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 42 79 37 121.34 0.46 2 43 79 36 122.27 0.01 3 45 50 5 276.96 3.55 4 45 79 34 131.19 1.04 5 45 80 35 122.44 0.00 6 46 49 3 295.41 0.15 7 46 50 4 283.18 0.44 8 47 50 3 286.78 2.17 9 47 51 4 282.46 1.86 10 47 80 33 131.31 1.07 11 47 86 39 129.88 1.37 12 47 89 42 122.41 0.01 13 47 90 43 122.34 0.01 14 47 93 46 122.26 0.02 15 48 52 4 288.13 0.28 16 48 102 54 122.23 0.03 17 48 103 55 122.24 0.03 18 49 52 3 295.75 3.15 19 49 53 4 288.18 0.30 20 50 53 3 289.83 1.12 21 50 54 4 291.81 0.14 22 50 73 23 132.44 1.18 23 50 77 27 132.65 1.24 24 50 80 30 132.47 1.16 25 51 54 3 292.85 0.65 26 51 55 4 285.35 1.72 27 51 69 18 132.44 1.18 28 51 73 22 132.88 1.12 29 51 90 39 129.86 1.38 30 51 93 42 126.94 0.53 31 51 94 43 123.96 0.54 32 51 103 52 123.69 0.48 33 52 55 3 287.58 2.25 34 52 56 4 285.92 1.44 35 52 102 50 123.83 0.54 36 52 103 51 123.82 0.54 37 52 115 63 82.84 0.26 38 53 56 3 299.17 2.38 39 53 57 4 290.06 0.74 40 53 72 19 133.29 1.12 41 53 77 24 133.28 1.11 42 54 57 3 293.60 1.04 43 54 58 4 285.98 1.15 44 54 69 15 133.19 1.12 45 54 72 18 133.27 1.12 46 55 58 3 295.93 0.12 47 55 59 4 286.19 1.03 48 55 64 9 133.91 1.27 49 55 69 14 133.28 1.11 50 55 103 48 123.86 0.55 51 55 113 58 91.14 1.36 52 55 114 59 86.35 0.02 53 55 115 60 84.61 0.22 54 56 59 3 295.92 0.12 55 56 115 59 86.19 0.04 56 58 64 6 133.95 1.27 57 58 68 10 133.77 1.33 58 58 69 11 133.72 1.31 59 59 62 3 269.58 4.80 60 59 63 4 153.12 2.43 61 61 107 46 123.87 0.57 62 62 106 44 123.87 0.57 63 62 114 52 91.94 1.45 64 63 113 50 91.94 1.46 65 63 114 51 91.23 1.20 66 64 68 4 283.36 0.35 67 64 112 48 91.93 1.46 68 64 113 49 91.91 1.45 69 65 68 3 297.58 1.35 70 65 69 4 284.74 0.34 71 65 111 46 91.99 1.46 72 65 112 47 91.90 1.45 73 65 113 48 91.86 1.43 74 66 69 3 287.33 0.96 75 66 70 4 284.31 0.80 76 66 90 24 137.99 0.83 77 66 91 25 137.55 1.01 78 66 94 28 136.47 0.61 79 66 105 39 123.79 0.52 80 66 110 44 92.02 1.48 81 66 111 45 91.95 1.45 82 66 113 47 91.59 1.35 83 67 70 3 286.93 1.16 84 67 71 4 284.32 0.80 85 68 71 3 293.06 1.90 86 68 72 4 284.31 0.79 87 69 72 3 285.37 0.27 88 69 73 4 285.38 0.26 89 69 90 21 138.25 0.72 90 69 94 25 138.04 0.76 91 69 113 44 91.78 1.44 92 70 73 3 298.64 1.05 93 70 74 4 285.38 0.26 94 70 86 16 139.63 0.78 95 70 87 17 139.30 0.93 96 70 90 20 138.26 0.71 97 70 91 21 138.29 0.72 98 71 74 3 291.47 2.54 99 71 75 4 285.36 0.25 100 72 75 3 287.87 1.00 101 72 76 4 281.60 1.09 102 73 76 3 286.80 0.01 103 73 77 4 271.39 1.53 104 73 80 7 204.34 0.82 105 73 81 8 191.91 5.28 106 73 86 13 139.76 0.83 107 73 90 17 138.33 0.71 108 74 78 4 240.25 7.17 109 74 81 7 167.78 3.46 110 74 86 12 139.78 0.83 111 77 80 3 313.10 3.71 112 77 81 4 243.97 5.33 113 78 81 3 271.27 3.27 114 78 82 4 237.75 2.43 115 79 83 4 273.12 1.11 116 80 83 3 273.12 1.11 117 80 86 6 203.52 0.43 118 81 86 5 208.88 2.23 119 83 86 3 286.23 1.79 120 85 88 3 290.32 0.26 121 85 89 4 290.33 0.27 122 86 89 3 290.32 0.27 123 86 90 4 290.31 0.27 124 87 90 3 294.08 0.27 125 87 91 4 292.21 0.67 126 88 91 3 292.57 0.49 127 88 92 4 292.20 0.67 128 89 92 3 292.16 0.69 129 89 93 4 292.14 0.69 130 90 93 3 292.88 1.05 131 90 94 4 292.14 0.69 132 91 94 3 290.99 3.83 133 91 95 4 287.80 2.25 134 92 95 3 298.75 3.22 135 92 96 4 287.79 2.25 136 93 96 3 303.94 2.65 137 93 97 4 287.80 2.25 138 93 103 10 206.96 2.94 139 94 97 3 293.55 0.61 140 94 98 4 293.54 0.61 141 94 103 9 206.91 2.91 142 94 105 11 203.58 1.39 143 94 113 19 167.97 0.48 144 95 98 3 294.50 0.14 145 95 99 4 281.98 1.70 146 96 99 3 293.25 0.77 147 96 100 4 277.94 0.33 148 97 100 3 285.16 3.29 149 97 101 4 278.95 0.20 150 97 102 5 248.28 2.45 151 97 103 6 207.28 3.10 152 98 101 3 285.38 3.02 153 98 103 5 207.26 3.08 154 98 104 6 203.84 1.39 155 98 105 7 203.84 1.39 156 98 129 31 19.39 0.24 157 101 116 15 168.05 0.58 158 102 115 13 170.89 0.79 159 102 116 14 165.78 0.55 160 103 113 10 174.64 2.51 161 103 114 11 170.96 0.76 162 103 116 13 159.91 2.39 163 104 113 9 174.68 2.51 164 104 114 10 170.99 0.73 165 104 115 11 170.95 0.75 166 104 116 12 162.21 3.35 167 105 108 3 295.62 0.52 168 105 109 4 287.25 3.49 169 105 110 5 278.73 0.78 170 105 111 6 211.48 2.31 171 105 112 7 204.49 5.73 172 105 113 8 174.69 2.50 173 105 126 21 36.13 0.16 174 106 112 6 211.47 2.31 175 106 113 7 204.86 5.61 176 106 114 8 193.72 0.10 177 106 123 17 39.46 1.17 178 106 125 19 36.61 0.06 179 107 111 4 248.19 16.04 180 107 112 5 217.50 0.70 181 107 125 18 36.63 0.07 182 108 111 3 292.00 1.03 183 108 125 17 36.61 0.07 184 108 126 18 36.15 0.16 185 109 126 17 36.27 0.23 186 109 127 18 36.44 0.14 187 109 129 20 30.37 0.71 188 120 123 3 329.19 0.50 189 123 126 3 319.21 0.53 190 126 129 3 285.54 0.39