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 2 20 18 87.55 0.10 2 2 22 20 86.36 0.26 3 2 48 46 84.23 0.14 4 3 20 17 103.62 8.02 5 3 21 18 87.02 0.26 6 3 22 19 86.91 0.28 7 3 48 45 85.86 0.49 8 3 49 46 85.87 0.51 9 3 50 47 84.80 0.14 10 4 19 15 147.91 14.10 11 4 20 16 103.62 8.02 12 4 50 46 86.44 0.29 13 5 19 14 180.75 2.31 14 6 21 15 195.68 5.32 15 6 27 21 86.75 0.30 16 6 29 23 85.93 0.48 17 6 50 44 86.72 0.32 18 7 29 22 86.73 0.30 19 7 50 43 173.23 1.91 20 9 29 20 86.75 0.35 21 9 30 21 86.73 0.34 22 9 53 44 86.73 0.34 23 9 56 47 85.20 0.30 24 10 55 45 85.96 0.53 25 10 56 46 85.20 0.30 26 10 57 47 84.25 0.14 27 11 32 21 86.48 0.35 28 11 56 45 86.11 0.45 29 12 30 18 86.59 0.41 30 12 31 19 86.14 0.47 31 12 32 20 86.45 0.35 32 12 56 44 85.91 0.49 33 13 29 16 86.59 0.41 34 13 30 17 86.19 0.51 35 14 27 13 86.89 0.29 36 14 29 15 86.20 0.49 37 14 30 16 86.20 0.49 38 15 27 12 86.89 0.29 39 15 30 15 86.19 0.50 40 21 45 24 147.96 14.09 41 23 45 22 87.04 0.26 42 23 46 23 87.51 0.03 43 23 47 24 207.80 0.24 44 24 45 21 87.00 0.24 45 24 46 22 87.04 0.26 46 25 44 19 87.00 0.25 47 25 45 20 86.69 0.33 48 26 42 16 87.05 0.25 49 26 43 17 86.91 0.24 50 26 44 18 86.64 0.31 51 27 42 15 86.80 0.28 52 27 43 16 86.75 0.30 53 28 41 13 86.98 0.28 54 28 42 14 86.53 0.33 55 29 43 14 86.08 0.42 56 31 37 6 133.27 1.53 57 34 58 24 140.41 5.70 58 35 56 21 201.18 0.70 59 35 57 22 87.02 0.27 60 35 58 23 86.77 0.31 61 36 56 20 87.00 0.28 62 36 57 21 86.81 0.29 63 36 58 22 86.75 0.29 64 36 59 23 86.20 0.35 65 36 81 45 37.79 1.38 66 37 41 4 208.48 0.01 67 37 54 17 208.47 0.14 68 37 55 18 87.05 0.27 69 37 56 19 86.80 0.29 70 38 54 16 87.06 0.24 71 38 55 17 86.83 0.29 72 38 57 19 86.75 0.30 73 38 59 21 75.38 0.05 74 38 81 43 28.80 1.39 75 38 105 67 25.88 0.49 76 39 54 15 86.80 0.29 77 40 52 12 204.41 0.88 78 40 54 14 86.78 0.30 79 43 50 7 87.05 0.27 80 43 51 8 86.75 0.30 81 43 52 9 86.38 0.33 82 43 53 10 83.50 0.46 83 43 54 11 82.23 0.77 84 44 50 6 86.45 0.29 85 44 51 7 86.05 0.43 86 45 49 4 86.45 0.29 87 45 50 5 85.69 0.43 88 59 80 21 113.81 0.59 89 59 81 22 94.78 0.56 90 59 103 44 83.23 5.20 91 59 105 46 94.58 0.79 92 59 106 47 117.33 0.58 93 60 79 19 117.39 0.54 94 60 80 20 117.40 0.54 95 60 107 47 117.36 0.57 96 61 79 18 117.48 0.57 97 61 107 46 117.52 0.53 98 61 108 47 117.46 0.52 99 61 109 48 117.46 0.52 100 62 107 45 117.78 0.55 101 62 108 46 117.75 0.55 102 62 109 47 117.73 0.56 103 63 75 12 202.99 0.28 104 63 76 13 202.94 0.25 105 63 77 14 201.54 0.43 106 