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 18 49 31 80.87 0.12 2 18 50 32 79.58 0.30 3 18 51 33 79.38 0.38 4 18 53 35 79.58 0.30 5 18 54 36 80.58 0.00 6 18 55 37 80.86 0.11 7 18 57 39 80.83 0.10 8 19 49 30 80.89 0.14 9 19 50 31 79.58 0.30 10 19 51 32 79.58 0.30 11 19 52 33 79.56 0.29 12 19 60 41 79.59 0.30 13 19 117 98 79.58 0.30 14 19 118 99 79.56 0.29 15 19 119 100 79.55 0.29 16 20 48 28 80.89 0.14 17 20 49 29 80.89 0.14 18 20 117 97 79.56 0.29 19 21 46 25 81.14 0.10 20 21 47 26 81.03 0.15 21 21 114 93 80.88 0.12 22 21 115 94 80.99 0.14 23 21 117 96 80.42 0.10 24 22 46 24 81.22 0.10 25 22 47 25 81.03 0.15 26 22 49 27 81.03 0.15 27 23 44 21 83.36 0.32 28 23 46 23 81.50 0.06 29 23 47 24 81.22 0.10 30 24 44 20 83.58 0.36 31 24 45 21 81.77 0.07 32 24 46 22 81.61 0.11 33 24 47 23 81.60 0.11 34 25 43 18 83.73 0.42 35 25 44 19 83.59 0.36 36 26 31 5 130.19 0.24 37 26 42 16 84.70 0.12 38 26 43 17 83.84 0.41 39 26 45 19 83.75 0.44 40 27 30 3 148.65 0.43 41 27 41 14 86.75 0.77 42 27 42 15 84.78 0.15 43 28 31 3 129.59 0.54 44 28 33 5 118.53 0.36 45 28 37 9 108.93 1.50 46 28 40 12 100.37 6.04 47 28 41 13 86.75 0.77 48 28 43 15 86.06 0.45 49 28 112 84 84.89 0.14 50 29 34 5 116.50 0.64 51 29 41 12 91.75 1.38 52 32 36 4 148.43 3.89 53 33 36 3 135.38 0.94 54 33 37 4 124.85 2.16 55 34 37 3 139.81 0.21 56 36 97 61 128.31 4.42 57 36 98 62 139.88 10.18 58 37 41 4 141.59 2.73 59 37 95 58 117.17 2.26 60 37 96 59 118.25 2.79 61 37 97 60 117.27 2.30 62 38 41 3 209.02 2.40 63 38 96 58 115.20 1.29 64 38 97 59 117.16 2.27 65 38 98 60 128.32 4.41 66 39 95 56 112.16 0.96 67 39 96 57 112.20 0.98 68 40 43 3 158.42 3.60 69 40 93 53 110.34 1.86 70 40 94 54 110.40 1.84 71 40 95 55 110.40 1.84 72 43 93 50 109.75 1.62 73 48 85 37 80.98 0.14 74 48 86 38 81.00 0.14 75 48 87 39 81.06 0.14 76 49 85 36 81.00 0.14 77 50 85 35 80.98 0.14 78 52 83 31 81.00 0.14 79 52 84 32 80.91 0.13 80 52 85 33 80.67 0.06 81 53 70 17 99.70 6.41 82 54 70 16 101.49 5.83 83 54 71 17 100.02 6.56 84 54 74 20 87.71 0.50 85 56 60 4 162.63 2.81 86 56 62 6 110.90 2.35 87 56 67 11 106.22 3.78 88 56 70 14 101.89 5.91 89 56 119 63 110.70 2.79 90 57 60 3 196.43 0.08 91 58 61 3 188.15 0.84 92 59 117 58 110.16 3.00 93 60 117 57 108.39 3.87 94 60 118 58 106.22 4.75 95 60 119 59 106.23 4.75 96 60 120 60 106.67 4.54 97 61 89 28 81.57 0.10 98 61 120 59 106.21 4.74 99 62 66 4 160.38 5.24 100 62 67 5 155.82 3.58 101 62 120 58 100.61 6.45 102 63 