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 74 72 29.50 0.07 2 2 75 73 28.03 0.30 3 3 50 47 43.80 0.05 4 3 73 70 37.94 0.53 5 3 74 71 30.16 0.39 6 3 75 72 29.51 0.07 7 3 76 73 29.50 0.07 8 4 50 46 43.92 0.04 9 4 70 66 51.19 0.07 10 4 72 68 43.61 0.17 11 4 73 69 39.23 0.12 12 5 34 29 49.58 0.88 13 5 49 44 43.93 0.03 14 5 50 45 43.92 0.04 15 5 69 64 57.31 0.35 16 5 70 65 53.73 0.45 17 5 71 66 51.18 0.08 18 5 72 67 47.19 0.07 19 5 74 69 42.34 0.03 20 6 49 43 50.99 0.17 21 6 68 62 57.50 0.42 22 6 69 63 56.18 0.22 23 6 70 64 54.06 0.32 24 6 71 65 53.54 0.54 25 7 10 3 313.39 0.59 26 7 46 39 54.84 0.03 27 7 65 58 63.88 0.91 28 7 66 59 63.94 0.89 29 7 67 60 61.79 0.15 30 7 68 61 60.93 0.56 31 7 69 62 58.24 0.79 32 7 71 64 55.01 0.15 33 8 46 38 57.73 1.12 34 8 47 39 56.35 0.43 35 8 67 59 63.94 0.89 36 9 67 58 65.47 0.21 37 10 15 5 251.74 4.17 38 10 37 27 98.43 15.49 39 10 44 34 98.42 15.48 40 10 46 36 62.24 0.15 41 10 66 56 69.80 0.45 42 10 67 57 69.78 0.44 43 13 66 53 107.77 0.17 44 14 64 50 120.48 0.04 45 14 66 52 111.02 1.45 46 15 37 22 186.10 0.99 47 15 38 23 186.73 1.27 48 15 64 49 120.49 0.04 49 15 65 50 120.36 0.01 50 16 37 21 187.12 1.08 51 16 38 22 187.47 1.22 52 16 39 23 188.16 1.48 53 16 63 47 120.56 0.01 54 16 64 48 120.53 0.02 55 16 65 49 120.49 0.04 56 17 20 3 286.20 0.19 57 17 35 18 187.60 1.65 58 17 36 19 188.09 1.51 59 17 37 20 188.03 1.54 60 17 59 42 120.86 0.02 61 17 60 43 120.84 0.03 62 17 61 44 120.80 0.03 63 17 62 45 120.70 0.01 64 17 63 46 120.63 0.01 65 17 65 48 120.59 0.01 66 18 36 18 188.51 1.31 67 18 38 20 188.65 1.34 68 18 61 43 120.91 0.03 69 19 35 16 188.53 1.30 70 19 36 17 188.53 1.30 71 19 61 42 121.02 0.03 72 20 23 3 323.08 1.40 73 20 35 15 188.65 1.31 74 20 57 37 136.79 0.95 75 20 61 41 121.04 0.03 76 21 33 12 188.81 1.38 77 21 34 13 188.81 1.38 78 21 35 14 188.85 1.38 79 21 36 15 188.87 1.37 80 22 26 4 262.99 0.69 81 22 28 6 236.50 0.12 82 22 34 12 188.85 1.38 83 22 54 32 164.59 0.15 84 22 72 50 120.44 0.02 85 23 26 3 270.05 1.06 86 23 54 31 167.15 1.13 87 24 54 30 167.15 1.13 88 24 55 31 162.38 0.82 89 24 56 32 162.01 0.99 90 24 57 33 161.93 0.96 91 25 54 29 170.25 0.40 92 26 53 27 174.90 1.70 93 26 54 28 173.88 2.19 94 27 52 25 184.59 0.94 95 27 53 26 178.05 0.12 96 28 34 6 233.01 7.70 97 28 48 20 189.28 1.26 98 28 51 23 188.44 1.45 99 28 52 24 183.67 0.48 100 28 54 26 180.08 0.91 101 28 74 46 120.39 0.04 102 29 32 3 272.48 2.80 103 29 48 19 189.28 1.27 104 29 50 21 188.93 1.44 105 29 51 22 188.00 1.67 106 30 48 18 189.28 1.26 107 30 50 20 188.99 1.41 108 30 51 21 188.93 1.44 109 31 47 16 196.98 1.31 110 32 47 15 197.19 1.23 111 32 48 16 197.01 1.30 112 33 45 12 200.84 0.85 113 33 46 13 199.75 0.53 114 33 47 14 197.25 1.26 115 34 46 12 201.16 1.02 116 34 47 13 199.25 0.29 117 34 48 14 199.12 0.35 118 34 49 15 199.26 0.29 119 34 72 38 120.44 0.01 120 34 74 40 120.39 0.02 121 35 45 10 201.46 1.08 122 35 46 11 201.18 1.02 123 35 65 30 120.83 0.01 124 35 71 36 120.42 0.01 125 35 72 37 120.42 0.01 126 36 44 8 201.72 1.15 127 36 45 9 201.46 1.08 128 37 44 7 201.73 1.15 129 37 45 8 201.72 1.15 130 37 46 9 201.69 1.13 131 37 65 28 120.59 0.01 132 38 42 4 246.07 1.25 133 38 43 5 221.58 3.62 134 46 71 25 120.43 0.01 135 50 74 24 120.44 0.02 136 50 76 26 117.59 0.17 137 51 76 25 116.64 0.31 138 52 76 24 110.98 0.39 139 52 77 25 108.03 0.20 140 53 74 21 120.37 0.05 141 53 75 22 120.29 0.03 142 53 77 24 104.75 1.25 143 54 72 18 120.51 0.04 144 54 74 20 120.28 0.08 145 55 73 18 120.39 0.04 146 55 74 19 120.24 0.11 147 55 75 20 120.17 0.10 148 56 72 16 120.45 0.06 149 56 73 17 120.20 0.09 150 57 71 14 120.46 0.05 151 57 72 15 120.20 0.12 152 59 63 4 260.39 1.21 153 59 65 6 243.68 0.70 154 59 71 12 120.28 0.07 155 60 63 3 268.20 1.70 156 65 69 4 250.22 3.91 157 66 69 3 273.23 0.89