76 118 84 88 4 187.94 0.82 119 85 88 3 217.75 1.51 120 85 89 4 193.16 2.71 121 85 102 17 123.70 0.78 122 85 138 53 124.84 0.71 123 85 139 54 124.48 0.70 124 86 89 3 223.94 3.33 125 86 90 4 193.17 2.71 126 87 90 3 229.27 8.94 127 87 91 4 193.18 2.71 128 88 91 3 208.38 4.89 129 88 92 4 200.78 1.09 130 88 99 11 124.05 0.75 131 88 100 12 124.01 0.77 132 88 101 13 123.70 0.78 133 88 102 14 123.70 0.79 134 89 92 3 219.67 4.87 135 89 93 4 200.78 1.09 136 89 102 13 123.70 0.79 137 90 93 3 218.46 3.01 138 90 94 4 200.78 1.09 139 91 94 3 242.78 1.07 140 91 95 4 200.69 1.11 141 91 98 7 130.94 2.68 142 91 99 8 124.09 0.74 143 92 95 3 229.71 4.41 144 92 96 4 169.22 2.53 145 92 99 7 124.09 0.74 146 92 100 8 124.07 0.75 147 92 101 9 124.03 0.76 148 93 96 3 246.75 0.89 149 95 98 3 240.86 2.98 150 96 99 3 268.04 0.58 151 102 139 37 123.70 0.78 152 103 137 34 123.84 0.81 153 103 138 35 123.70 0.78 154 103 139 36 123.34 0.61 155 104 136 32 123.81 0.80 156 104 137 33 123.70 0.78 157 105 136 31 123.81 0.80 158 105 137 32 123.76 0.79 159 105 139 34 123.70 0.78 160 106 133 27 123.84 0.84 161 106 135 29 123.86 0.82 162 106 136 30 123.83 0.81 163 106 139 33 123.80 0.80 164 107 135 28 123.91 0.81 165 107 136 29 123.95 0.78 166 107 137 30 123.93 0.79 167 107 139 32 123.87 0.81 168 108 133 25 123.99 0.80 169 108 134 26 123.98 0.79 170 108 135 27 123.97 0.79 171 109 130 21 123.98 0.84 172 109 132 23 124.00 0.80 173 109 133 24 124.00 0.80 174 109 134 25 123.98 0.79 175 110 130 20 124.06 0.82 176 110 131 21 124.06 0.81 177 110 132 22 124.03 0.80 178 110 134 24 124.14 0.72 179 111 127 16 124.56 0.66 180 111 128 17 124.47 0.68 181 111 129 18 124.40 0.69 182 111 130 19 124.38 0.70 183 112 127 15 124.79 0.72 184 112 128 16 124.51 0.66 185 112 131 19 124.40 0.69 186 112 132 20 124.38 0.70 187 113 125 12 138.84 1.55 188 113 126 13 129.17 0.51 189 113 127 14 124.79 0.72 190 114 125 11 140.52 2.39 191 114 126 12 135.11 2.01 192 114 128 14 131.47 1.52 193 115 123 8 148.13 1.11 194 115 124 9 143.91 3.20 195 115 125 10 141.30 2.00 196 116 123 7 148.12 1.11 197 116 124 8 147.97 1.18 198 116 126 10 144.03 3.14 199 116 128 12 143.83 3.11 200 117 122 5 150.18 1.61 201 117 123 6 148.18 1.11 202 118 121 3 199.09 3.93 203 118 122 4 163.22 2.15 204 118 124 6 148.58 0.93 205 128 131 3 269.42 0.87 206 133 136 3 267.89 1.38