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 37 69 32 68.10 1.13 2 37 70 33 67.78 1.02 3 38 68 30 68.59 1.18 4 38 69 31 68.10 1.13 5 38 70 32 68.11 1.13 6 38 71 33 68.09 1.13 7 38 79 41 68.35 1.10 8 38 136 98 68.53 1.18 9 38 137 99 68.10 1.14 10 39 67 28 68.67 1.16 11 39 68 29 68.65 1.16 12 39 78 39 68.57 1.19 13 39 136 97 68.31 1.21 14 40 65 25 69.20 1.18 15 40 66 26 68.78 1.15 16 40 67 27 68.69 1.15 17 40 133 93 68.71 1.17 18 40 134 94 68.71 1.17 19 40 136 96 68.52 1.16 20 41 65 24 69.24 1.17 21 41 66 25 68.91 1.19 22 41 68 27 68.97 1.16 23 42 65 23 69.31 1.21 24 42 66 24 69.25 1.17 25 43 63 20 70.88 1.36 26 43 64 21 70.22 1.30 27 43 65 22 69.66 1.24 28 43 66 23 69.66 1.24 29 44 61 17 82.60 0.15 30 44 62 18 74.77 0.54 31 44 63 19 70.89 1.36 32 45 50 5 132.15 5.06 33 45 61 16 82.61 0.15 34 45 62 17 76.28 0.22 35 45 64 19 72.11 0.76 36 46 49 3 135.56 3.37 37 46 50 4 132.15 5.06 38 46 60 14 96.28 2.72 39 46 61 15 87.67 1.44 40 47 50 3 132.15 5.06 41 47 51 4 132.15 5.07 42 47 52 5 132.00 5.07 43 47 53 6 129.19 4.12 44 47 56 9 108.73 2.15 45 47 59 12 102.16 4.82 46 47 60 13 96.57 2.77 47 47 61 14 96.32 2.70 48 47 62 15 96.82 2.95 49 48 51 3 133.43 4.43 50 48 52 4 132.14 5.07 51 48 53 5 131.78 5.09 52 51 54 3 242.55 0.40 53 52 55 3 142.53 0.07 54 52 56 4 134.78 3.60 55 53 56 3 140.09 1.14 56 55 116 61 132.49 4.96 57 55 117 62 132.53 4.96 58 56 59 3 227.72 5.15 59 56 114 58 131.50 4.81 60 56 115 59 132.08 5.09 61 56 116 60 132.17 5.05 62 57 115 58 130.92 4.62 63 57 116 59 131.50 4.81 64 57 117 60 132.24 5.08 65 58 114 56 112.26 1.23 66 58 115 57 121.08 0.73 67 59 62 3 156.36 0.97 68 59 113 54 111.37 0.79 69 59 114 55 112.26 0.38 70 62 112 50 102.14 5.34 71 67 104 37 68.73 1.16 72 67 105 38 68.77 1.15 73 67 106 39 69.14 1.20 74 68 104 36 68.73 1.16 75 69 104 35 68.70 1.15 76 70 79 9 131.19 5.64 77 70 101 31 69.17 1.19 78 71 75 4 186.53 5.52 79 71 79 8 131.14 5.63 80 71 102 31 68.73 1.14 81 71 104 33 68.59 1.19 82 72 75 3 207.09 4.84 83 72 101 29 69.11 1.21 84 73 89 16 78.39 2.30 85 73 92 19 78.39 2.30 86 73 93 20 71.67 1.02 87 73 101 28 69.14 1.21 88 75 79 4 187.47 4.96 89 75 81 6 131.09 5.65 90 75 86 11 88.42 9.20 91 75 89 14 71.86 0.98 92 75 138 63 131.27 5.65 93 76 79 3 238.13 2.57 94 79 137 58 131.12 5.63 95 79 138 59 131.10 5.64 96 80 136 56 131.15 5.63 97 80 137 57 131.09 5.65 98 80 138 58 131.09 5.65 99 81 85 4 172.81 3.12 100 81 86 5 169.69 4.67 101 81 138 57 126.41 3.44 102 82 85 3 196.55 8.73 103 82 86 4 176.80 1.16 104 82 138 56 127.03 3.71 105 83 86 3 189.94 1.16 106 83 87 4 179.13 2.33 107 84 87 3 225.69 0.26 108 84 88 4 185.09 5.30 109 85 88 3 207.38 1.66 110 85 89 4 181.71 1.04 111 85 102 17 68.10 1.14 112 85 138 53 93.13 2.79 113 85 139 54 76.47 1.43 114 86 89 3 204.31 3.20 115 86 90 4 186.06 1.14 116 87 90 3 223.12 2.95 117 87 91 4 184.42 1.96 118 88 91 3 200.93 1.51 119 88 92 4 180.19 4.07 120 88 99 11 68.93 1.18 121 88 100 12 68.93 1.18 122 88 101 13 68.67 1.16 123 88 102 14 68.56 1.20 124 89 92 3 210.28 10.96 125 89 93 4 177.07 1.77 126 89 102 13 68.67 1.15 127 90 93 3 214.01 12.85 128 90 94 4 176.33 2.14 129 91 94 3 221.03 6.78 130 91 95 4 182.96 1.18 131 91 99 8 68.95 1.18 132 92 95 3 186.15 0.41 133 92 96 4 113.52 13.05 134 92 99 7 68.98 1.18 135 92 100 8 68.85 1.21 136 92 101 9 68.61 1.19 137 95 98 3 217.80 10.90 138 102 138 36 68.66 1.16 139 102 139 37 68.12 1.14 140 103 138 35 68.58 1.19 141 103 139 36 68.09 1.14 142 104 136 32 68.63 1.17 143 104 137 33 68.48 1.18 144 105 136 31 68.67 1.15 145 105 137 32 68.59 1.19 146 105 139 34 68.10 1.14 147 106 133 27 69.25 1.18 148 106 135 29 69.06 1.22 149 106 136 30 68.66 1.14 150 106 139 33 68.67 1.15 151 107 135 28 69.22 1.19 152 107 136 29 69.08 1.21 153 107 137 30 68.92 1.18 154 107 139 32 68.70 1.15 155 108 133 25 70.09 1.19 156 108 134 26 69.30 1.18 157 108 135 27 69.26 1.18 158 109 130 21 73.04 0.27 159 109 132 23 70.58 1.02 160 109 133 24 70.10 1.20 161 109 134 25 70.00 1.19 162 110 130 20 82.12 1.09 163 110 131 21 74.59 1.05 164 110 132 22 70.77 0.96 165 111 127 16 102.64 5.09 166 111 128 17 101.58 5.55 167 111 129 18 94.79 2.38 168 111 130 19 91.02 0.59 169 112 127 15 102.94 4.96 170 112 128 16 101.78 5.53 171 112 131 19 97.31 3.73 172 112 132 20 97.30 3.73 173 113 126 13 105.47 3.73 174 113 127 14 102.94 4.96 175 114 125 11 108.71 5.21 176 114 126 12 108.64 5.19 177 115 123 8 118.16 1.88 178 115 124 9 110.11 5.88 179 115 125 10 108.96 5.32 180 116 123 7 118.30 1.92 181 116 124 8 110.77 5.57 182 116 126 10 110.12 5.88 183 116 128 12 110.15 5.87 184 117 121 4 146.02 1.19 185 117 122 5 129.62 0.36 186 117 123 6 118.52 2.03 187 118 121 3 169.23 5.72 188 118 122 4 137.15 3.23 189 128 131 3 241.84 0.88 190 133 136 3 237.06 2.56