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 40 46 6 283.37 1.64 2 41 46 5 289.22 1.28 3 41 47 6 276.69 4.98 4 41 50 9 272.60 1.19 5 41 70 29 217.21 1.20 6 41 81 40 173.21 0.57 7 42 47 5 301.00 1.85 8 42 81 39 173.46 0.65 9 42 82 40 173.46 0.64 10 42 116 74 46.88 1.14 11 42 117 75 46.83 1.14 12 42 118 76 46.76 1.13 13 43 46 3 314.44 0.26 14 43 47 4 310.39 0.11 15 43 118 75 46.77 1.12 16 44 47 3 310.42 0.12 17 44 48 4 310.45 0.11 18 44 65 21 234.46 0.03 19 44 66 22 234.33 0.04 20 44 118 74 46.85 1.16 21 44 119 75 46.62 1.18 22 44 120 76 46.52 1.22 23 45 48 3 319.12 2.50 24 45 49 4 312.43 0.86 25 45 120 75 46.48 1.25 26 46 49 3 319.13 2.50 27 46 50 4 313.56 0.30 28 47 50 3 320.63 1.75 29 47 51 4 319.81 2.16 30 47 65 18 235.36 0.42 31 47 68 21 235.34 0.42 32 47 69 22 235.30 0.44 33 47 70 23 235.11 0.42 34 47 81 34 196.59 1.20 35 47 82 35 196.59 1.20 36 47 117 70 46.90 1.15 37 48 51 3 319.33 2.58 38 48 61 13 235.85 0.47 39 48 62 14 235.82 0.45 40 48 65 17 235.36 0.42 41 48 120 72 46.53 1.23 42 49 52 3 331.81 0.40 43 50 70 20 235.30 0.46 44 50 71 21 235.16 0.41 45 50 73 23 235.13 0.42 46 51 54 3 308.97 1.05 47 51 61 10 235.94 0.44 48 51 64 13 235.94 0.44 49 51 65 14 235.93 0.43 50 51 69 18 235.69 0.50 51 51 70 19 235.41 0.52 52 51 71 20 235.17 0.42 53 51 78 27 197.40 1.07 54 52 71 19 235.44 0.50 55 52 73 21 235.16 0.42 56 53 71 18 235.66 0.49 57 54 59 5 298.75 0.01 58 54 61 7 236.18 0.49 59 54 64 10 236.18 0.50 60 54 71 17 235.65 0.48 61 54 76 22 234.00 0.35 62 54 78 24 231.22 1.03 63 55 71 16 235.69 0.48 64 55 75 20 235.08 0.41 65 56 59 3 310.67 1.48 66 56 76 20 234.92 0.45 67 56 90 34 192.04 3.20 68 58 90 32 192.02 3.20 69 58 91 33 192.00 3.19 70 58 92 34 187.91 1.93 71 59 64 5 301.57 1.13 72 59 90 31 192.00 3.19 73 59 94 35 147.19 1.68 74 59 96 37 125.62 1.09 75 60 63 3 311.56 1.49 76 60 64 4 304.25 0.21 77 61 64 3 305.79 0.56 78 61 65 4 304.25 0.21 79 62 65 3 312.86 0.84 80 62 66 4 304.24 0.21 81 63 66 3 307.23 1.28 82 63 67 4 307.22 1.28 83 63 96 33 125.16 1.31 84 63 128 65 38.20 0.14 85 64 67 3 313.57 1.86 86 64 68 4 307.47 1.16 87 64 69 5 277.74 1.76 88 64 78 14 197.38 1.09 89 64 90 26 192.00 3.19 90 64 96 32 125.11 1.29 91 65 68 3 313.28 0.64 92 65 69 4 297.72 2.89 93 66 124 58 44.77 0.45 94 66 125 59 42.76 0.39 95 66 128 62 37.88 0.12 96 67 97 30 125.09 1.30 97 67 100 33 125.08 1.30 98 67 109 42 96.35 2.95 99 67 128 61 37.88 0.12 100 67 129 62 36.91 0.42 101 68 80 12 196.88 1.06 102 68 81 13 196.88 1.07 103 68 82 14 196.86 1.06 104 68 109 41 96.36 2.95 105 69 78 9 197.30 1.07 106 69 79 10 197.20 1.04 107 69 80 11 196.88 1.07 108 69 85 16 193.30 2.68 109 69 87 18 193.12 2.71 110 69 100 31 125.06 1.30 111 70 78 8 197.28 