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 28 36 8 276.72 5.56 2 29 32 3 313.73 0.72 3 29 33 4 310.92 0.69 4 30 33 3 311.75 0.28 5 30 34 4 310.92 0.69 6 31 34 3 311.76 0.28 7 31 35 4 310.93 0.69 8 32 35 3 317.19 1.00 9 32 36 4 313.60 0.65 10 33 36 3 313.60 0.65 11 33 37 4 311.38 1.76 12 34 37 3 313.28 0.82 13 34 38 4 311.56 1.67 14 35 38 3 313.27 0.81 15 35 39 4 311.55 1.66 16 36 39 3 313.38 0.87 17 36 40 4 313.25 0.81 18 37 40 3 315.89 0.49 19 37 41 4 311.82 1.51 20 38 41 3 320.56 2.87 21 38 42 4 313.64 1.61 22 39 42 3 318.19 1.69 23 39 43 4 309.36 0.53 24 39 88 49 60.73 0.45 25 39 107 68 43.65 1.17 26 39 110 71 40.73 0.28 27 40 43 3 307.93 0.18 28 40 44 4 307.89 0.19 29 41 44 3 317.95 4.95 30 42 48 6 282.65 7.60 31 42 86 44 61.12 0.57 32 42 88 46 61.79 0.24 33 43 49 6 261.61 2.68 34 43 52 9 238.91 5.28 35 43 88 45 65.34 0.65 36 43 110 67 43.69 1.15 37 45 48 3 318.06 3.42 38 45 49 4 309.45 1.23 39 46 49 3 315.94 4.48 40 46 50 4 309.45 1.23 41 47 50 3 316.36 1.84 42 47 51 4 309.45 1.23 43 47 79 32 158.16 0.48 44 48 51 3 316.29 1.85 45 48 52 4 309.42 1.25 46 48 82 34 158.16 0.48 47 48 83 35 158.12 0.48 48 48 86 38 158.06 0.44 49 49 52 3 310.38 0.75 50 49 53 4 303.98 1.45 51 50 53 3 321.93 2.35 52 50 54 4 317.98 4.33 53 50 69 19 159.58 0.02 54 51 54 3 321.93 2.35 55 51 55 4 310.98 2.05 56 51 65 14 159.55 0.04 57 51 69 18 159.56 0.04 58 51 79 28 158.31 0.46 59 51 83 32 158.23 0.45 60 52 55 3 312.10 1.49 61 52 56 4 310.54 2.27 62 52 83 31 158.28 0.47 63 52 89 37 157.84 0.42 64 52 102 50 146.22 0.35 65 53 56 3 317.15 1.03 66 53 111 58 57.66 2.05 67 54 57 3 325.21 2.99 68 54 58 4 312.03 1.52 69 54 60 6 258.22 8.94 70 54 65 11 164.55 2.30 71 54 68 14 159.95 0.03 72 54 69 15 159.94 0.04 73 55 58 3 315.44 1.89 74 55 59 4 300.61 2.73 75 55 60 5 275.38 9.36 76 55 65 10 187.96 3.31 77 55 89 34 157.94 0.40 78 55 100 45 157.13 0.39 79 55 101 46 150.12 0.93 80 55 102 47 148.74 1.02 81 56 102 46 149.38 1.29 82 56 111 55 64.01 1.50 83 59 92 33 157.82 0.37 84 59 99 40 157.24 0.44 85 59 100 41 157.21 0.43 86 59 101 42 157.03 0.36 87 60 64 4 304.57 0.37 88 60 65 5 300.72 1.48 89 60 99 39 157.22 0.43 90 60 100 40 157.21 0.43 91 61 64 3 317.60 0.15 92 61 65 4 314.11 1.92 93 61 97 36 157.30 0.44 94 61 98 37 157.28 0.43 95 61 99 38 157.22 0.43 96 62 65 3 317.62 0.16 97 62 66 4 311.63 3.16 98 62 73 11 170.84 4.15 99 62 76 14 160.92 0.14 100 62 77 15 160.85 0.15 101 62 80 18 160.81 0.14 102 62 100 38 157.18 0.43 103 63 66 3 317.62 0.16 104 63 67 4 312.12 2.91 105 63 73 10 