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 11 17 6 130.47 2.46 2 11 44 33 103.22 1.44 3 11 45 34 45.20 0.18 4 11 46 35 45.78 0.12 5 12 45 33 103.22 1.45 6 12 46 34 72.83 1.02 7 13 45 32 103.28 1.45 8 13 46 33 102.38 1.02 9 14 44 30 103.42 1.38 10 14 45 31 103.29 1.45 11 14 46 32 103.29 1.45 12 14 47 33 103.25 1.45 13 14 55 41 103.30 1.45 14 14 111 97 103.28 1.44 15 14 112 98 103.25 1.45 16 14 113 99 103.20 1.45 17 15 43 28 103.31 1.45 18 15 44 29 103.44 1.39 19 15 111 96 103.25 1.45 20 16 41 25 103.64 1.43 21 16 42 26 103.62 1.43 22 16 108 92 103.53 1.41 23 16 109 93 103.60 1.43 24 16 111 95 103.30 1.45 25 17 41 24 103.64 1.43 26 17 42 25 103.62 1.43 27 17 44 27 103.62 1.43 28 18 41 23 103.66 1.43 29 18 42 24 103.66 1.43 30 19 39 20 103.72 1.42 31 19 40 21 103.70 1.42 32 19 41 22 103.67 1.43 33 19 42 23 103.67 1.43 34 20 36 16 104.03 1.40 35 20 37 17 103.86 1.45 36 20 38 18 103.74 1.42 37 20 39 19 103.73 1.42 38 21 26 5 132.69 0.09 39 21 37 16 103.91 1.43 40 21 38 17 103.80 1.44 41 21 40 19 103.70 1.43 42 22 25 3 141.56 1.46 43 22 26 4 136.62 1.01 44 22 36 14 104.02 1.40 45 22 37 15 103.92 1.43 46 23 26 3 143.21 0.74 47 23 27 4 132.71 0.09 48 23 28 5 128.76 0.06 49 23 29 6 125.82 0.31 50 23 32 9 118.98 1.06 51 23 35 12 108.70 0.90 52 23 36 13 104.01 1.40 53 23 37 14 103.94 1.42 54 23 38 15 103.95 1.42 55 24 27 3 132.64 0.11 56 24 29 5 130.65 0.17 57 27 30 3 154.82 0.79 58 28 31 3 145.16 1.65 59 28 32 4 132.01 0.19 60 29 32 3 137.75 0.39 61 31 89 58 133.63 0.36 62 31 91 60 132.74 0.09 63 31 92 61 133.77 0.33 64 31 103 72 189.50 2.47 65 32 35 3 240.09 0.65 66 32 89 57 131.81 0.26 67 32 90 58 132.62 0.14 68 32 91 59 132.63 0.14 69 33 90 57 130.46 0.56 70 33 91 58 131.73 0.07 71 33 92 59 132.72 0.10 72 34 89 55 117.08 0.07 73 34 90 56 124.79 0.02 74 35 38 3 165.84 2.31 75 35 88 53 116.84 0.08 76 35 89 54 116.82 0.07 77 38 87 49 104.12 1.39 78 43 79 36 103.61 1.43 79 43 80 37 103.62 1.43 80 43 81 38 103.64 1.43 81 44 79 35 103.61 1.43 82 45 79 34 103.58 1.44 83 46 76 30 103.66 1.43 84 47 76 29 103.63 1.43 85 47 77 30 103.61 1.43 86 47 78 31 103.58 1.44 87 47 79 32 103.31 1.45 88 48 51 3 177.08 0.68 89 48 55 7 118.24 4.53 90 48 65 17 104.20 1.35 91 49 65 16 104.17 1.33 92 49 66 17 104.17 1.33 93 49 69 20 103.81 1.43 94 51 62 11 104.88 1.62 95 51 65 14 104.56 1.54 96 52 55 3 172.53 1.78 97 55 111 56 118.25 4.54 98 55 112 57 118.20 4.53 99 55 113 58 118.20 4.54 100 56 112 56 118.09 4.54 101 56 113 57 118.09 4.54 102 56 114 58 118.09 4.54 103 57 61 4 160.45 2.04 104 57 62 5 