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 8 26 18 96.53 0.52 2 8 27 19 96.95 0.58 3 9 25 16 96.99 0.58 4 9 57 48 97.25 0.61 5 9 58 49 97.16 0.65 6 9 59 50 97.09 0.64 7 10 57 47 97.45 0.58 8 10 59 49 97.34 0.60 9 12 22 10 186.97 1.85 10 12 25 13 97.50 0.58 11 12 31 19 97.41 0.58 12 12 59 47 97.44 0.58 13 13 33 20 97.42 0.58 14 13 62 49 97.28 0.60 15 14 33 19 97.44 0.58 16 14 63 49 97.25 0.61 17 15 33 18 97.43 0.58 18 15 41 26 97.48 0.51 19 15 63 48 97.34 0.58 20 15 64 49 97.34 0.58 21 15 66 51 87.64 0.49 22 16 66 50 96.83 0.61 23 17 35 18 97.41 0.57 24 17 36 19 97.37 0.59 25 17 39 22 97.39 0.57 26 18 34 16 97.43 0.58 27 18 35 17 97.33 0.56 28 18 36 18 97.41 0.58 29 19 33 14 97.48 0.58 30 19 34 15 97.42 0.57 31 19 35 16 97.37 0.55 32 19 36 17 97.41 0.57 33 20 31 11 97.57 0.54 34 20 32 12 97.50 0.56 35 20 33 13 97.42 0.55 36 21 31 10 97.56 0.54 37 21 32 11 97.50 0.56 38 22 31 9 97.54 0.53 39 24 29 5 210.31 0.18 40 25 49 24 97.45 0.59 41 26 49 23 97.48 0.58 42 27 49 22 97.47 0.58 43 27 50 23 97.47 0.58 44 27 51 24 97.48 0.58 45 28 49 21 97.37 0.56 46 29 48 19 97.45 0.58 47 29 49 20 97.34 0.58 48 30 46 16 97.48 0.58 49 30 47 17 97.43 0.58 50 30 48 18 97.33 0.59 51 31 46 15 97.42 0.58 52 31 47 16 97.37 0.59 53 32 45 13 97.43 0.59 54 32 46 14 97.33 0.58 55 33 41 8 97.53 0.58 56 33 45 12 97.34 0.60 57 33 47 14 97.25 0.61 58 34 41 7 97.49 0.58 59 35 39 4 97.52 0.58 60 35 40 5 97.49 0.58 61 35 41 6 97.41 0.60 62 38 68 30 97.22 0.57 63 38 69 31 97.03 0.63 64 38 91 53 43.15 0.42 65 39 66 27 97.45 0.58 66 39 67 28 97.37 0.59 67 39 68 29 97.00 0.61 68 39 69 30 96.78 0.60 69 40 66 26 97.39 0.60 70 40 67 27 97.34 0.61 71 40 69 29 76.67 4.50 72 41 44 3 182.42 2.15 73 41 45 4 97.22 0.49 74 41 64 23 97.48 0.58 75 41 65 24 97.39 0.60 76 41 66 25 97.27 0.61 77 42 64 22 97.44 0.59 78 42 65 23 97.31 0.59 79 43 65 22 97.33 0.59 80 44 61 17 97.50 0.58 81 44 64 20 97.27 0.61 82 45 64 19 97.03 0.61 83 46 61 15 97.42 0.59 84 47 59 12 97.46 0.58 85 47 60 13 97.35 0.60 86 47 61 14 97.10 0.64 87 47 62 15 95.78 0.35 88 48 59 11 97.42 0.58 89 48 60 12 97.15 0.67 90 48 61 13 97.09 0.64 91 49 58 9 97.44 0.59 92 49 59 10 97.16 0.65 93 50 57 7 97.48 0.58 94 50 58 8 97.43 0.58 95 50 60 10 97.33 0.61 96 51 55 4 97.51 0.57 97 51 56 5 97.50 0.58 98 51 58 7 97.48 0.58 99 52 56 4 97.51 0.58 100 52 58 6 97.50 0.58 101 59 62 3 200.72 3.58 102 68 90 22 125.75 0.30 103 69 89 20 132.75 0.06 104 69 90 21 132.41 0.10 105 69 91 22 129.09 0.28 106 