176.53 1.29 106 64 67 3 316.79 0.58 107 64 68 4 309.54 1.61 108 65 68 3 312.58 0.09 109 65 69 4 308.86 1.95 110 65 76 11 161.63 0.49 111 65 80 15 160.86 0.16 112 66 69 3 316.65 0.68 113 66 70 4 308.82 1.97 114 66 71 5 217.97 5.00 115 66 72 6 204.12 1.71 116 66 73 7 185.25 3.06 117 66 76 10 170.13 4.46 118 67 70 3 312.53 0.10 119 71 75 4 308.67 1.34 120 71 76 5 304.56 0.70 121 72 75 3 310.93 2.47 122 72 76 4 311.75 0.18 123 73 76 3 317.58 0.05 124 73 77 4 311.78 0.17 125 74 77 3 320.81 0.72 126 74 78 4 319.06 1.60 127 75 78 3 316.92 2.67 128 75 79 4 316.86 2.69 129 76 79 3 312.39 0.34 130 76 80 4 311.56 0.06 131 77 80 3 311.58 0.06 132 77 81 4 309.07 0.55 133 78 81 3 310.62 0.23 134 78 82 4 313.99 1.92 135 79 82 3 324.57 1.55 136 79 83 4 313.99 1.92 137 80 83 3 315.50 3.86 138 80 84 4 312.06 2.15 139 80 89 9 193.97 3.93 140 80 100 20 157.09 0.46 141 81 84 3 316.32 3.08 142 81 85 4 315.12 3.68 143 82 85 3 321.12 0.68 144 82 86 4 309.87 0.70 145 83 86 3 316.32 3.08 146 83 87 4 304.41 1.07 147 83 88 5 240.03 5.27 148 83 89 6 199.09 1.36 149 84 87 3 308.68 0.10 150 84 89 5 207.81 10.84 151 84 91 7 193.97 3.93 152 87 103 16 151.66 0.44 153 88 102 14 154.00 0.30 154 88 103 15 151.75 0.40 155 88 107 19 136.84 0.12 156 89 100 11 157.22 0.45 157 89 101 12 156.81 0.37 158 89 102 13 152.12 0.58 159 89 103 14 151.75 0.40 160 90 100 10 157.25 0.45 161 90 101 11 157.18 0.46 162 90 103 13 151.79 0.42 163 91 98 7 157.42 0.41 164 91 99 8 157.27 0.44 165 91 100 9 157.25 0.44 166 91 101 10 157.24 0.45 167 92 98 6 159.69 1.54 168 92 99 7 157.35 0.41 169 92 101 9 157.28 0.44 170 93 97 4 244.25 20.88 171 93 98 5 159.71 1.54 172 94 97 3 315.03 1.42 173 94 99 5 197.38 3.58 174 102 107 5 294.49 0.26 175 102 108 6 263.69 1.27 176 103 107 4 316.21 3.49 177 104 107 3 326.45 1.64 178 104 108 4 317.97 2.60 179 105 108 3 320.70 1.24 180 105 109 4 309.64 0.39 181 106 109 3 315.93 3.53 182 106 110 4 305.73 2.34 183 107 110 3 317.01 2.99 184 107 111 4 311.92 0.68 185 108 111 3 320.12 1.44 186 108 112 4 312.31 0.49 187 109 112 3 316.48 0.40 188 109 113 4 311.93 0.69 189 110 113 3 313.98 1.71 190 110 114 4 305.82 2.65 191 111 114 3 315.68 0.85 192 111 115 4 310.91 0.10 193 112 115 3 317.38 1.70 194 112 116 4 311.69 1.53 195 113 116 3 312.83 0.96 196 113 117 4 311.75 1.56 197 114 117 3 315.19 0.17 198 114 118 4 311.80 1.53 199 115 118 3 318.09 3.59 200 115 119 4 312.90 0.99 201 116 119 3 315.45 0.28 202 116 120 4 312.91 0.99 203 117 120 3 315.84 0.45 204 117 121 4 312.91 0.99 205 118 121 3 314.26 0.58