----------------------------------------------------------------------------------------------- //SSM_code.zip ----------------------------------------------------------------------------------------------- The SSM Simulation contains: SSM_final_version.c RUN_SSM mtt.c VMAX.dat ----------------------------------------------------------------------------------------------- //Synthetase sequestration model (SSM) ----------------------------------------------------------------------------------------------- Description: The synthetase sequestration model simulates the charging cycle of tRNAs in a yeast cell: We assume that the uncharged tRNA population is divided between a ‘bound’ state (b), where the tRNA is uncharged but bound to the corresponding synthetase enzyme and an ‘empty’ (uncharged and unbound) state (e). The third state is the charged state (c) where the tRNA is charged with its corresponding amino acid. There are 20 different amino acids. Doxycycline reduces the number of Glutamine synthetase molecules only. But the cycles of all amino acid types are affected, since the cell growth is reduced, which is reflected in the usage rates. Motivation: To address the paradox that experimentally treating the teO-GLN4 cells with doxycycline induces a GCN4 amino acid starvation response, indicative of the accumulation of uncharged tRNA, but another experiment showed that proportion of glutamine tRNAs charged with glutamine is not affected by glutamine synthetase depletion. Idea: In the bound state (b), tRNA is not available to react with Gcn2 kinase, which is thought to activate the GCN4 amino acid starvation response. Therefore, when the glutamine synthetase concentration drops in response to doxycycline, there are fewer glutamine synthetase molecules available to bind to the Gutamin tRNA, so that the empty level increases at the expense of bound level. Crucially, the increased amount of ‘empty’ (e) tRNA is now available to react with Gcn2, and trigger the GCN4 response. ----------------------------------------------------------------------------------------------- //INSTALLATION and RUN ----------------------------------------------------------------------------------------------- This code is written in C. Linux: No installation needed. 1.) The following files are required to be in the same directory: SSM_final_version.c (this is the original code) RUN_SSM (this is the executable program) mtt.c (get from http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html ) VMAX.dat (can be reproduced by copying lns 570-590 from the SSM_final_version.c) 2.) Open a terminal and go to the directory where your files are. If you changed (parameters or settings within) the code go to step 3.a) otherwise go directly to step 3.b) 3.a) compile the code using gcc -O3 -o RUN_SSM SSM_final_version.c -lm (or set your own programm name intstead of 'RUN_SSM'.) 3.b) Run the programm with ./RUN_SSM (or use your own name you chose in 3.a) instead of 'RUN_SSM'.) 4.) The program creates a folder named 'OUTPUT_SynSeq' and prints the output to this folder. You should see the following files: Parameters.dat (which gives you the information about all the parameters used in this run) Levels_i.dat (with i=0,...19; one for each of the 20 amino acids) (4 columns: Gln4 protein ration, empty level, bound level, charged level) Comp_times_steps_i.dat (with 10^i=the number of Gillespie iterations skipped (transient time) and used) (this file shows you the computational time for each doxycycline loop) ----------------------------------------------------------------------------------------------- //NOTES ----------------------------------------------------------------------------------------------- You may use any other random number generator; adjust the initiatisation. The default in the code is a loop (arg_d in ln 117) where the glutamine synthetase concentration is reduced to 1% for arg_d=0 and stepwise recovered to 100% for arg_d=26. To run the simulation for a distinct Gln4 protein ratio, the loop must be commented and arg_d or d (=Gln4 protein ratio) must be manually set. If you run the programm 'RUN_SSM' a second time, the terminal will show: 'mkdir: cannot create directory ‘OUTPUT_SynSeq’: File exists' and overwrite or add to the files in the OUTPUT_SynSeq folder. Rename the folder before you restart the programm. The number of Gillespie iterations is set to 10^10. For the small Gln4 protein ratio (=0.01) the programm runs 300 min. Note that for demonstration, in the Example, 10^7 Gillespie steps have been used, which is not enough to reach a steady state, but takes only 8s for the small Gln4 protein ratio (=0.01). ----------------------------------------------------------------------------------------------- //EXAMPLES ----------------------------------------------------------------------------------------------- Parameters.dat shows first blocks for each aminoacid of the rate constants k2, k3, k0,k1 in one line; the initial number of T_c,T_e,T_b,E[j] in the second row and the initial rates charge, usage, dissociation, binding in the third row. After the 20th amino acid, the global parameters are listed: the scaling factor (for a smaller cell fraction), the chargeing factor a (which adjusts the average cell charging level of 80%), the Gln4 protein ratio and the iteration steps. The third part lists the amino acid, the total number of tRNAs and synthetase molecules for this amino acid type. Should look like this for Gln4 protein ratio=0.5: *********************************EXAMPLE******************************************** --------------------------- aminoacid, k2=a*kcat, k3=d*hopp*USE, k0,k1 T_c,T_e,T_b,E[j] charge, usage, degredation, bind. rate --------------------------- 0: 