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 1107 1154 47 53.63 0.93 2 1107 1155 48 49.25 1.66 3 1108 1127 19 112.23 2.37 4 1108 1128 20 104.83 1.09 5 1108 1129 21 104.62 1.11 6 1108 1130 22 104.70 1.08 7 1108 1152 44 186.43 0.48 8 1108 1155 47 81.30 1.44 9 1109 1127 18 129.72 1.09 10 1109 1128 19 104.87 1.07 11 1109 1155 46 104.53 1.13 12 1109 1156 47 102.53 0.23 13 1109 1157 48 79.72 0.50 14 1110 1126 16 187.24 0.35 15 1110 1128 18 170.00 8.95 16 1110 1157 47 104.70 1.08 17 1111 1125 14 187.44 0.38 18 1111 1126 15 187.35 0.40 19 1111 1128 17 186.02 1.04 20 1111 1157 46 104.84 1.10 21 1112 1134 22 104.77 1.11 22 1112 1136 24 104.75 1.11 23 1112 1157 45 104.88 1.09 24 1113 1136 23 104.78 1.11 25 1113 1157 44 132.47 10.00 26 1113 1160 47 104.56 1.11 27 1115 1136 21 104.87 1.10 28 1115 1160 45 104.81 1.12 29 1115 1161 46 104.80 1.12 30 1115 1163 48 90.42 1.46 31 1116 1163 47 103.69 0.79 32 1117 1138 21 104.77 1.12 33 1117 1139 22 104.77 1.12 34 1117 1142 25 177.67 6.52 35 1117 1163 46 104.51 1.02 36 1117 1165 48 97.73 1.05 37 1118 1137 19 104.79 1.13 38 1118 1138 20 104.70 1.11 39 1118 1139 21 104.78 1.13 40 1118 1163 45 104.70 1.11 41 1119 1136 17 177.87 6.57 42 1119 1137 18 127.68 12.51 43 1120 1135 15 177.88 6.56 44 1120 1136 16 177.88 6.56 45 1121 1136 15 177.88 6.56 46 1121 1137 16 177.87 6.57 47 1128 1152 24 177.40 5.32 48 1129 1152 23 177.26 5.32 49 1130 1152 22 104.92 1.07 50 1131 1151 20 105.09 1.02 51 1131 1152 21 104.87 1.10 52 1132 1151 19 104.88 1.09 53 1132 1152 20 104.81 1.11 54 1133 1149 16 106.56 1.76 55 1133 1150 17 104.86 1.10 56 1133 1151 18 104.73 1.10 57 1134 1149 15 104.88 1.09 58 1134 1150 16 104.83 1.10 59 1135 1148 13 104.90 1.10 60 1135 1149 14 104.70 1.09 61 1136 1148 12 104.78 1.09 62 1136 1150 14 104.67 1.09 63 1138 1144 6 117.20 4.21 64 1140 1192 52 89.93 1.28 65 1141 1166 25 102.69 1.79 66 1141 1190 49 84.75 2.97 67 1141 1192 51 84.82 2.95 68 1142 1163 21 173.94 3.64 69 1142 1164 22 104.89 1.09 70 1142 1165 23 104.80 1.12 71 1142 1166 24 104.30 1.14 72 1142 1192 50 85.22 2.77 73 1143 1163 20 104.87 1.10 74 1143 1164 21 104.81 1.12 75 1143 1192 49 78.95 0.90 76 1143 1193 50 64.03 0.19 77 1144 1162 18 104.90 1.09 78 1144 1163 19 104.84 1.10 79 1145 1161 16 104.95 1.06 80 1145 1162 17 104.84 1.10 81 1145 1164 19 104.73 1.09 82 1147 1161 14 104.80 1.11 83 1148 1161 13 104.67 1.09 84 1150 1157 7 104.89 1.09 85 1150 1158 8 104.73 1.09 86 1150 1159 9 104.71 1.11 87 1150 1160 10 85.76 0.17 88 1150 1161 11 93.81 0.25 89 1151 1157 6 104.79 1.12 90 1151 1158 7 104.66 1.09 91 1152 1156 4 104.79 1.12 92 1152 1157 5 102.81 0.44 93 1153 1156 3 104.81 1.12 94 1164 1193 29 64.06 0.21 95 1164 1219 55 59.12 0.93 96 1164 1220 56 57.01 0.01 97 1165 1193 28 91.70 0.54 98 1165 1220 55 59.12 0.93 99 1165 1221 56 57.05 0.03 100 1166 1191 25 98.88 3.16 101 1166 1192 26 98.86 3.16 102 1166 1221 55 60.01 0.49 103 1167 1190 23 99.42 3.29 104 1167 1191 24 98.96 3.21 105 1167 1221 54 60.17 0.42 106 1167 1222 55 60.16 0.42 107 1167 1223 56 60.01 0.49 108 1168 1189 21 99.45 3.27 109 1168 1190 22 99.45 3.27 110 1169 1181 12 99.20 3.33 111 1169 1188 19 99.91 3.49 112 1169 1189 20 99.91 3.50 113 1169 1197 28 99.36 3.33 114 1169 1199 30 99.20 3.33 115 1169 1223 54 99.22 3.31 116 1169 1225 56 77.75 0.59 117 1170 1225 55 93.03 0.25 118 1173 1225 52 170.26 1.12 119 1175 1202 27 179.31 4.32 120 1177 1226 49 187.28 0.29 121 1177 1227 50 102.55 6.37 122 1177 1228 51 100.53 5.74 123 1178 1201 23 184.68 1.02 124 1178 1202 24 187.25 0.34 125 1178 1205 27 175.69 3.44 126 1178 1228 50 143.94 11.74 127 1179 1201 22 187.30 0.29 128 1179 1202 23 187.34 0.31 129 1179 1228 49 183.59 1.54 130 1191 1218 27 100.39 3.68 131 1192 1218 26 111.02 5.17 132 1193 1218 25 111.02 5.17 133 1193 1219 26 117.34 4.99 134 1193 1220 27 165.97 3.02 135 1194 1217 23 114.77 6.15 136 1194 1218 24 107.64 6.74 137 1194 1219 25 143.39 8.04 138 1195 1217 22 107.64 6.75 139 1195 1218 23 99.42 3.40 140 1196 1215 19 131.34 1.54 141 1196 1216 20 100.45 3.51 142 1196 1217 21 99.28 3.35 143 1197 1215 18 100.89 3.35 144 1197 1216 19 100.17 3.65 145 1198 1214 16 107.53 6.67 146 1198 1215 17 99.30 3.34 147 1199 1214 15 100.14 3.67 148 1200 1214 14 99.78 3.54 149 1201 1214 13 99.78 3.54 150 1207 1211 4 185.12 0.92 151 1207 1212 5 180.00 1.65 152 1207 1214 7 124.61 18.41 153 1208 1229 21 104.90 3.33 154 1211 1226 15 138.80 9.01 155 1211 1227 16 100.52 3.82 156 1212 1226 14 100.18 3.65 157 1213 1226 13 100.14 3.67 158 1214 1226 12 99.26 3.32 159 1214 1228 14 93.08 0.28 160 1216 1224 8 99.27 3.33 161 1217 1223 6 99.24 3.32 162 1218 1221 3 100.12 3.67 163 1218 1222 4 93.08 0.27 164 1218 1223 5 63.36 1.04 165 1219 1222 3 99.21 3.33