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 16 50 34 57.22 0.00 2 17 49 32 111.73 9.03 3 17 50 33 84.79 1.09 4 17 56 39 111.74 9.03 5 17 58 41 111.75 9.03 6 17 59 42 111.74 9.03 7 18 48 30 111.78 9.01 8 18 49 31 111.73 9.03 9 18 50 32 111.73 9.03 10 18 51 33 111.72 9.03 11 18 59 41 111.74 9.03 12 18 116 98 111.73 9.04 13 18 117 99 111.70 9.04 14 18 118 100 103.10 4.77 15 19 47 28 111.74 9.03 16 19 48 29 111.81 9.00 17 19 116 97 111.72 9.04 18 20 45 25 111.89 8.98 19 20 46 26 111.85 9.00 20 20 47 27 111.84 8.99 21 20 113 93 111.75 9.03 22 20 114 94 111.81 9.02 23 20 116 96 111.75 9.03 24 21 45 24 111.92 8.97 25 21 46 25 111.89 8.98 26 21 48 27 111.87 8.99 27 22 45 23 111.94 8.97 28 22 46 24 111.94 8.97 29 23 43 20 112.00 8.96 30 23 44 21 111.97 8.96 31 23 45 22 111.97 8.96 32 23 46 23 111.97 8.96 33 24 41 17 112.25 8.85 34 24 42 18 112.14 8.90 35 24 43 19 112.01 8.96 36 25 41 16 112.25 8.86 37 25 42 17 112.19 8.88 38 25 44 19 112.01 8.96 39 26 29 3 137.58 2.28 40 26 40 14 112.27 8.86 41 26 41 15 112.25 8.86 42 27 30 3 132.78 0.12 43 27 32 5 124.02 3.10 44 27 36 9 116.48 6.79 45 27 39 12 112.41 8.80 46 27 40 13 112.27 8.85 47 27 42 15 112.26 8.85 48 27 111 84 112.31 8.84 49 28 33 5 124.90 2.64 50 28 40 12 112.38 8.79 51 31 35 4 150.60 3.52 52 32 35 3 145.09 0.76 53 32 36 4 128.75 0.76 54 33 36 3 143.44 1.58 55 35 96 61 127.07 1.76 56 35 97 62 129.03 0.81 57 35 98 63 140.80 0.18 58 36 40 4 136.91 0.40 59 36 94 58 125.94 2.25 60 36 95 59 125.97 2.23 61 36 96 60 125.94 2.25 62 37 40 3 197.62 3.74 63 37 95 58 125.73 2.27 64 37 96 59 125.94 2.25 65 37 97 60 127.06 1.77 66 38 94 56 119.14 5.50 67 38 95 57 122.68 3.75 68 39 92 53 117.25 6.44 69 39 93 54 117.27 6.44 70 39 94 55 118.54 5.80 71 42 92 50 115.08 7.48 72 47 84 37 111.84 9.00 73 47 85 38 111.87 8.99 74 47 86 39 111.92 8.97 75 48 84 36 111.85 9.00 76 49 84 35 111.84 9.00 77 51 55 4 228.15 0.97 78 51 82 31 111.86 9.00 79 51 83 32 111.84 9.00 80 51 84 33 111.75 9.03 81 52 55 3 251.00 0.72 82 52 69 17 112.55 8.75 83 53 69 16 112.56 8.75 84 53 70 17 112.56 8.75 85 53 73 20 112.21 8.88 86 55 61 6 115.62 7.33 87 55 66 11 115.19 7.49 88 55 69 14 115.12 7.49 89 55 118 63 155.47 4.33 90 56 59 3 245.84 2.66 91 57 60 3 189.06 0.21 92 59 116 57 116.12 7.12 93 59 117 58 115.48 7.42 94 59 118 59 115.53 7.39 95 60 88 28 111.95 8.97 96 60 119 59 115.45 7.42 97 61 65 4 156.50 0.85 98 61 66 5 151.55 1.61 99 61 118 57 