1.66 0.10 43.00 0.003 178330 0 0 22920 0.0e+00 1.8e+04 0.0e+00 0.0e+00 1: 1.19 0.10 43.00 0.006 220290 0 0 17540 0.0e+00 2.2e+04 0.0e+00 0.0e+00 ... (for all 20 amino acids) 19: 4.87 0.10 43.00 0.004 199310 0 0 6750 0.0e+00 2.0e+04 0.0e+00 0.0e+00 --------------------------- Scaling factor=1 a=0.200000 Gln4 protein ratio=0.500000 Gillespie steps=10000000 --------------------------- j t[j] Etotal[j] 0: 178330 22920 1: 220290 17540 2: 115390 5950 3: 167840 17660 4: 41960 12970 5: 104900 51660 6: 178330 46100 7: 220290 51950 8: 83920 16730 9: 167840 19790 10: 220290 80830 11: 230780 26230 12: 115390 50790 13: 115390 10270 14: 125880 13480 15: 188820 18440 16: 178330 30520 17: 62940 11250 18: 83920 9500 19: 199310 6750 --------------------------- *********************************************************************************** Levels_5.dat The Glutamine levels for 27 different Gln4 protein ratios: Gln4 protein ratio, empty level, bound level, charged level *********************************EXAMPLE******************************************** 0.010000 0.115628 0.006509 0.877863 0.012000 0.115349 0.007800 0.876851 0.014000 0.114942 0.009091 0.875967 0.016000 0.114462 0.010376 0.875161 0.018000 0.114245 0.011661 0.874095 0.020000 0.114028 0.012950 0.873022 0.030000 0.112010 0.019303 0.868687 0.040000 0.110665 0.025627 0.863708 0.050000 0.108529 0.031813 0.859657 0.060000 0.107047 0.037996 0.854958 0.070000 0.105612 0.044111 0.850277 0.080000 0.104127 0.050153 0.845719 0.090000 0.102833 0.056164 0.841003 0.100000 0.101242 0.062047 0.836711 0.120000 0.098081 0.073581 0.828338 0.140000 0.095820 0.085086 0.819093 0.160000 0.093203 0.096209 0.810588 0.180000 0.090712 0.107086 0.802202 0.200000 0.088363 0.117744 0.793893 0.300000 0.042653 0.123412 0.833935 0.400000 0.027792 0.125476 0.846732 0.500000 0.020533 0.126398 0.853069 0.600000 0.016282 0.127022 0.856696 0.700000 0.013486 0.127450 0.859064 0.800000 0.011481 0.127502 0.861017 0.900000 0.010014 0.127755 0.862231 1.000000 0.008875 0.127893 0.863232 *********************************************************************************** Comp_times_steps_7.dat showsthe computational time for all 27 Gln4 protein ratios for 2 x 10^7 Gillespie iterations (transient +real time): Gln4 protein ratio, time in seconds, in minutes, in hours, in days *********************************EXAMPLE******************************************** 0.01 8.00 s 0.13 min 0.00 h 0.00 d 0.01 16.00 s 0.27 min 0.00 h 0.00 d 0.01 24.00 s 0.40 min 0.01 h 0.00 d 0.02 33.00 s 0.55 min 0.01 h 0.00 d 0.02 41.00 s 0.68 min 0.01 h 0.00 d 0.02 49.00 s 0.82 min 0.01 h 0.00 d 0.03 57.00 s 0.95 min 0.02 h 0.00 d 0.04 64.00 s 1.07 min 0.02 h 0.00 d 0.05 72.00 s 1.20 min 0.02 h 0.00 d 0.06 80.00 s 1.33 min 0.02 h 0.00 d 0.07 88.00 s 1.47 min 0.02 h 0.00 d 0.08 97.00 s 1.62 min 0.03 h 0.00 d 0.09 104.00 s 1.73 min 0.03 h 0.00 d 0.10 113.00 s 1.88 min 0.03 h 0.00 d 0.12 120.00 s 2.00 min 0.03 h 0.00 d 0.14 129.00 s 2.15 min 0.04 h 0.00 d 0.16 136.00 s 2.27 min 0.04 h 0.00 d 0.18 144.00 s 2.40 min 0.04 h 0.00 d 0.20 152.00 s 2.53 min 0.04 h 0.00 d 0.30 160.00 s 2.67 min 0.04 h 0.00 d 0.40 168.00 s 2.80 min 0.05 h 0.00 d 0.50 176.00 s 2.93 min 0.05 h 0.00 d 0.60 184.00 s 3.07 min 0.05 h 0.00 d 0.70 191.00 s 3.18 min 0.05 h 0.00 d 0.80 199.00 s 3.32 min 0.06 h 0.00 d 0.90 207.00 s 3.45 min 0.06 h 0.00 d 1.00 215.00 s 3.58 min 0.06 h 0.00 d *********************************************************************************** ----------------------------------------------------------------------------------------------- //ATTRIBUTION PARTIES ----------------------------------------------------------------------------------------------- The SSM model and its iterations has been developed by Corina Keller, M.Carmen Romano and Ian Stansfield. The work has been carried out at University of Aberdeen, UK, and has been funded by BBSRC. ----------------------------------------------------------------------------------------------- //AUTHORS ----------------------------------------------------------------------------------------------- The SSM code has been developed by Corina Keller. ----------------------------------------------------------------------------------------------- //PUBLICATIONS ----------------------------------------------------------------------------------------------- The SSM model was developed to support the following publication. If you use the code, please refer to this publication: - to be added - (* submitted to NUCLEIC ACIDS RESEARCH The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Matthew R. McFarland, Corina Keller, Brandon Childers, Holly Corrigall, Adélaïde Raguin, M. Carmen Romano, Ian Stansfield. *) ----------------------------------------------------------------------------------------------- //CORRESPONDENCE ----------------------------------------------------------------------------------------------- i.stansfield@abdn.ac.uk ----------------------------------------------------------------------------------------------- //LICENSE ----------------------------------------------------------------------------------------------- Creative Commoms BY-NC find here: https://creativecommons.org/licenses/by-nc/4.0/ You are free to: Share — copy and redistribute the material in any medium or format Adapt — remix, transform, and build upon the material The licensor cannot revoke these freedoms as long as you follow the license terms. Under the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. NonCommercial — You may not use the material for commercial purposes. No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. Notices: You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation. No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.