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 12 16 4 86.06 2.29 2 12 44 32 70.73 1.06 3 12 93 81 74.11 0.39 4 12 98 86 72.44 0.58 5 13 42 29 73.42 0.43 6 13 43 30 69.84 1.29 7 13 44 31 70.81 1.02 8 14 41 27 82.06 2.56 9 14 42 28 78.50 0.79 10 14 43 29 74.38 0.04 11 15 40 25 110.52 1.41 12 15 41 26 82.14 2.52 13 15 120 105 154.16 2.31 14 16 41 25 99.92 1.18 15 16 42 26 99.91 1.18 16 16 96 80 154.18 2.33 17 16 97 81 154.10 2.33 18 16 98 82 153.20 2.50 19 16 118 102 153.22 2.50 20 16 119 103 154.12 2.33 21 16 120 104 154.33 2.25 22 17 118 101 154.12 2.33 23 17 119 102 154.19 2.33 24 17 121 104 159.94 1.48 25 18 117 99 155.34 1.75 26 18 118 100 154.66 2.10 27 18 149 131 74.38 0.43 28 19 117 98 160.68 1.82 29 19 124 105 160.81 1.82 30 19 148 129 74.53 0.46 31 19 149 130 74.40 0.45 32 19 150 131 73.86 0.47 33 20 116 96 160.84 1.88 34 20 117 97 160.84 1.88 35 20 124 104 161.05 1.82 36 20 129 109 160.85 1.80 37 20 132 112 160.74 1.85 38 20 146 126 75.42 0.47 39 20 147 127 75.19 0.45 40 20 148 128 74.50 0.45 41 20 149 129 74.41 0.45 42 20 150 130 74.41 0.45 43 21 115 94 160.96 1.85 44 21 116 95 160.84 1.88 45 21 132 111 160.92 1.83 46 21 146 125 75.47 0.48 47 21 147 126 75.20 0.45 48 21 149 128 74.54 0.48 49 22 114 92 161.03 1.85 50 22 115 93 161.00 1.84 51 22 132 110 160.99 1.86 52 22 141 119 103.33 0.29 53 22 145 123 75.61 0.44 54 22 146 124 75.48 0.48 55 23 112 89 161.43 1.80 56 23 113 90 161.23 1.85 57 23 114 91 161.05 1.84 58 23 141 118 111.03 2.69 59 23 145 122 76.81 0.92 60 24 112 88 161.44 1.80 61 24 113 89 161.42 1.80 62 24 141 117 111.06 2.69 63 25 112 87 161.47 1.79 64 26 145 119 77.09 0.82 65 28 106 78 161.62 1.78 66 28 112 84 161.48 1.78 67 29 145 116 76.99 0.86 68 29 147 118 75.80 0.43 69 30 152 122 75.19 0.44 70 31 152 121 75.15 0.46 71 32 58 26 75.10 0.47 72 32 59 27 75.12 0.46 73 32 60 28 75.14 0.44 74 32 61 29 75.10 0.45 75 34 82 48 159.33 0.72 76 34 83 49 159.33 0.71 77 35 82 47 159.35 0.72 78 35 83 48 159.36 0.72 79 35 86 51 161.22 1.67 80 35 104 69 161.34 1.80 81 35 114 79 161.08 1.82 82 36 57 21 74.61 0.42 83 36 147 111 75.48 0.48 84 36 149 113 75.12 0.48 85 36 152 116 74.61 0.42 86 37 55 18 74.67 0.39 87 37 56 19 74.44 0.43 88 37 149 112 75.10 0.48 89 38 55 17 74.25 0.52 90 38 56 18 74.22 0.52 91 38 57 19 73.69 0.34 92 38 58 20 74.20 0.54 93 38 149 111 74.56 0.42 94 38 152 114 74.37 0.45 95 38 153 115 69.14 0.25 96 38 155 117 47.87 0.74 97 39 54 15 74.25 0.52 98 39 55 16 73.67 0.35 99 39 118 79 159.21 1.40 100 40 54 14 73.70 0.35 101 40 55 15 73.38 0.23 102 40 56 16 73.41 0.21 103 40 153 113 69.81 0.09 104 40 155 115 36.17 1.22 105 40 156 116 25.69 0.37 106 40 157 117 16.70 0.14 107 41 53 12 74.25 0.49 108 41 54 13 73.95 0.40 109 42 51 9 75.06 0.62 110 42 52 10 74.73 0.51 111 42 53 11 74.20 0.49 112 42 98 56 161.10 1.84 113 42 100 58 160.95 1.85 114 42 118 76 161.09 1.81 115 43 51 8 75.14 0.58 116 43 52 9 74.78 0.49 117 44 50 6 89.33 2.13 118 44 51 7 75.16 0.59 119 44 78 34 157.94 0.42 120 44 90 46 161.22 1.88 121 45 48 3 111.27 0.89 122 45 49 4 107.09 0.66 123 45 50 5 91.96 0.92 124 45 52 7 78.83 0.20 125 46 49 3 107.12 0.65 126 46 72 26 137.83 0.27 127 49 71 22 157.95 0.44 128 49 72 23 157.96 0.44 129 50 69 19 157.91 0.44 130 50 70 20 157.95 0.44 131 50 71 21 157.96 0.44 132 51 69 18 157.95 0.43 133 51 70 19 157.97 0.44 134 51 78 27 161.95 1.86 135 51 88 37 162.13 1.88 136 52 68 16 157.95 0.43 137 52 69 17 157.96 0.44 138 53 67 14 157.95 0.43 139 53 68 15 157.96 0.43 140 53 80 27 162.28 1.88 141 53 88 35 187.53 13.31 142 54 65 11 157.94 0.43 143 54 66 12 157.94 0.43 144 54 67 13 157.95 0.43 145 55 65 10 157.94 0.43 146 55 66 11 157.94 0.43 147 55 68 13 158.23 0.44 148 55 82 27 238.42 0.78 149 56 63 7 156.34 0.41 150 56 64 8 157.94 0.43 151 56 65 9 157.94 0.43 152 56 155 99 78.50 1.00 153 56 156 100 38.43 0.10 154 57 63 6 157.94 0.43 155 57 64 7 157.96 0.44 156 57 66 9 158.00 0.43 157 58 61 3 157.97 0.44 158 58 62 4 157.97 0.44 159 58 63 5 157.94 0.43 160 58 154 96 157.97 0.44 161 58 155 97 157.94 0.43 162 59 62 3 157.98 0.43 163 59 64 5 157.99 0.44 164 122 150 28 222.28 8.36 165 124 150 26 238.96 0.02