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 2 5 3 258.85 0.20 2 2 6 4 256.73 0.86 3 3 6 3 256.73 0.86 4 3 7 4 256.62 0.83 5 3 50 47 90.28 2.69 6 3 69 66 32.05 0.01 7 3 72 69 28.79 0.56 8 3 73 70 27.78 0.34 9 3 76 73 20.38 1.07 10 4 7 3 262.31 1.92 11 4 8 4 256.62 0.83 12 4 24 20 120.12 0.12 13 4 69 65 32.19 0.04 14 5 8 3 262.29 1.93 15 5 9 4 255.91 0.63 16 6 9 3 260.79 1.24 17 6 10 4 256.82 0.18 18 6 49 43 92.13 2.15 19 6 50 44 92.09 2.12 20 7 10 3 261.05 1.40 21 7 11 4 256.83 0.18 22 7 46 39 92.14 2.14 23 7 50 43 92.14 2.15 24 7 69 62 32.90 0.32 25 7 72 65 34.09 2.10 26 8 11 3 256.83 0.18 27 8 12 4 255.61 0.43 28 8 19 11 127.51 1.93 29 8 22 14 122.14 0.57 30 8 23 15 122.03 0.62 31 8 24 16 121.97 0.63 32 8 65 57 55.09 1.49 33 9 12 3 264.45 1.04 34 9 13 4 255.60 0.43 35 9 19 10 123.53 0.04 36 10 13 3 264.45 1.04 37 10 14 4 252.21 1.25 38 10 42 32 92.66 2.18 39 10 45 35 92.37 2.19 40 10 46 36 92.32 2.21 41 10 49 39 92.25 2.14 42 10 50 40 92.27 2.15 43 11 14 3 259.70 1.33 44 11 15 4 252.21 1.25 45 11 22 11 123.48 0.08 46 11 28 17 117.85 0.90 47 11 32 21 117.19 0.28 48 11 42 31 92.50 2.13 49 11 65 54 55.21 1.49 50 12 15 3 262.60 1.93 51 12 16 4 248.05 3.31 52 12 17 5 197.21 3.56 53 12 22 10 123.50 0.07 54 13 16 3 260.22 0.77 55 14 41 27 92.74 2.22 56 14 42 28 92.66 2.18 57 14 45 31 92.70 2.21 58 15 28 13 121.17 0.65 59 15 32 17 117.45 0.18 60 15 34 19 116.05 0.14 61 15 38 23 100.12 0.66 62 15 42 27 92.80 2.19 63 17 22 5 228.99 3.40 64 17 32 15 119.80 1.35 65 18 21 3 262.89 0.95 66 18 22 4 254.06 0.24 67 19 22 3 255.66 0.45 68 21 32 11 118.20 0.46 69 22 32 10 123.26 3.35 70 22 65 43 83.42 0.86 71 23 26 3 257.38 1.13 72 23 65 42 85.06 1.75 73 24 64 40 85.89 2.00 74 24 65 41 83.44 0.88 75 24 66 42 83.31 0.90 76 24 69 45 83.26 0.85 77 25 64 39 85.91 2.01 78 26 31 5 160.79 0.88 79 26 32 6 160.79 0.88 80 26 64 38 85.92 2.02 81 26 65 39 85.86 2.00 82 27 30 3 265.89 5.13 83 27 31 4 162.53 1.75 84 27 32 5 162.53 1.75 85 27 63 36 86.00 2.00 86 27 64 37 85.95 2.03 87 28 32 4 165.06 0.48 88 28 33 5 160.80 0.88 89 28 34 6 160.72 0.90 90 28 42 14 126.70 0.57 91 28 62 34 86.14 1.99 92 28 63 35 85.97 2.02 93 28 64 36 85.95 2.03 94 28 65 37 85.95 2.03 95 28 68 40 83.38 0.76 96 29 33 4 160.78 0.89 97 29 34 5 160.75 0.89 98 32 65 33 85.94 2.02 99 34 38 4 249.37 4.08 100 35 38 3 258.99 0.72 101 35 39 4 254.75 1.39 102 36 39 3 261.06 0.09 103 36 40 4 258.99 0.72 104 37 40 3 260.24 0.11 105 37 41 4 257.32 0.10 106 38 41 3 261.88 0.66 107 38 42 4 256.99 0.04 108 39 42 3 264.02 0.41 109 39 43 4 257.02 0.07 110 40 43 3 261.98 0.70 111 40 44 4 254.81 1.03 112 41 44 3 262.38 0.50 113 41 45 4 254.79 1.04 114 42 45 3 256.70 1.39 115 42 46 4 253.03 0.18 116 43 46 3 265.00 2.42 117 43 47 4 252.53 0.36 118 43 54 11 128.36 0.49 119 43 59 16 86.16 1.99 120 44 47 3 253.67 0.19 121 44 48 4 252.61 0.40 122 45 48 3 263.76 4.86 123 45 49 4 252.91 0.25 124 46 49 3 253.66 0.18 125 46 50 4 252.47 0.39 126 46 72 26 33.60 0.58 127 47 50 3 265.87 2.64 128 47 51 4 247.00 2.15 129 47 52 5 197.28 2.81 130 47 53 6 166.55 1.40 131 47 54 7 153.43 5.16 132 48 51 3 250.66 0.32 133 50 72 22 33.61 0.58 134 50 76 26 19.93 0.30 135 54 58 4 256.93 2.02 136 54 59 5 238.37 2.62 137 54 62 8 193.27 3.41 138 54 71 17 61.41 1.13 139 55 58 3 256.94 2.03 140 55 59 4 251.22 0.83 141 55 71 16 71.74 0.71 142 56 59 3 256.94 2.03 143 56 60 4 251.22 0.83 144 57 60 3 257.67 1.67 145 58 61 3 259.25 0.28 146 58 62 4 251.25 3.35 147 59 62 3 254.84 1.56 148 62 67 5 220.25 7.08 149 62 68 6 182.78 4.42 150 62 71 9 177.56 0.93 151 63 67 4 253.00 0.04 152 64 67 3 262.12 4.29 153 64 68 4 253.31 0.12 154 65 68 3 263.11 3.80 155 65 69 4 252.99 0.04 156 66 69 3 255.08 0.38 157 66 70 4 253.27 0.12 158 67 70 3 252.66 1.32 159 67 71 4 250.25 1.64 160 68 71 3 254.97 1.05 161 68 72 4 250.25 1.64 162 69 72 3 256.30 0.38 163 69 73 4 251.88 0.82 164 70 73 3 262.23 3.35 165 70 74 4 253.29 1.12 166 71 74 3 251.60 1.97 167 71 75 4 246.92 1.66 168 72 75 3 261.88 3.79 169 72 76 4 244.84 2.69