63 79 16 135.59 6.58 107 63 109 46 117.77 0.55 108 63 113 50 115.12 0.53 109 64 75 11 203.41 0.09 110 64 79 15 201.46 0.43 111 64 85 21 117.75 0.55 112 64 87 23 117.33 0.56 113 64 109 45 117.77 0.55 114 64 113 49 110.31 0.64 115 65 87 22 117.70 0.53 116 65 113 48 117.38 0.56 117 66 87 21 117.77 0.55 118 66 95 29 115.56 0.30 119 66 113 47 117.64 0.52 120 66 114 48 117.34 0.57 121 66 115 49 110.05 0.17 122 66 116 50 98.88 0.19 123 67 115 48 117.19 0.51 124 67 116 49 101.53 0.56 125 68 89 21 117.54 0.48 126 68 90 22 117.53 0.48 127 68 116 48 116.97 0.40 128 69 87 18 117.83 0.56 129 69 88 19 117.70 0.55 130 69 89 20 117.53 0.48 131 69 90 21 117.70 0.55 132 69 95 26 125.55 4.67 133 69 116 47 117.33 0.58 134 70 87 17 117.86 0.57 135 70 88 18 117.82 0.56 136 71 85 14 117.98 0.56 137 71 86 15 117.93 0.57 138 71 87 16 117.86 0.57 139 71 88 17 117.85 0.56 140 72 86 14 117.98 0.57 141 72 88 16 117.85 0.58 142 73 86 13 117.95 0.59 143 74 85 11 150.38 16.80 144 75 85 10 159.13 21.18 145 79 103 24 119.37 0.26 146 80 103 23 117.89 0.55 147 80 104 24 119.47 0.21 148 81 103 22 117.86 0.55 149 81 104 23 117.87 0.55 150 81 105 24 117.92 0.56 151 82 102 20 117.84 0.54 152 82 103 21 117.75 0.54 153 83 102 19 117.77 0.54 154 83 103 20 117.75 0.55 155 84 100 16 117.88 0.54 156 84 101 17 117.77 0.54 157 84 102 18 117.61 0.51 158 85 100 15 117.79 0.55 159 85 101 16 117.76 0.55 160 85 102 17 117.63 0.52 161 86 99 13 117.80 0.55 162 86 100 14 117.51 0.52 163 87 95 8 170.12 0.56 164 87 98 11 117.85 0.54 165 87 99 12 117.42 0.57 166 87 101 14 117.39 0.55 167 88 95 7 119.13 0.01 168 89 93 4 123.55 1.36 169 89 94 5 117.95 0.57 170 89 95 6 117.84 0.54 171 93 116 23 117.84 0.54 172 93 117 24 117.78 0.55 173 93 118 25 117.74 0.56 174 94 115 21 117.92 0.55 175 94 116 22 117.78 0.55 176 94 117 23 117.75 0.55 177 95 99 4 117.27 0.52 178 95 114 19 117.88 0.54 179 95 115 20 117.78 0.55 180 95 116 21 117.75 0.55 181 96 114 18 117.84 0.55 182 96 115 19 117.75 0.56 183 96 117 21 117.48 0.60 184 97 114 17 117.75 0.55 185 98 111 13 117.91 0.53 186 98 112 14 117.88 0.54 187 98 114 16 117.55 0.51 188 99 114 15 117.42 0.57 189 100 111 11 117.84 0.53 190 101 109 8 117.84 0.53 191 101 110 9 117.75 0.56 192 101 111 10 117.64 0.53 193 101 113 12 117.36 0.56 194 101 114 13 117.25 0.54 195 102 109 7 117.75 0.55 196 102 110 8 117.65 0.53 197 103 108 5 117.76 0.55 198 103 109 6 117.48 0.51 199 104 107 3 117.86 0.53 200 104 110 6 117.37 0.55 201 109 112 3 117.88 0.55 202 109 113 4 108.46 5.24