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 9.13 0.50 2 81 85 4 350.63 0.49 3 82 85 3 353.25 0.21 4 82 89 7 152.30 0.16 5 82 93 11 118.22 10.38 6 85 89 4 308.72 3.73 7 87 159 72 55.45 0.81 8 89 92 3 276.13 9.38 9 89 93 4 296.20 0.47 10 90 93 3 303.78 3.14 11 90 94 4 296.20 0.46 12 91 94 3 299.25 1.99 13 91 95 4 299.24 1.98 14 92 95 3 306.54 2.17 15 92 96 4 299.25 1.99 16 92 159 67 62.99 2.15 17 92 162 70 62.73 2.15 18 93 96 3 299.24 2.00 19 93 97 4 299.23 2.00 20 93 158 65 64.38 1.49 21 93 159 66 63.09 2.11 22 93 161 68 63.05 2.09 23 93 162 69 62.86 2.08 24 94 97 3 308.17 3.67 25 94 98 4 296.23 0.50 26 95 98 3 308.50 0.14 27 95 99 4 296.19 0.50 28 96 99 3 296.06 0.48 29 96 104 8 219.87 7.38 30 96 107 11 203.66 1.39 31 96 161 65 63.13 2.09 32 96 162 66 62.91 2.10 33 96 165 69 61.99 1.68 34 99 103 4 296.00 0.89 35 99 104 5 290.05 3.83 36 99 165 66 62.99 2.07 37 100 103 3 311.19 4.22 38 100 104 4 298.22 1.99 39 101 104 3 313.17 3.23 40 101 105 4 298.22 1.99 41 102 105 3 302.85 0.09 42 102 106 4 298.22 1.99 43 103 106 3 312.76 1.26 44 103 107 4 298.19 2.00 45 103 165 62 64.28 1.49 46 104 107 3 302.67 3.79 47 104 108 4 299.06 2.14 48 105 108 3 299.57 2.32 49 105 109 4 299.30 2.10 50 106 109 3 306.58 0.38 51 106 110 4 302.11 0.70 52 107 110 3 305.44 0.96 53 107 111 4 303.63 0.06 54 107 161 54 65.20 1.32 55 107 164 57 65.05 1.33 56 107 165 58 64.95 1.29 57 108 111 3 306.94 0.20 58 108 112 4 306.91 0.21 59 109 112 3 328.33 1.92 60 110 113 3 318.93 0.74 61 110 114 4 300.07 1.90 62 110 140 30 119.84 0.29 63 110 144 34 118.75 0.52 64 110 145 35 118.66 0.54 65 110 148 38 118.51 0.58 66 110 164 54 67.86 0.85 67 111 114 3 318.93 0.74 68 111 115 4 299.30 2.27 69 111 160 49 72.33 0.53 70 111 164 53 71.52 0.71 71 112 115 3 300.17 1.97 72 112 116 4 302.89 0.38 73 113 116 3 308.51 0.37 74 113 117 4 302.89 0.38 75 113 134 21 122.08 0.73 76 113 138 25 120.19 0.21 77 113 145 32 118.75 0.51 78 114 117 3 305.27 0.41 79 114 118 4 302.87 0.36 80 114 145 31 118.76 0.51 81 114 149 35 118.50 0.57 82 114 152 38 118.31 0.66 83 114 160 46 86.63 0.69 84 115 118 3 306.16 0.80 85 115 119 4 304.94 1.40 86 116 119 3 306.16 0.80 87 116 120 4 303.31 2.21 88 117 120 3 305.00 3.06 89 117 121 4 303.07 2.08 90 117 134 17 124.02 0.23 91 117 145 28 119.84 0.29 92 117 149 32 118.71 0.51 93 118 121 3 306.48 0.39 94 118 122 4 303.06 2.09 95 118 149 31 118.84 0.49 96 119 122 3 305.29 0.98 97 119 123 4 301.46 2.89 98 120 123 3 305.29 0.98 99 120 124 4 301.46 2.89 100 120 125 5 275.90 2.53 101 120 130 10 152.30 1.30 102 120 133 13 152.25 1.28 103 121 124 3 301.45 2.89 104 121 127 6 222.88 2.27 105 121 130 9 175.78 3.33 106 121 149 28 120.16 0.40 107 125 129 4 289.79 2.58 108 125 130 5 282.94 0.84 109 126 129 3 300.10 3.58 110 126 130 4 288.25 3.34 111 127 130 3 294.53 2.21 112 127 131 4 288.25 3.33 113 128 131 3 308.22 0.04 114 128 132 4 288.24 3.33 115 129 132 3 296.13 2.56 116 129 133 4 288.25 3.33 117 130 133 3 314.82 3.29 118 130 134 4 288.69 3.10 119 131 134 3 300.05 3.68 120 131 135 4 286.44 2.33 121 131 142 11 131.69 3.35 122 131 145 14 131.69 3.35 123 131 146 15 124.04 0.48 124 132 135 3 301.56 1.72 125 132 136 4 295.01 1.90 126 133 136 3 303.60 2.39 127 133 137 4 295.01 1.91 128 134 137 3 308.35 0.59 129 134 138 4 292.93 2.94 130 134 145 11 141.80 1.28 131 135 138 3 303.59 2.39 132 135 140 5 201.55 0.77 133 135 142 7 145.58 0.26 134 141 144 3 304.94 2.87 135 141 145 4 306.05 2.31 136 142 145 3 311.47 1.52 137 142 146 4 305.44 1.50 138 143 146 3 314.44 0.03 139 143 147 4 308.44 0.01 140 144 147 3 314.38 0.07 141 144 148 4 306.93 0.78 142 145 148 3 311.35 1.45 143 145 149 4 305.43 1.51 144 146 149 3 305.56 1.46 145 146 150 4 305.56 1.46 146 147 150 3 308.48 0.01 147 147 151 4 306.38 1.00 148 148 151 3 308.44 0.03 149 148 152 4 306.39 0.99 150 149 152 3 313.22 0.40 151 149 153 4 303.51 0.45 152 150 153 3 313.22 0.40 153 151 154 3 327.95 1.33 154 151 155 4 311.24 1.39 155 152 155 3 305.31 0.45 156 152 160 8 182.66 0.43 157 152 164 12 154.21 0.04 158 153 160 7 209.34 5.15 159 155 159 4 286.85 0.32 160 155 160 5 245.06 12.69 161 155 163 8 210.23 4.59 162 156 159 3 308.57 0.58 163 156 160 4 304.19 1.60 164 157 160 3 304.19 1.60 165 159 162 3 304.82 1.55 166 159 163 4 300.89 0.41 167 160 163 3 302.43 0.35 168 160 164 4 302.44 0.36 169 161 164 3 307.12 0.78 170 161 165 4 302.46 0.37 171 162 165 3 305.34 0.07 172 162 166 4 302.45 0.38 173 163 166 3 305.34 0.07