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 43 3 311.02 1.77 2 40 46 6 274.85 4.38 3 41 46 5 287.85 1.98 4 41 47 6 274.86 4.38 5 41 50 9 274.86 4.38 6 41 70 29 212.06 1.59 7 41 81 40 132.70 21.73 8 42 47 5 310.24 0.01 9 42 81 39 132.74 21.74 10 42 82 40 132.74 21.75 11 42 116 74 48.47 1.05 12 42 117 75 48.41 1.06 13 42 118 76 48.41 1.07 14 43 46 3 314.47 0.01 15 43 47 4 311.07 0.42 16 43 118 75 48.41 1.08 17 44 47 3 314.36 0.57 18 44 48 4 311.08 0.42 19 44 65 21 235.16 0.28 20 44 66 22 236.71 0.99 21 44 118 74 48.47 1.05 22 44 119 75 48.37 1.08 23 44 120 76 48.33 1.08 24 45 48 3 313.98 0.76 25 45 49 4 314.00 0.76 26 45 120 75 48.30 1.09 27 46 49 3 316.18 0.48 28 46 50 4 319.56 2.03 29 47 50 3 321.96 1.02 30 47 51 4 319.57 2.02 31 47 65 18 237.81 0.66 32 47 68 21 237.85 0.68 33 47 69 22 237.78 0.67 34 47 70 23 237.75 0.66 35 47 81 34 198.32 0.93 36 47 82 35 198.32 0.93 37 47 117 70 48.49 1.06 38 48 51 3 324.12 0.07 39 48 61 13 238.24 0.72 40 48 62 14 238.20 0.73 41 48 65 17 237.81 0.67 42 48 120 72 48.37 1.10 43 49 52 3 334.44 0.92 44 50 70 20 237.83 0.68 45 50 71 21 237.74 0.65 46 50 73 23 237.59 0.70 47 51 54 3 303.85 1.29 48 51 61 10 238.34 0.76 49 51 64 13 238.34 0.76 50 51 65 14 238.30 0.74 51 51 69 18 238.09 0.73 52 51 70 19 237.91 0.65 53 51 71 20 237.75 0.66 54 51 78 27 204.65 2.41 55 52 71 19 237.99 0.69 56 52 73 21 237.72 0.64 57 53 71 18 238.00 0.69 58 54 59 5 302.91 2.16 59 54 61 7 238.50 0.72 60 54 64 10 238.56 0.70 61 54 71 17 238.00 0.69 62 54 76 22 236.74 0.59 63 54 78 24 236.58 0.53 64 55 71 16 238.02 0.70 65 55 75 20 237.31 0.74 66 55 76 21 237.19 0.70 67 56 59 3 318.12 2.07 68 56 76 20 237.22 0.70 69 56 90 34 196.88 0.78 70 58 90 32 196.94 0.72 71 58 91 33 196.93 0.73 72 58 92 34 193.20 0.13 73 59 64 5 310.03 0.36 74 59 90 31 196.84 0.78 75 59 94 35 174.36 1.93 76 59 96 37 147.75 11.33 77 60 63 3 325.01 4.06 78 60 64 4 310.04 0.36 79 61 64 3 310.05 0.36 80 61 65 4 310.03 0.36 81 62 65 3 312.62 0.96 82 62 66 4 310.01 0.35 83 63 66 3 310.25 0.23 84 63 67 4 310.01 0.35 85 63 96 33 140.16 15.10 86 63 128 65 43.18 0.10 87 64 67 3 314.05 1.62 88 64 68 4 310.24 0.24 89 64 69 5 289.99 3.51 90 64 78 14 202.05 1.11 91 64 90 26 196.86 0.77 92 64 96 32 140.16 15.10 93 65 68 3 317.64 0.18 94 65 69 4 286.57 3.56 95 66 124 58 46.61 0.32 96 66 125 59 46.27 0.42 97 66 128 62 42.67 0.15 98 67 97 30 140.09 15.06 99 67 100 33 140.08 15.06 100 67 109 42 124.22 19.03 101 67 128 61 42.47 0.26 102 68 80 12 200.64 1.67 103 68 81 13 200.63 1.66 104 68 82 14 200.60 1.65 105 68 109 41 124.22 19.04 106 69 78 9 201.97 1.09 107 69 79 10 201.48 1.28 108 69 80 11 200.63 1.66 109 69 85 16 197.59 0.69 110 69 87 18 197.31 0.69 111 69 100 31 140.08 15.06 112 70 78 8 201.98 1.09 113 