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 12 45 33 87.77 0.36 2 12 46 34 74.92 0.90 3 13 44 31 88.27 0.48 4 13 45 32 87.93 0.33 5 13 46 33 86.15 0.15 6 14 44 30 88.38 0.43 7 14 45 31 87.94 0.33 8 14 46 32 87.94 0.33 9 14 47 33 87.91 0.32 10 14 55 41 87.94 0.33 11 14 111 97 87.92 0.34 12 14 112 98 87.84 0.35 13 14 113 99 87.84 0.35 14 15 43 28 88.36 0.44 15 15 44 29 88.41 0.42 16 15 111 96 87.91 0.34 17 16 41 25 88.66 0.41 18 16 42 26 88.61 0.40 19 16 43 27 88.43 0.41 20 16 108 92 88.04 0.37 21 16 109 93 88.54 0.43 22 16 111 95 87.95 0.33 23 17 41 24 88.70 0.41 24 17 42 25 88.62 0.39 25 17 44 27 88.62 0.39 26 18 41 23 88.84 0.42 27 18 42 24 88.81 0.42 28 19 39 20 89.97 0.44 29 19 40 21 89.06 0.52 30 19 41 22 88.85 0.42 31 19 42 23 88.84 0.42 32 20 37 17 90.37 0.40 33 20 38 18 90.17 0.47 34 20 39 19 89.98 0.43 35 21 26 5 128.78 1.29 36 21 37 16 90.50 0.35 37 21 38 17 90.28 0.42 38 21 40 19 90.02 0.43 39 22 25 3 138.30 1.28 40 22 26 4 131.01 0.19 41 22 36 14 91.97 0.31 42 22 37 15 90.52 0.35 43 23 26 3 133.72 1.17 44 23 27 4 130.98 0.18 45 23 28 5 123.59 0.06 46 23 29 6 124.91 0.73 47 23 32 9 118.05 2.02 48 23 35 12 109.03 0.63 49 23 36 13 92.67 0.04 50 23 37 14 91.71 0.24 51 23 38 15 91.77 0.21 52 24 27 3 131.00 0.19 53 24 29 5 124.12 0.35 54 27 30 3 164.64 1.08 55 28 31 3 140.81 0.44 56 28 32 4 128.11 0.65 57 29 32 3 134.38 2.54 58 31 91 60 128.32 1.52 59 31 92 61 128.34 1.51 60 31 103 72 201.96 2.60 61 32 35 3 234.29 0.08 62 32 89 57 125.67 0.35 63 32 90 58 125.70 0.35 64 32 91 59 125.83 0.42 65 33 90 57 123.78 0.07 66 33 91 58 125.68 0.35 67 33 92 59 128.31 1.52 68 34 89 55 118.43 2.06 69 34 90 56 118.47 2.06 70 35 88 53 118.42 2.06 71 35 89 54 118.42 2.06 72 38 87 49 115.15 2.25 73 43 79 36 88.61 0.40 74 43 80 37 88.61 0.39 75 43 81 38 88.69 0.42 76 44 79 35 88.61 0.39 77 45 79 34 88.54 0.41 78 46 76 30 88.73 0.39 79 47 51 4 182.88 5.06 80 47 65 18 91.53 0.70 81 47 77 30 88.50 0.43 82 47 78 31 88.45 0.42 83 47 79 32 88.31 0.41 84 48 65 17 91.45 0.74 85 48 76 28 88.67 0.41 86 49 65 16 91.31 0.72 87 49 66 17 91.22 0.76 88 51 55 4 141.39 3.52 89 51 57 6 116.95 1.58 90 51 61 10 105.59 1.24 91 51 62 11 99.58 1.66 92 51 65 14 99.58 1.66 93 51 113 62 117.95 2.41 94 52 55 3 180.24 3.68 95 53 56 3 211.52 3.33 96 55 112 57 105.35 0.11 97 55 113 58 112.88 3.88 98 56 82 26 88.60 0.40 99 56 114 58 100.24 1.37 100 57 61 4 166.17 2.79 