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 95.23 7.00 2 6 24 18 94.99 7.06 3 6 25 19 95.34 6.88 4 6 55 49 95.91 7.03 5 7 24 17 95.71 7.05 6 7 55 48 96.11 7.13 7 7 56 49 95.91 7.04 8 7 57 50 95.88 7.04 9 8 56 48 96.42 7.16 10 8 57 49 96.22 7.08 11 9 24 15 96.94 7.21 12 10 20 10 218.90 0.55 13 10 24 14 96.98 7.22 14 10 30 20 96.42 7.21 15 10 57 47 96.88 7.25 16 10 61 51 94.98 6.64 17 12 61 49 96.23 7.08 18 13 32 19 96.62 7.21 19 13 61 48 96.44 7.16 20 13 62 49 96.17 7.11 21 13 64 51 84.70 7.04 22 14 64 50 95.87 7.04 23 15 34 19 96.22 7.10 24 15 35 20 96.45 7.21 25 15 38 23 96.16 7.11 26 15 64 49 95.91 7.04 27 16 33 17 96.67 7.25 28 16 34 18 96.24 7.08 29 16 35 19 96.49 7.21 30 16 64 48 96.08 7.12 31 17 32 15 96.86 7.25 32 17 33 16 96.75 7.21 33 17 35 18 96.69 7.25 34 18 30 12 97.10 7.18 35 18 31 13 97.06 7.19 36 18 32 14 96.84 7.26 37 18 61 43 96.98 7.20 38 19 30 11 97.12 7.17 39 19 31 12 97.08 7.19 40 20 30 10 97.14 7.20 41 22 28 6 218.70 0.17 42 24 30 6 218.72 0.18 43 24 48 24 96.90 7.22 44 25 48 23 96.92 7.23 45 26 48 22 96.87 7.21 46 26 50 24 96.95 7.22 47 27 47 20 96.91 7.23 48 27 48 21 96.16 7.09 49 28 47 19 96.81 7.22 50 28 48 20 96.16 7.09 51 29 45 16 96.95 7.21 52 29 46 17 96.79 7.22 53 29 47 18 96.09 7.12 54 30 45 15 96.84 7.23 55 30 46 16 96.49 7.19 56 31 44 13 96.86 7.24 57 31 45 14 96.12 7.11 58 32 40 8 97.02 7.21 59 32 43 11 96.92 7.21 60 32 44 12 96.46 7.21 61 32 45 13 95.95 7.02 62 32 46 14 96.12 7.11 63 33 40 7 96.98 7.21 64 34 38 4 97.00 7.21 65 34 39 5 96.98 7.22 66 34 40 6 96.94 7.21 67 35 38 3 97.02 7.21 68 36 89 53 47.54 3.30 69 37 66 29 96.81 7.27 70 37 67 30 95.36 7.28 71 37 89 52 47.48 3.33 72 37 113 76 51.70 0.95 73 38 64 26 96.97 7.22 74 38 65 27 96.73 7.19 75 38 66 28 95.82 7.05 76 38 67 29 95.52 6.91 77 39 64 25 96.85 7.24 78 39 65 26 96.47 7.13 79 39 67 28 93.48 7.24 80 39 116 77 60.34 0.89 81 40 44 4 96.09 7.12 82 40 62 22 96.98 7.21 83 40 63 23 96.89 7.24 84 40 64 24 96.19 7.13 85 41 62 21 96.85 7.24 86 41 63 22 96.62 7.20 87 41 65 24 95.89 7.04 88 42 62 20 96.16 7.11 89 43 59 16 96.98 7.21 90 43 60 17 96.94 7.21 91 43 62 19 96.13 7.11 92 45 59 14 96.84 7.23 93 46 57 11 96.89 7.24 94 46 58 12 96.57 7.23 95 46 59 13 96.09 7.12 96 47 57 10 96.56 7.17 97 47 58 11 96.11 7.13 98 48 55 7 96.89 7.25 99 48 56 8 96.48 7.17 100 48 57 9 96.08 7.12 101 49 55 6 96.95 7.22 102 49 56 7 96.80 7.29 103 49 58 9 95.87 7.03 104 50 55 5 96.95 7.22 