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 1 49 48 57.65 17.08 2 1 73 72 24.05 0.28 3 1 74 73 24.07 0.28 4 1 77 76 24.00 0.26 5 2 5 3 278.26 0.03 6 2 6 4 279.48 0.65 7 2 66 64 37.09 1.21 8 2 70 68 26.45 0.92 9 3 6 3 286.21 0.64 10 3 7 4 275.01 1.58 11 4 7 3 276.27 1.08 12 4 8 4 279.50 0.66 13 4 45 41 69.25 11.96 14 4 48 44 69.25 11.95 15 5 8 3 286.21 0.64 16 5 9 4 283.88 0.53 17 5 41 36 69.25 11.96 18 5 45 40 69.25 11.96 19 5 53 48 69.02 11.86 20 5 66 61 47.05 0.88 21 5 70 65 43.94 0.67 22 5 73 68 43.90 0.66 23 6 9 3 282.39 0.59 24 6 19 13 81.05 13.09 25 6 22 16 78.64 14.20 26 6 66 60 44.02 0.62 27 7 10 3 283.22 0.19 28 7 19 12 81.05 13.09 29 8 11 3 279.80 0.52 30 8 12 4 256.60 4.13 31 8 13 5 202.60 1.23 32 8 40 32 70.00 11.95 33 8 41 33 69.38 11.93 34 8 44 36 69.40 11.95 35 8 45 37 69.36 11.94 36 9 13 4 202.15 1.44 37 9 15 6 159.40 2.91 38 9 19 10 82.59 12.35 39 9 33 24 78.51 13.88 40 9 37 28 71.68 11.13 41 9 41 32 69.91 11.92 42 10 19 9 82.59 12.35 43 12 40 28 70.09 11.90 44 12 44 32 69.99 11.92 45 13 37 24 71.69 11.13 46 13 40 27 70.11 11.90 47 14 37 23 75.02 9.46 48 15 19 4 275.24 1.23 49 15 22 7 207.68 0.54 50 15 31 16 90.59 8.02 51 15 32 17 90.50 7.99 52 15 33 18 88.59 8.85 53 15 37 22 85.24 8.31 54 16 31 15 90.69 7.96 55 16 32 16 90.58 8.01 56 17 21 4 282.79 2.48 57 17 31 14 90.70 7.96 58 18 21 3 291.14 0.28 59 19 22 3 284.45 2.85 60 22 26 4 212.46 0.37 61 22 28 6 181.54 4.62 62 22 31 9 123.64 15.47 63 23 26 3 244.97 5.58 64 23 28 5 201.75 1.15 65 24 65 41 73.05 0.94 66 24 66 42 72.97 0.96 67 24 67 43 72.97 0.96 68 25 67 42 73.05 0.94 69 27 30 3 278.66 0.46 70 27 64 37 78.92 3.85 71 28 31 3 274.25 0.62 72 28 32 4 271.94 0.09 73 28 33 5 216.01 0.53 74 28 63 35 83.04 5.79 75 28 66 38 82.92 5.85 76 29 32 3 274.38 1.31 77 29 33 4 216.02 0.53 78 29 64 35 83.43 5.99 79 33 37 4 258.20 3.00 80 33 38 5 252.53 1.15 81 33 63 30 94.20 11.35 82 34 37 3 261.06 1.93 83 34 38 4 264.54 0.17 84 35 38 3 271.55 2.00 85 35 39 4 264.58 0.18 86 36 39 3 281.96 3.31 87 36 40 4 269.31 2.54 88 37 40 3 276.00 3.29 89 37 41 4 267.41 1.86 90 38 41 3 269.04 2.68 91 38 42 4 271.66 0.26 92 39 42 3 273.26 0.54 93 39 43 4 279.66 2.66 94 40 43 3 280.42 3.04 95 40 44 4 279.66 2.66 96 41 44 3 287.82 0.66 97 41 45 4 273.56 0.31 98 41 53 12 162.24 3.33 99 41 63 22 140.52 2.72 100 42 45 3 283.39 1.55 101 42 46 4 273.56 0.32 102 42 52 10 162.24 3.33 103 42 53 11 162.24 3.33 104 42 58 16 148.85 3.35 105 42 63 21 143.96 1.05 106 43 46 3 285.92 0.96 107 43 47 4 285.91 0.96 108 44 47 3 285.91 0.96 109 44 48 4 273.50 0.32 110 45 48 3 280.35 3.75 111 45 49 4 273.50 0.32 112 45 51 6 252.03 3.56 113 45 52 7 180.10 7.25 114 45 53 8 180.30 7.16 115 46 49 3 283.18 0.42 116 46 50 4 260.89 0.67 117 46 51 5 202.44 3.85 118 46 52 6 180.12 7.25 119 49 73 24 95.52 25.19 120 49 77 28 95.36 25.19 121 50 77 27 95.36 25.19 122 50 80 30 95.02 25.06 123 51 73 22 95.52 25.19 124 51 76 25 95.45 25.21 125 51 77 26 95.38 25.19 126 51 80 29 90.96 25.23 127 53 57 4 255.78 0.18 128 53 63 10 177.72 2.89 129 53 69 16 100.23 23.17 130 53 73 20 95.51 25.19 131 54 57 3 282.34 0.17 132 54 58 4 247.89 3.77 133 54 76 22 97.47 24.20 134 55 58 3 264.92 2.04 135 55 59 4 254.68 7.16 136 57 60 3 275.19 0.70 137 57 62 5 199.81 0.38 138 57 63 6 199.81 0.38 139 57 69 12 135.46 5.71 140 57 72 15 100.35 23.21 141 57 73 16 100.36 23.21 142 57 76 19 100.36 23.21 143 58 63 5 201.28 2.58 144 61 64 3 278.66 2.60 145 62 65 3 281.31 2.10 146 62 69 7 156.75 4.92 147 63 69 6 203.28 5.49 148 65 68 3 277.68 2.10 149 65 69 4 269.56 2.02 150 66 69 3 277.75 2.06 151 66 70 4 268.90 2.36 152 67 70 3 280.18 3.27 153 67 71 4 280.17 3.27 154 68 71 3 283.66 1.52 155 68 72 4 270.33 1.66 156 69 72 3 270.33 1.66 157 69 73 4 270.43 1.60 158 70 73 3 275.17 0.33 159 70 74 4 270.35 0.47 160 71 74 3 272.56 0.98 161 71 75 4 270.38 0.45 162 72 75 3 278.86 2.81 163 72 76 4 272.51 0.62 164 73 76 3 277.85 3.31 165 73 77 4 272.50 0.64 166 74 77 3 279.64 2.42 167 74 78 4 272.56 0.60 168 75 78 3 273.13 0.74 169 75 79 4 273.94 0.67 170 76 79 3 276.44 0.58 171 76 80 4 267.25 0.30 172 77 80 3 274.01 0.70 173 79 82 3 271.75 0.34 174 79 83 4 259.85 3.80 175 80 83 3 276.55 1.49