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 46 50 4 247.24 2.44 2 47 50 3 251.76 0.18 3 47 51 4 247.24 2.44 4 47 86 39 92.61 1.83 5 47 89 42 83.97 2.44 6 47 90 43 83.92 2.44 7 47 93 46 82.18 1.61 8 48 51 3 251.76 0.18 9 48 52 4 247.24 2.44 10 48 93 45 82.20 1.61 11 48 97 49 81.16 1.10 12 48 102 54 78.78 0.09 13 48 103 55 78.77 0.09 14 49 52 3 249.21 1.45 15 49 53 4 242.28 0.12 16 49 54 5 242.34 0.15 17 50 53 3 248.71 1.20 18 50 54 4 240.22 1.18 19 50 69 19 116.52 0.15 20 50 72 22 116.41 0.18 21 50 73 23 116.18 0.19 22 50 77 27 116.23 0.17 23 50 80 30 116.05 0.20 24 50 86 36 98.50 4.41 25 50 90 40 84.39 2.39 26 51 54 3 245.55 1.46 27 51 55 4 245.55 1.46 28 51 69 18 116.49 0.15 29 51 90 39 85.34 2.86 30 51 93 42 82.50 1.68 31 51 94 43 82.18 1.60 32 51 103 52 78.77 0.09 33 51 113 62 46.77 0.32 34 52 55 3 250.31 0.92 35 52 56 4 245.56 1.47 36 52 103 51 78.77 0.09 37 53 56 3 249.41 0.46 38 53 57 4 245.55 1.47 39 53 72 19 116.52 0.15 40 53 77 24 116.44 0.16 41 54 57 3 245.56 1.47 42 54 58 4 238.41 2.04 43 54 69 15 116.53 0.15 44 54 72 18 116.46 0.17 45 55 58 3 247.08 0.70 46 55 69 14 116.62 0.18 47 55 103 48 78.78 0.09 48 55 113 58 48.02 0.30 49 55 114 59 46.30 0.29 50 55 115 60 36.15 0.53 51 57 72 15 116.52 0.15 52 58 64 6 134.38 3.77 53 58 68 10 116.69 0.18 54 58 69 11 116.64 0.18 55 60 63 3 251.02 0.96 56 60 64 4 231.03 2.50 57 61 114 53 48.19 0.24 58 62 114 52 48.20 0.24 59 63 114 51 48.04 0.29 60 64 68 4 238.60 1.16 61 64 69 5 239.59 0.66 62 64 112 48 48.20 0.26 63 64 113 49 48.06 0.29 64 65 68 3 252.40 2.69 65 65 69 4 245.31 2.19 66 65 111 46 48.18 0.30 67 65 112 47 48.09 0.28 68 65 113 48 48.04 0.29 69 66 69 3 253.20 1.75 70 66 70 4 247.96 0.46 71 66 90 24 98.25 4.52 72 66 91 25 98.16 4.48 73 66 111 45 48.16 0.30 74 66 113 47 48.03 0.29 75 67 70 3 247.96 0.46 76 67 71 4 241.91 0.51 77 68 71 3 251.17 3.43 78 68 72 4 243.93 1.56 79 69 72 3 244.91 1.06 80 69 73 4 244.84 1.02 81 69 90 21 98.16 4.53 82 69 113 44 47.95 0.28 83 70 73 3 246.81 0.12 84 70 74 4 244.84 1.02 85 70 87 17 98.51 4.42 86 70 90 20 98.20 4.54 87 70 91 21 98.34 4.48 88 71 74 3 244.93 1.06 89 71 75 4 244.84 1.02 90 71 76 5 244.83 1.02 91 72 75 3 249.80 1.45 92 72 76 4 236.95 2.89 93 72 77 5 230.82 5.95 94 73 77 4 227.31 4.19 95 73 78 5 227.31 4.19 96 73 80 7 191.24 3.46 97 73 81 8 161.58 4.46 98 73 86 13 128.72 0.24 99 73 90 17 98.15 4.53 100 74 77 3 242.84 0.86 101 74 78 4 227.27 4.17 102 74 81 7 167.46 1.53 103 74 82 8 161.58 4.47 104 77 80 3 281.05 0.19 105 78 81 3 262.62 1.79 106 78 82 4 249.78 0.43 107 79 82 3 237.43 3.27 108 79 83 4 237.43 3.27 109 80 83 3 253.78 0.96 110 80 86 6 182.94 4.14 111 81 86 5 214.54 1.03 112 83 86 3 264.00 1.34 113 84 87 3 251.22 0.21 114 85 88 3 252.35 1.22 115 85 89 4 247.56 0.39 116 86 89 3 247.56 0.38 117 86 90 4 247.56 0.38 118 87 90 3 252.09 0.45 119 87 91 4 249.89 1.54 120 88 91 3 249.89 1.54 121 88 92 4 249.41 0.72 122 89 92 3 250.03 0.42 123 89 93 4 247.47 1.70 124 90 93 3 255.40 2.07 125 90 94 4 247.47 1.70 126 91 94 3 247.47 1.71 127 91 95 4 246.04 2.42 128 92 95 3 248.88 1.19 129 92 96 4 242.06 1.38 130 93 96 3 248.03 0.71 131 93 97 4 237.36 0.95 132 93 103 10 170.30 2.78 133 94 97 3 247.32 0.92 134 94 98 4 230.88 4.19 135 94 103 9 167.05 4.40 136 94 105 11 152.99 0.48 137 94 113 19 47.81 0.30 138 95 98 3 242.16 1.40 139 95 99 4 236.12 1.20 140 96 99 3 243.19 0.02 141 96 100 4 238.94 0.21 142 97 100 3 246.87 1.81 143 97 101 4 241.25 0.95 144 97 102 5 189.02 3.82 145 97 103 6 170.31 2.79 146 98 101 3 244.37 0.56 147 98 102 4 223.12 7.70 148 98 103 5 181.38 3.79 149 98 104 6 167.06 4.40 150 98 105 7 166.97 4.39 151 101 117 16 30.66 0.42 152 101 118 17 29.24 0.04 153 102 116 14 34.91 0.81 154 102 117 15 30.20 0.19 155 103 113 10 48.02 0.29 156 103 114 11 46.41 0.40 157 103 115 12 38.10 0.12 158 103 116 13 33.91 0.57 159 104 112 8 48.41 0.28 160 104 113 9 48.04 0.29 161 104 114 10 46.71 0.25 162 104 116 12 45.51 0.02 163 104 117 13 40.84 0.43 164 104 118 14 30.97 0.60 165 105 112 7 48.41 0.29 166 105 113 8 48.05 0.29 167 106 111 5 123.98 1.35 168 106 112 6 123.93 1.36 169 107 110 3 247.52 0.63 170 107 111 4 133.53 0.58