66 3 199.61 6.02 103 63 67 4 176.29 7.49 104 63 120 57 95.02 4.03 105 64 67 3 198.39 3.56 106 64 68 4 186.38 2.44 107 65 68 3 221.35 4.00 108 65 69 4 174.29 6.44 109 66 69 3 184.48 1.34 110 66 70 4 170.46 1.02 111 66 83 17 80.85 0.12 112 66 119 53 94.99 4.04 113 66 120 54 85.11 0.17 114 67 70 3 219.14 5.11 115 67 71 4 172.34 0.85 116 68 71 3 190.37 2.23 117 68 72 4 179.97 2.96 118 69 72 3 215.27 12.58 119 69 73 4 179.97 2.96 120 69 80 11 94.09 6.26 121 69 81 12 94.03 6.28 122 69 82 13 81.26 0.01 123 69 83 14 80.92 0.11 124 70 73 3 204.72 6.87 125 70 74 4 171.35 0.34 126 70 83 13 80.98 0.14 127 71 74 3 190.02 3.29 128 71 75 4 171.35 0.34 129 72 75 3 188.66 3.98 130 72 76 4 171.35 0.34 131 72 80 8 94.08 6.28 132 73 76 3 195.09 0.76 133 73 77 4 141.65 12.88 134 73 80 7 93.97 6.32 135 73 81 8 93.95 6.32 136 73 82 9 93.89 6.32 137 76 79 3 231.74 1.86 138 76 80 4 182.25 5.28 139 77 80 3 220.21 3.90 140 83 119 36 79.59 0.30 141 83 120 37 79.57 0.29 142 84 118 34 80.91 0.14 143 84 119 35 79.58 0.30 144 84 120 36 79.55 0.29 145 85 117 32 80.89 0.13 146 85 118 33 79.59 0.30 147 85 119 34 79.58 0.30 148 86 117 31 80.91 0.13 149 86 118 32 80.89 0.12 150 86 120 34 79.59 0.30 151 87 90 3 247.73 0.30 152 87 114 27 81.20 0.12 153 87 116 29 81.02 0.14 154 87 117 30 80.91 0.13 155 88 116 28 81.15 0.13 156 88 117 29 81.06 0.14 157 88 118 30 81.01 0.14 158 88 120 32 80.92 0.13 159 89 114 25 82.45 0.18 160 89 115 26 81.55 0.09 161 89 116 27 81.34 0.08 162 90 111 21 82.30 0.48 163 90 113 23 83.75 0.44 164 90 114 24 83.28 0.43 165 90 115 25 81.70 0.10 166 91 111 20 83.28 0.11 167 91 112 21 84.06 0.29 168 91 113 22 83.82 0.44 169 91 115 24 83.70 0.47 170 92 108 16 109.98 1.77 171 92 109 17 109.32 1.45 172 92 110 18 87.73 1.77 173 92 111 19 84.06 0.10 174 93 108 15 110.11 1.79 175 93 109 16 110.00 1.76 176 93 112 19 84.59 0.05 177 93 113 20 84.72 0.02 178 94 106 12 111.39 1.21 179 94 107 13 110.18 1.79 180 94 108 14 110.14 1.80 181 95 106 11 111.49 1.21 182 95 107 12 110.21 1.79 183 95 109 14 110.16 1.80 184 95 112 17 110.16 1.80 185 96 104 8 116.86 1.48 186 96 105 9 113.25 0.34 187 96 106 10 112.31 0.80 188 97 104 7 116.91 1.47 189 97 105 8 113.28 0.35 190 97 107 10 113.31 0.36 191 97 109 12 113.32 0.37 192 98 102 4 133.30 5.69 193 98 103 5 119.11 0.71 194 98 104 6 116.92 1.47 195 99 102 3 154.69 12.75 196 99 103 4 131.88 4.98 197 99 105 6 119.05 0.74 198 109 112 3 248.46 0.06 199 114 117 3 225.86 5.29