153.47 0.10 105 57 113 56 115.88 3.46 106 57 114 57 114.64 2.85 107 58 61 3 176.16 0.35 108 58 62 4 169.19 2.32 109 58 113 55 115.88 3.46 110 58 114 56 104.74 1.57 111 59 62 3 201.04 0.57 112 59 63 4 170.00 1.91 113 60 63 3 178.83 3.10 114 60 64 4 170.00 1.91 115 61 64 3 191.62 5.29 116 61 65 4 166.09 1.38 117 61 77 16 103.25 1.46 118 61 113 52 104.80 1.55 119 61 114 53 104.14 1.38 120 62 65 3 202.90 5.65 121 62 66 4 169.65 0.07 122 63 66 3 186.57 1.53 123 63 67 4 174.55 0.93 124 64 67 3 182.25 0.41 125 64 68 4 176.93 0.27 126 64 74 10 103.67 1.44 127 64 75 11 103.64 1.43 128 64 76 12 103.44 1.38 129 64 77 13 103.43 1.38 130 65 68 3 186.72 1.35 131 65 69 4 180.74 1.64 132 65 77 12 103.45 1.36 133 66 69 3 197.45 1.86 134 66 70 4 180.74 1.64 135 67 70 3 205.12 7.79 136 67 71 4 169.19 1.80 137 67 74 7 105.62 2.42 138 68 71 3 170.10 0.32 139 68 72 4 157.08 2.26 140 68 74 6 105.62 2.41 141 68 75 7 103.66 1.43 142 68 76 8 103.45 1.36 143 71 74 3 250.74 1.54 144 77 113 36 103.28 1.45 145 77 114 37 103.25 1.45 146 78 112 34 103.58 1.44 147 78 113 35 103.26 1.45 148 78 114 36 102.92 1.43 149 79 111 32 103.56 1.44 150 79 112 33 103.29 1.45 151 79 113 34 103.28 1.45 152 80 111 31 103.58 1.44 153 80 112 32 103.53 1.42 154 80 114 34 103.30 1.45 155 81 108 27 103.45 1.53 156 81 110 29 103.63 1.43 157 81 111 30 103.59 1.44 158 82 110 28 103.64 1.43 159 82 111 29 103.62 1.43 160 82 112 30 103.62 1.43 161 82 114 32 103.61 1.43 162 83 108 25 103.71 1.42 163 83 109 26 103.69 1.42 164 83 110 27 103.67 1.43 165 84 105 21 103.86 1.41 166 84 107 23 103.73 1.42 167 84 108 24 103.71 1.42 168 84 109 25 103.70 1.42 169 85 105 20 104.01 1.38 170 85 106 21 103.98 1.39 171 85 107 22 103.77 1.43 172 85 109 24 103.72 1.42 173 86 102 16 106.83 0.03 174 86 103 17 104.11 1.36 175 86 104 18 104.06 1.38 176 86 106 20 104.02 1.38 177 87 102 15 107.25 0.23 178 87 103 16 104.20 1.34 179 87 106 19 104.06 1.38 180 87 107 20 104.06 1.38 181 88 100 12 124.51 1.09 182 88 101 13 117.00 0.10 183 88 102 14 107.28 0.24 184 89 99 10 131.55 0.12 185 89 100 11 127.26 0.07 186 89 101 12 119.89 1.34 187 89 103 14 113.91 1.46 188 89 106 17 109.58 0.46 189 90 98 8 132.62 0.14 190 90 99 9 131.55 0.12 191 90 100 10 128.44 0.51 192 91 97 6 142.60 0.93 193 91 98 7 134.78 0.18 194 91 99 8 131.74 0.07 195 91 101 10 131.55 0.12 196 91 103 12 130.56 0.53 197 92 96 4 154.22 0.88 198 92 97 5 142.59 0.93 199 92 98 6 134.79 0.18 200 93 96 3 233.59 5.46 201 93 97 4 158.97 1.23 202 93 99 6 136.44 0.59 203 103 106 3 257.63 0.10 204 108 111 3 233.46 6.73