2024_Ramos_Martinez_BGHI

Data for Ramos, Martínez, 2024

This repository contains the BGHI structures in complex with glucose dimers selected in the study, obtained at different concentrations of the cosolvent (125 mM, 250 mM, 500 and 1000 mM).

The system.gro and system.pdb files have the initial atomic coordinates of the systems with all their components: the BGHI crystal structure, water, glucose and sodium ions. The files traj_protein+2BGL.pdb are PDB trajectories containing only the BGHI enzyme and glucose dimers with $S \geq 50 ~\mathrm{\mathring{A}}^{-1}$. The trajectories can be loaded by using VMD just typing:

vmd traj_protein+2BGL.pdb

Or using the VMD visualization state available in the root directory:

vmd -e state.vmd

The visualization state loads the trajectory and a representation indicating the catalytic dyad (E166 and E377), the residues BGL1 (red) and BGL2 (blue) and the distances $d_1$ and $d_2$, such as the following:

The VMD script print_scores.tcl can be used to print out the distances $d_1$, $d_2$ and $d_3$, as well as the value of $S$:

vmd -dispdev text -e print_scores.tcl

To work properly, both the files state.vmd and print_scores.tcl must be in the same directory as traj_protein+2BGL.pdb, thus we created symbolic links to then inside each system's directory.

The solvated_structures directories contain PDB files with all system components for frames with $S \geq 50 ~\mathrm{\mathring{A}}^{-1}$.

It is possible to open them as a trajectory in the following way:

vmd output_*.pdb

For better visualization, it may be convenient to align the protein structures. To do this simply do the following: Extensions > Analysis > RMSD Trajectory Tool, then type "protein" in the dialog box and click on "ALIGN". You can also choose to use just the protein backbone atoms as reference by click on "Backbone" before perform the alignment.

Another option is to add the follow macro to the .vmdrc file:

atomselect macro R { protein and resid 3 4 5 6 7 8 9 10 11 12 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 }

With this macro it is possible to use "R" instead of "protein" and align all structures over the rigid part of the BGHI.

It is also possible to select the protein highly flexible F segments (F1-5) by defining the following macros:

atomselect macro F { protein and ((resid  13 to 57) or (resid 177 to 197 ) or (resid 308 to 353) or (resid 379 to 400) or (resid 431 to 463)) }

atomselect macro F1 { protein and resid 13 to 57 }
atomselect macro F2 { protein and resid 177 to 197 }
atomselect macro F3 { protein and resid 308 to 353 }
atomselect macro F4 { protein and resid 379 to 400 }
atomselect macro F5 { protein and resid 431 to 463 }

OBS¹: The macros simplify the selection of system components in the VMD software. After defining the selections above you can use them in the "Graphical Representations" (Graphics > Representations...) menu by simply typing, for example, "F1" instead of "protein and resid 13 to 57" in the "Selected Atoms" dialog box.

OBS²: If you are not familiar with VMD, please visit the following link for strunctions about how to install and use it: VMD 1.9.3 Documentation