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 99.70 1.75 2 12 44 32 70.79 0.99 3 12 93 81 73.95 0.49 4 12 98 86 72.79 0.52 5 13 42 29 68.54 2.87 6 13 43 30 70.36 1.85 7 13 44 31 71.75 0.55 8 14 41 27 91.34 1.61 9 14 42 28 79.51 0.96 10 14 43 29 75.60 0.66 11 15 40 25 108.97 0.36 12 15 41 26 91.35 1.61 13 15 120 105 155.65 1.53 14 16 41 25 101.30 1.27 15 16 42 26 101.29 1.27 16 16 96 80 155.83 1.45 17 16 97 81 155.60 1.52 18 16 98 82 154.87 1.60 19 16 118 102 155.38 1.60 20 16 119 103 155.63 1.52 21 16 120 104 155.68 1.52 22 17 118 101 155.66 1.53 23 17 119 102 155.70 1.51 24 17 121 104 157.22 0.98 25 17 153 136 58.86 0.12 26 18 117 99 155.69 1.51 27 18 118 100 155.71 1.51 28 18 149 131 74.02 0.39 29 19 117 98 157.28 0.96 30 19 124 105 157.50 0.93 31 19 148 129 74.39 0.39 32 19 149 130 74.03 0.40 33 19 150 131 73.66 0.36 34 20 116 96 157.56 0.95 35 20 117 97 157.56 0.95 36 20 124 104 157.62 0.91 37 20 129 109 157.47 0.94 38 20 132 112 157.34 1.01 39 20 146 126 75.25 0.45 40 20 147 127 75.12 0.48 41 20 148 128 74.38 0.43 42 20 149 129 74.23 0.33 43 20 150 130 74.13 0.38 44 21 115 94 157.66 0.94 45 21 116 95 157.62 0.96 46 21 132 111 157.53 0.96 47 21 146 125 75.26 0.44 48 21 147 126 75.14 0.48 49 21 149 128 74.67 0.53 50 22 114 92 157.85 0.91 51 22 115 93 157.81 0.93 52 22 132 110 157.65 0.96 53 22 141 119 108.09 2.27 54 22 145 123 75.35 0.41 55 22 146 124 75.28 0.43 56 23 112 89 158.63 1.08 57 23 113 90 158.49 1.02 58 23 114 91 157.92 0.94 59 23 141 118 110.94 0.86 60 23 145 122 75.84 0.42 61 24 112 88 158.63 1.08 62 24 113 89 158.58 1.07 63 24 141 117 118.72 3.04 64 25 112 87 158.65 1.08 65 26 145 119 76.36 0.38 66 28 106 78 158.80 1.06 67 28 112 84 158.65 1.08 68 29 145 116 76.17 0.47 69 29 147 118 75.59 0.33 70 31 152 121 75.11 0.47 71 32 58 26 75.09 0.47 72 32 59 27 75.11 0.47 73 32 60 28 75.11 0.47 74 32 61 29 75.09 0.47 75 34 82 48 158.72 1.04 76 34 83 49 158.72 1.05 77 35 82 47 158.71 1.04 78 35 83 48 158.72 1.04 79 35 86 51 158.62 1.08 80 35 104 69 158.62 1.06 81 35 114 79 157.97 0.95 82 36 57 21 74.47 0.35 83 36 147 111 75.25 0.45 84 36 149 113 75.11 0.48 85 36 152 116 74.42 0.33 86 37 55 18 74.48 0.35 87 37 56 19 74.28 0.27 88 37 149 112 74.98 0.54 89 38 55 17 73.97 0.39 90 38 56 18 73.72 0.34 91 38 57 19 73.70 0.33 92 38 58 20 73.78 0.35 93 38 149 111 74.44 0.34 94 38 152 114 73.73 0.35 95 38 153 115 70.14 0.25 96 38 155 117 48.58 0.99 97 39 53 14 74.53 0.36 98 39 54 15 74.03 0.41 99 39 55 16 73.47 0.25 100 39 118 79 155.85 1.44 101 40 54 14 73.73 0.34 102 40 55 15 73.46 0.25 103 40 56 16 73.47 0.26 104 40 153 113 70.70 0.62 105 40 155 115 45.58 0.30 106 40 156 116 29.05 1.55 107 40 157 117 16.70 0.14 108 41 53 12 74.00 0.38 109 41 54 13 73.75 0.39 110 42 51 9 74.92 0.56 111 42 52 10 74.74 0.51 112 42 53 11 74.47 0.62 113 42 98 56 157.91 0.97 114 42 100 58 157.80 0.89 115 42 118 76 157.90 0.94 116 43 51 8 74.92 0.57 117 43 52 9 74.80 0.52 118 44 50 6 83.78 1.04 119 44 51 7 74.93 0.57 120 44 78 34 156.48 1.12 121 44 90 46 158.25 0.94 122 45 48 3 110.30 0.20 123 45 49 4 102.85 0.76 124 45 50 5 91.46 1.19 125 45 52 7 77.92 0.10 126 46 49 3 105.55 0.59 127 46 72 26 144.89 0.77 128 49 71 22 156.44 1.12 129 49 72 23 156.46 1.13 130 50 69 19 156.41 1.13 131 50 70 20 156.42 1.13 132 50 71 21 156.45 1.13 133 51 69 18 156.43 1.13 134 51 70 19 156.46 1.13 135 51 78 27 159.05 1.05 136 51 88 37 159.38 1.18 137 52 68 16 156.44 1.13 138 52 69 17 156.45 1.13 139 53 67 14 156.43 1.12 140 53 68 15 156.45 1.13 141 53 80 27 159.49 1.18 142 53 88 35 196.93 16.90 143 54 65 11 156.42 1.13 144 54 66 12 156.43 1.13 145 54 67 13 156.44 1.13 146 55 65 10 156.43 1.12 147 55 66 11 156.44 1.13 148 55 68 13 156.91 1.10 149 55 82 27 235.62 0.51 150 56 63 7 155.16 0.99 151 56 64 8 156.43 1.12 152 56 65 9 156.43 1.12 153 56 155 99 88.53 0.75 154 56 156 100 57.56 9.47 155 57 63 6 156.42 1.12 156 57 64 7 156.44 1.13 157 57 66 9 157.27 0.75 158 58 61 3 156.47 1.12 159 58 62 4 156.47 1.13 160 58 63 5 156.43 1.12 161 58 154 96 156.47 1.13 162 58 155 97 156.43 1.12 163 59 62 3 156.47 1.12 164 59 64 5 156.72 1.01 165 122 150 28 221.00 7.57 166 124 150 26 231.82 2.19