114.98 7.42 100 62 65 3 181.91 7.63 101 62 66 4 170.37 0.73 102 62 119 57 112.43 8.70 103 63 66 3 192.90 4.04 104 63 67 4 175.65 1.90 105 64 67 3 196.75 2.12 106 64 68 4 174.48 2.79 107 65 68 3 190.88 0.82 108 65 69 4 179.74 6.39 109 65 82 17 111.69 9.06 110 65 118 53 112.57 8.77 111 65 119 54 112.23 8.79 112 66 69 3 197.69 3.23 113 66 70 4 189.73 1.39 114 67 70 3 191.88 0.32 115 67 71 4 177.94 4.50 116 68 71 3 218.41 9.51 117 68 72 4 169.55 1.20 118 68 79 11 111.92 8.99 119 68 80 12 111.91 8.99 120 68 81 13 111.87 9.01 121 68 82 14 111.76 9.05 122 69 72 3 203.69 5.33 123 69 73 4 179.77 1.65 124 69 82 13 111.86 9.01 125 70 73 3 202.75 4.86 126 70 74 4 197.77 7.34 127 71 74 3 204.55 3.96 128 71 75 4 176.88 3.09 129 71 79 8 111.92 9.00 130 72 75 3 187.00 5.01 131 72 76 4 134.30 1.18 132 72 79 7 111.91 8.98 133 72 80 8 111.91 8.98 134 72 81 9 111.90 8.98 135 75 78 3 237.72 3.19 136 75 79 4 173.22 0.80 137 76 79 3 220.30 10.41 138 82 118 36 111.73 9.03 139 82 119 37 111.62 9.01 140 83 117 34 111.84 9.00 141 83 118 35 111.58 8.98 142 83 119 36 102.72 4.73 143 84 116 32 111.83 8.99 144 84 117 33 111.73 9.04 145 85 116 31 111.84 9.00 146 85 117 32 111.83 8.99 147 85 119 34 111.73 9.03 148 86 113 27 111.77 9.05 149 86 115 29 111.87 8.99 150 86 116 30 111.84 9.00 151 87 115 28 111.92 8.97 152 87 116 29 111.91 8.97 153 87 117 30 111.86 9.00 154 87 119 32 111.84 9.00 155 88 113 25 111.92 9.00 156 88 114 26 111.95 8.96 157 88 115 27 111.96 8.96 158 89 110 21 112.14 8.90 159 89 112 23 111.95 8.98 160 89 113 24 111.89 9.01 161 89 114 25 111.97 8.96 162 90 110 20 112.27 8.86 163 90 111 21 112.25 8.86 164 90 112 22 112.00 8.96 165 90 114 24 112.00 8.96 166 91 107 16 115.20 7.42 167 91 108 17 114.99 7.51 168 91 109 18 112.31 8.85 169 91 110 19 112.30 8.85 170 91 111 20 112.26 8.86 171 92 107 15 115.27 7.40 172 92 108 16 115.13 7.46 173 92 111 19 112.31 8.85 174 92 112 20 112.30 8.85 175 93 105 12 117.28 6.44 176 93 106 13 117.23 6.43 177 93 107 14 115.27 7.40 178 94 105 11 119.16 5.50 179 94 106 12 117.28 6.44 180 94 108 14 115.55 7.28 181 95 103 8 126.09 2.25 182 95 104 9 125.84 2.21 183 95 105 10 121.16 4.51 184 96 103 7 127.09 1.78 185 96 104 8 126.04 2.25 186 96 106 10 125.83 2.21 187 97 101 4 143.49 0.57 188 97 102 5 131.21 0.23 189 97 103 6 127.10 1.78 190 98 101 3 166.05 1.54 191 98 102 4 141.34 0.53 192 98 104 6 129.83 0.45 193 108 111 3 251.34 0.47 194 113 116 3 243.81 0.54