101 57 62 5 145.37 0.35 102 57 113 56 97.77 2.40 103 57 114 57 91.60 0.63 104 58 61 3 191.47 0.99 105 58 62 4 172.38 0.32 106 58 114 56 91.78 0.57 107 59 62 3 189.38 1.52 108 59 63 4 172.38 0.32 109 60 63 3 176.94 1.79 110 60 64 4 166.71 3.16 111 61 64 3 179.17 0.67 112 61 65 4 163.67 1.55 113 61 77 16 87.63 0.31 114 61 113 52 91.56 0.68 115 61 114 53 90.64 0.36 116 62 65 3 166.96 0.24 117 62 66 4 172.31 2.77 118 63 66 3 182.48 2.32 119 63 67 4 164.90 0.94 120 64 67 3 168.66 1.08 121 64 68 4 164.88 0.94 122 64 74 10 104.54 4.85 123 64 75 11 103.87 4.52 124 64 76 12 99.87 5.25 125 65 68 3 171.95 1.70 126 65 69 4 167.66 0.45 127 65 77 12 99.81 5.28 128 66 69 3 168.30 0.14 129 66 70 4 168.31 0.14 130 67 70 3 171.33 1.65 131 67 71 4 168.30 0.14 132 67 74 7 111.70 1.28 133 68 71 3 168.31 0.14 134 68 72 4 140.01 0.27 135 68 74 6 108.44 2.90 136 68 75 7 104.42 4.79 137 68 76 8 99.91 5.28 138 71 74 3 206.63 13.38 139 77 113 36 87.95 0.33 140 77 114 37 87.92 0.33 141 78 112 34 88.51 0.43 142 78 113 35 87.90 0.33 143 78 114 36 87.72 0.35 144 79 111 32 88.42 0.42 145 79 112 33 87.94 0.33 146 79 113 34 87.93 0.33 147 80 111 31 88.47 0.42 148 80 112 32 88.39 0.42 149 80 114 34 87.95 0.33 150 81 84 3 252.21 1.00 151 81 108 27 88.24 0.18 152 81 110 29 88.64 0.39 153 81 111 30 88.47 0.42 154 82 110 28 88.70 0.42 155 82 111 29 88.67 0.41 156 82 112 30 88.61 0.39 157 82 114 32 88.53 0.43 158 83 108 25 89.72 0.32 159 83 109 26 88.81 0.42 160 83 110 27 88.76 0.42 161 84 105 21 90.03 0.39 162 84 107 23 90.01 0.42 163 84 108 24 89.87 0.40 164 84 109 25 89.03 0.44 165 85 105 20 90.05 0.39 166 85 106 21 90.06 0.40 167 85 107 22 90.04 0.41 168 85 109 24 89.97 0.42 169 86 103 17 107.84 2.02 170 86 104 18 89.53 0.14 171 87 102 15 117.86 1.95 172 87 103 16 117.83 1.96 173 87 106 19 90.30 0.45 174 87 107 20 90.34 0.43 175 88 100 12 118.27 2.06 176 88 101 13 118.27 2.07 177 88 102 14 118.16 2.09 178 89 100 11 118.28 2.06 179 89 101 12 118.28 2.07 180 89 103 14 118.25 2.06 181 89 106 17 118.25 2.08 182 90 98 8 120.30 3.07 183 90 99 9 119.72 2.79 184 90 100 10 118.29 2.06 185 91 98 7 120.48 3.14 186 91 99 8 120.31 3.06 187 91 101 10 120.30 3.02 188 91 103 12 118.39 2.06 189 92 96 4 142.84 1.09 190 92 97 5 130.19 0.58 191 92 98 6 129.00 1.11 192 93 96 3 192.63 1.75 193 93 97 4 148.41 2.06 194 93 99 6 130.18 0.58 195 103 106 3 252.41 0.89 196 108 111 3 230.78 3.65