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 77 161 84 18.92 1.19 2 82 85 3 400.56 0.50 3 82 89 7 168.58 2.99 4 85 89 4 284.94 17.01 5 87 156 69 66.65 1.95 6 89 92 3 322.49 1.51 7 89 93 4 309.08 3.92 8 90 93 3 319.68 3.59 9 90 94 4 306.22 2.48 10 91 94 3 310.23 0.49 11 91 95 4 314.88 0.34 12 92 95 3 329.06 0.77 13 92 96 4 321.54 2.99 14 92 159 67 75.61 0.65 15 92 162 70 75.53 0.63 16 93 96 3 326.43 0.55 17 93 97 4 314.08 0.72 18 93 159 66 75.62 0.65 19 93 161 68 75.62 0.65 20 93 162 69 75.56 0.61 21 94 97 3 322.75 1.82 22 94 98 4 313.13 2.98 23 95 98 3 319.70 3.51 24 95 99 4 309.87 1.38 25 96 99 3 315.56 3.14 26 96 104 8 285.78 6.03 27 96 107 11 280.00 5.29 28 96 161 65 75.73 0.63 29 96 162 66 75.56 0.61 30 96 165 69 74.78 0.31 31 97 104 7 310.02 1.77 32 98 104 6 316.70 0.07 33 99 103 4 316.72 0.07 34 99 104 5 316.70 0.07 35 99 165 66 75.58 0.58 36 100 103 3 319.97 1.50 37 100 104 4 324.74 1.15 38 101 104 3 327.09 0.02 39 101 105 4 321.83 2.60 40 102 105 3 321.84 2.60 41 102 106 4 321.83 2.61 42 103 106 3 321.82 2.62 43 103 107 4 321.81 2.62 44 103 165 62 75.82 0.57 45 104 107 3 324.20 0.18 46 104 108 4 318.25 1.26 47 105 108 3 323.02 0.77 48 105 109 4 322.91 1.07 49 106 109 3 323.82 0.63 50 106 110 4 322.93 1.08 51 107 110 3 334.31 0.17 52 107 111 4 324.16 1.70 53 107 161 54 94.77 0.21 54 107 164 57 91.53 1.60 55 108 111 3 338.85 2.10 56 108 112 4 331.11 1.77 57 109 112 3 350.04 0.78 58 109 140 31 134.93 1.83 59 110 114 4 315.28 0.01 60 110 140 30 134.93 1.83 61 110 144 34 134.66 1.97 62 110 145 35 133.89 1.58 63 110 164 54 94.97 0.30 64 111 114 3 324.18 0.15 65 111 115 4 311.00 2.15 66 111 160 49 95.14 0.23 67 111 161 50 95.10 0.24 68 111 164 53 95.00 0.29 69 112 116 4 308.03 0.64 70 113 116 3 318.33 1.56 71 113 117 4 308.07 0.61 72 113 134 21 135.22 1.76 73 113 145 32 134.59 1.88 74 114 117 3 323.92 2.51 75 114 118 4 321.95 2.27 76 114 145 31 134.68 1.88 77 114 149 35 132.62 2.16 78 114 152 38 132.52 2.10 79 114 160 46 95.41 0.14 80 115 118 3 325.82 1.55 81 115 119 4 322.72 1.89 82 116 119 3 327.38 0.78 83 116 120 4 313.18 3.14 84 117 120 3 329.38 1.43 85 117 121 4 313.85 1.87 86 117 134 17 147.88 4.25 87 117 145 28 135.01 1.88 88 117 149 32 134.63 1.89 89 118 121 3 332.12 3.14 90 118 122 4 321.44 1.23 91 118 149 31 134.78 1.97 92 119 122 3 324.66 0.96 93 119 123 4 326.23 1.16 94 120 123 3 332.35 1.18 95 120 125 5 299.13 0.81 96 120 130 10 164.03 1.10 97 120 133 13 162.41 1.45 98 121 124 3 332.35 1.18 99 121 127 6 225.12 0.08 100 121 130 9 186.26 2.80 101 121 149 28 135.35 1.74 102 125 129 4 318.37 1.49 103 125 130 5 290.10 1.17 104 126 129 3 318.38 1.49 105 126 130 4 311.31 1.76 106 127 130 3 312.95 2.57 107 127 131 4 311.31 1.75 108 128 131 3 326.38 4.14 109 128 132 4 313.21 1.34 110 129 132 3 317.00 0.55 111 129 133 4 313.22 1.34 112 130 133 3 322.04 0.70 113 130 134 4 314.06 0.93 114 131 134 3 328.75 2.46 115 131 135 4 314.06 0.95 116 131 142 11 136.13 1.48 117 131 146 15 136.08 1.50 118 132 135 3 321.73 1.26 119 132 136 4 314.73 0.60 120 133 136 3 314.73 0.60 121 133 137 4 314.72 0.60 122 134 137 3 323.59 1.14 123 134 138 4 295.66 4.58 124 134 145 11 169.53 2.06 125 135 138 3 318.65 2.57 126 135 140 5 213.84 6.25 127 135 142 7 172.91 0.38 128 141 144 3 321.37 1.39 129 141 145 4 319.94 0.64 130 142 145 3 324.17 0.01 131 142 146 4 319.94 0.64 132 143 146 3 322.71 0.74 133 143 147 4 319.95 0.63 134 144 147 3 331.30 1.18 135 144 148 4 316.64 1.10 136 144 168 24 94.97 0.16 137 145 148 3 324.38 1.01 138 145 149 4 315.75 1.48 139 146 149 3 322.54 1.92 140 146 150 4 322.54 1.92 141 147 150 3 327.44 0.53 142 147 151 4 319.93 0.61 143 148 151 3 322.30 1.03 144 148 152 4 319.94 0.62 145 148 168 20 95.00 0.23 146 148 169 21 94.83 0.21 147 149 152 3 324.82 1.24 148 149 153 4 320.21 0.76 149 150 153 3 320.20 0.77 150 151 154 3 343.56 3.36 151 151 155 4 324.31 0.07 152 151 169 18 94.88 0.21 153 152 155 3 324.31 0.07 154 152 160 8 172.25 1.10 155 155 159 4 317.34 3.45 156 155 160 5 308.94 0.73 157 156 159 3 323.03 0.61 158 156 160 4 323.02 0.61 159 157 160 3 334.06 3.18 160 159 162 3 316.12 0.90 161 159 163 4 293.96 4.98 162 160 163 3 303.51 9.75 163 160 164 4 293.96 4.98 164 161 164 3 316.10 0.89 165 162 165 3 328.49 2.27 166 163 166 3 332.67 0.54