69 115 46 101.19 0.13 107 69 116 47 47.82 0.14 108 70 88 18 166.43 13.42 109 70 89 19 132.75 0.05 110 70 90 20 132.66 0.06 111 71 88 17 196.55 1.37 112 71 89 18 132.77 0.06 113 71 90 19 132.75 0.05 114 71 116 45 132.02 0.14 115 71 117 46 126.78 0.33 116 71 118 47 117.28 1.54 117 72 87 15 197.51 1.75 118 72 88 16 196.72 1.38 119 72 89 17 196.53 1.38 120 72 118 46 132.66 0.05 121 73 87 14 202.04 1.12 122 73 89 16 197.50 1.77 123 74 89 15 206.47 1.90 124 74 95 21 132.74 0.08 125 74 97 23 131.99 0.15 126 74 118 44 132.74 0.04 127 75 97 22 132.75 0.07 128 75 118 43 132.81 0.06 129 75 121 46 132.37 0.03 130 77 97 20 132.81 0.06 131 77 105 28 204.77 0.92 132 77 122 45 132.66 0.09 133 77 123 46 122.42 1.48 134 77 124 47 109.84 0.56 135 78 124 46 127.91 0.11 136 79 99 20 132.75 0.06 137 79 100 21 132.74 0.06 138 79 103 24 144.46 5.17 139 79 124 45 132.13 0.03 140 80 98 18 132.79 0.06 141 80 99 19 132.67 0.09 142 80 100 20 132.74 0.06 143 80 124 44 132.56 0.12 144 81 97 16 145.03 4.86 145 81 98 17 144.48 4.61 146 81 99 18 142.72 4.91 147 81 100 19 143.32 5.21 148 82 95 13 168.00 6.54 149 82 96 14 145.34 4.76 150 82 97 15 145.03 4.86 151 83 95 12 145.41 4.76 152 83 96 13 145.34 4.76 153 83 98 15 145.12 4.87 154 84 95 11 145.41 4.76 155 89 113 24 196.96 1.45 156 90 113 23 196.54 1.38 157 91 113 22 136.16 1.60 158 91 114 23 136.30 1.68 159 92 112 20 166.71 13.52 160 92 113 21 132.75 0.06 161 92 114 22 136.25 1.65 162 93 112 19 132.81 0.06 163 93 113 20 132.74 0.05 164 94 110 16 136.43 1.72 165 94 111 17 132.81 0.06 166 94 112 18 132.77 0.07 167 95 109 14 175.27 9.01 168 95 110 15 132.78 0.06 169 95 111 16 132.78 0.06 170 96 109 13 132.78 0.06 171 96 110 14 132.77 0.07 172 97 109 12 132.75 0.06 173 97 111 14 132.69 0.07 174 99 105 6 169.06 4.08 175 103 124 21 174.28 0.74 176 103 125 22 132.78 0.06 177 103 126 23 132.68 0.07 178 104 124 20 132.77 0.05 179 104 125 21 132.75 0.05 180 104 126 22 132.69 0.07 181 105 122 17 210.18 0.10 182 105 123 18 132.78 0.06 183 105 124 19 132.69 0.07 184 106 122 16 132.78 0.06 185 106 123 17 132.76 0.05 186 106 124 18 132.68 0.09 187 106 125 19 132.66 0.09 188 108 120 12 181.97 4.26 189 108 122 14 132.71 0.07 190 109 122 13 132.65 0.09 191 110 120 10 132.78 0.07 192 111 118 7 132.78 0.06 193 111 119 8 132.76 0.07 194 111 121 10 115.39 0.63 195 111 122 11 116.50 1.19 196 112 118 6 132.69 0.07 197 112 119 7 132.53 0.10 198 113 117 4 132.77 0.06 199 113 118 5 128.41 0.73 200 114 117 3 132.78 0.06