70 79 9 201.85 1.11 114 70 81 11 201.40 1.25 115 71 75 4 339.19 0.02 116 71 76 5 270.95 4.71 117 71 77 6 216.93 3.75 118 71 78 7 201.99 1.09 119 72 77 5 222.02 1.22 120 72 78 6 202.08 1.10 121 72 79 7 202.08 1.10 122 74 77 3 323.28 2.22 123 76 88 12 197.16 0.69 124 76 89 13 197.16 0.69 125 76 90 14 196.94 0.76 126 77 86 9 197.41 0.64 127 77 87 10 197.30 0.69 128 77 88 11 197.16 0.69 129 78 86 8 197.40 0.65 130 78 87 9 197.30 0.69 131 78 90 12 197.15 0.68 132 79 84 5 198.21 0.96 133 79 85 6 197.60 0.70 134 79 86 7 197.31 0.69 135 80 83 3 318.84 1.75 136 80 84 4 197.59 0.70 137 80 85 5 197.58 0.70 138 80 100 20 140.12 15.09 139 80 107 27 126.44 20.15 140 82 107 25 126.44 20.16 141 82 108 26 126.41 20.14 142 82 109 27 126.28 20.07 143 82 115 33 49.02 1.07 144 82 117 35 48.45 1.05 145 83 100 17 140.16 15.11 146 83 104 21 138.66 14.84 147 83 107 24 126.44 20.16 148 83 108 25 126.45 20.15 149 85 100 15 140.18 15.09 150 85 103 18 139.22 14.88 151 85 104 19 138.09 14.48 152 87 90 3 383.17 2.62 153 87 99 12 140.19 15.09 154 87 100 13 140.16 15.08 155 87 103 16 139.37 14.80 156 90 94 4 284.20 0.07 157 90 95 5 292.17 3.92 158 90 96 6 273.75 5.29 159 90 99 9 204.45 17.02 160 91 94 3 315.78 1.04 161 94 99 5 289.57 2.70 162 95 98 3 323.52 2.73 163 95 99 4 303.31 2.35 164 96 100 4 304.74 1.64 165 97 100 3 315.68 3.83 166 97 101 4 303.25 0.89 167 97 110 13 140.80 11.08 168 97 128 31 44.09 0.54 169 97 130 33 40.05 0.69 170 98 101 3 316.86 0.10 171 98 102 4 310.85 2.90 172 99 102 3 312.93 1.86 173 99 103 4 311.92 2.37 174 100 103 3 326.08 4.56 175 100 104 4 300.86 0.37 176 100 107 7 287.69 5.76 177 100 110 10 211.77 24.37 178 101 104 3 316.28 0.18 179 101 105 4 289.14 5.05 180 101 110 9 252.31 4.09 181 101 130 29 40.19 0.66 182 102 105 3 324.04 0.91 183 104 107 3 311.88 1.92 184 105 111 6 286.83 7.79 185 106 111 5 286.85 7.79 186 106 113 7 286.83 7.79 187 107 110 3 315.21 2.02 188 107 111 4 295.92 3.29 189 107 113 6 286.87 7.81 190 108 111 3 306.98 0.98 191 108 112 4 301.47 1.76 192 108 113 5 286.83 7.79 193 108 115 7 282.93 9.58 194 109 112 3 316.20 0.61 195 109 115 6 286.71 7.77 196 109 117 8 253.91 0.81 197 109 125 16 46.52 0.36 198 109 129 20 40.20 0.64 199 110 129 19 40.20 0.64 200 110 130 20 40.05 0.70 201 111 133 22 32.69 1.85 202 111 135 24 20.93 0.07 203 112 126 14 46.38 0.44 204 112 129 17 40.23 0.65 205 112 130 18 40.20 0.64 206 117 125 8 276.38 1.11 207 119 122 3 320.52 0.75 208 119 125 6 284.12 4.98 209 121 124 3 316.13 2.15 210 121 125 4 308.56 0.10 211 122 125 3 313.39 2.15 212 122 126 4 308.57 0.11 213 123 126 3 308.73 0.19 214 123 127 4 308.56 0.12 215 124 127 3 313.52 0.34 216 124 128 4 307.54 0.65 217 125 128 3 315.32 0.56 218 125 129 4 307.19 0.82 219 126 129 3 316.92 1.29