1.04 112 70 79 9 197.24 1.04 113 70 80 10 197.19 1.03 114 70 81 11 197.06 0.98 115 71 75 4 335.72 1.38 116 71 76 5 281.53 6.84 117 71 77 6 197.44 1.06 118 71 78 7 197.28 1.04 119 72 77 5 206.16 0.29 120 72 78 6 197.43 1.07 121 72 79 7 197.41 1.07 122 74 77 3 316.72 2.89 123 76 88 12 192.66 2.92 124 76 89 13 192.66 2.92 125 76 90 14 192.06 3.20 126 77 86 9 193.31 2.69 127 77 87 10 193.12 2.71 128 77 88 11 192.66 2.92 129 78 86 8 193.17 2.71 130 78 87 9 193.11 2.71 131 78 90 12 192.66 2.92 132 79 84 5 193.72 2.55 133 79 85 6 193.25 2.71 134 79 86 7 193.15 2.72 135 80 83 3 305.12 1.41 136 80 84 4 193.56 2.56 137 80 85 5 193.28 2.68 138 80 100 20 125.06 1.31 139 80 107 27 96.62 2.88 140 82 107 25 96.62 2.88 141 82 108 26 96.54 2.92 142 82 109 27 96.51 2.91 143 82 115 33 46.93 1.14 144 82 117 35 46.88 1.16 145 83 100 17 125.12 1.33 146 83 104 21 122.98 1.38 147 83 107 24 96.62 2.88 148 83 108 25 96.62 2.88 149 85 100 15 125.12 1.34 150 85 103 18 124.87 1.40 151 85 104 19 124.00 1.80 152 87 90 3 373.79 2.49 153 87 99 12 125.11 1.30 154 87 103 16 124.37 1.65 155 90 94 4 280.12 0.99 156 90 96 6 259.74 5.70 157 90 99 9 125.88 1.26 158 91 94 3 313.72 0.01 159 94 99 5 280.83 1.52 160 95 98 3 312.94 2.21 161 95 99 4 280.99 1.59 162 96 100 4 298.51 0.59 163 97 100 3 303.24 0.20 164 97 101 4 297.66 1.01 165 97 110 13 96.36 2.96 166 97 128 31 40.73 0.57 167 97 130 33 36.93 0.41 168 98 101 3 308.25 4.19 169 98 102 4 305.95 5.34 170 99 102 3 311.79 2.44 171 99 103 4 308.91 3.87 172 100 103 3 318.35 0.45 173 100 104 4 300.39 0.53 174 100 107 7 271.37 0.33 175 100 110 10 170.22 33.97 176 101 104 3 317.06 0.21 177 101 105 4 282.00 1.18 178 101 110 9 98.28 3.77 179 101 130 29 36.95 0.41 180 102 105 3 324.29 0.78 181 104 107 3 322.79 2.69 182 105 111 6 286.50 7.64 183 106 111 5 286.50 7.64 184 107 110 3 308.00 0.01 185 107 111 4 295.56 3.13 186 108 111 3 308.00 0.01 187 108 112 4 296.67 3.67 188 108 113 5 262.03 0.49 189 108 115 7 173.22 34.16 190 109 112 3 306.74 0.62 191 109 115 6 247.65 1.62 192 109 117 8 77.06 13.92 193 109 125 16 43.22 0.61 194 109 129 20 36.92 0.42 195 110 129 19 36.93 0.42 196 110 130 20 36.91 0.42 197 111 132 21 34.75 0.47 198 111 133 22 32.71 1.05 199 111 135 24 20.03 0.67 200 112 126 14 43.19 0.66 201 112 129 17 36.92 0.42 202 112 130 18 36.91 0.42 203 112 132 20 33.38 0.72 204 117 125 8 252.88 1.34 205 119 122 3 319.19 1.67 206 119 125 6 280.80 7.86 207 121 124 3 314.82 2.81 208 121 125 4 308.57 0.11 209 122 125 3 312.87 2.04 210 122 126 4 308.56 0.11 211 123 126 3 310.46 1.06 212 123 127 4 308.56 0.11 213 124 127 3 310.81 1.01 214 124 128 4 307.51 0.64 215 125 128 3 314.51 0.10 216 125 129 4 305.00 1.89 217 126 129 3 311.55 1.39