105 51 54 3 109.91 10.09 106 51 55 4 96.97 7.23 107 51 56 5 96.97 7.23 108 67 88 21 96.69 8.81 109 67 113 46 98.13 8.41 110 67 116 49 98.23 8.35 111 67 117 50 98.09 8.39 112 67 118 51 96.81 8.36 113 68 86 18 97.30 8.52 114 68 87 19 97.35 8.54 115 68 118 50 97.95 8.46 116 69 87 18 97.37 8.55 117 69 118 49 98.16 8.35 118 69 119 50 98.04 8.42 119 69 120 51 97.94 8.46 120 70 118 48 98.81 8.32 121 70 120 50 98.48 8.29 122 71 120 49 98.82 8.34 123 72 83 11 192.15 4.42 124 72 87 15 98.87 8.34 125 72 93 21 98.58 8.29 126 72 95 23 98.23 8.35 127 72 120 48 98.83 8.34 128 73 95 22 98.53 8.28 129 73 120 47 98.88 8.34 130 73 124 51 94.33 7.25 131 75 95 20 98.73 8.34 132 75 124 49 98.50 8.26 133 75 125 50 98.35 8.32 134 75 127 52 85.78 5.54 135 76 127 51 97.22 8.25 136 77 97 20 98.47 8.26 137 77 98 21 98.41 8.26 138 77 101 24 98.17 8.37 139 77 127 50 97.42 8.31 140 78 96 18 98.73 8.32 141 78 97 19 98.47 8.26 142 78 98 20 98.58 8.31 143 78 127 49 98.34 8.31 144 79 95 16 98.78 8.31 145 79 96 17 98.72 8.30 146 80 93 13 98.94 8.30 147 80 94 14 98.88 8.32 148 80 95 15 98.76 8.28 149 81 94 13 98.89 8.31 150 81 96 15 98.77 8.28 151 87 111 24 98.84 8.34 152 88 111 23 98.84 8.35 153 89 111 22 98.84 8.33 154 89 113 24 98.85 8.31 155 90 110 20 98.84 8.34 156 90 111 21 98.75 8.34 157 91 110 19 98.81 8.34 158 91 111 20 98.38 8.28 159 92 109 17 98.83 8.34 160 92 110 18 98.14 8.29 161 93 108 15 98.83 8.34 162 93 109 16 98.73 8.35 163 94 107 13 98.83 8.34 164 94 108 14 98.24 8.34 165 95 103 8 98.92 8.35 166 95 107 12 98.73 8.32 167 95 109 14 98.28 8.36 168 96 103 7 98.89 8.35 169 97 101 4 98.90 8.35 170 97 102 5 98.88 8.34 171 97 103 6 98.82 8.34 172 98 101 3 98.92 8.35 173 101 127 26 98.84 8.33 174 101 128 27 98.81 8.34 175 101 129 28 98.59 8.37 176 102 126 24 98.89 8.34 177 102 127 25 98.80 8.34 178 102 128 26 98.69 8.35 179 103 107 4 97.30 8.29 180 103 125 22 98.87 8.34 181 103 126 23 98.81 8.34 182 103 127 24 98.69 8.35 183 104 125 21 98.82 8.33 184 104 126 22 98.73 8.35 185 104 128 24 98.25 8.35 186 105 125 20 98.62 8.34 187 106 125 19 98.25 8.35 188 109 120 11 98.84 8.34 189 109 121 12 98.69 8.37 190 109 122 13 98.37 8.32 191 109 124 15 96.67 8.37 192 110 120 10 98.68 8.36 193 110 121 11 98.28 8.36 194 111 119 8 98.75 8.36 195 111 120 9 98.16 8.38 196 112 118 6 98.84 8.34 197 112 119 7 98.81 8.34 198 112 121 9 98.28 8.36 199 113 117 4 98.88 8.33 200 114 117 3 98.91 8.34 201 114 119 5 98.86 8.32