###################################################################################################################################### ----------------------------------- Electron Transfer (ET) Rate CALCULATION ------------------------------------------------- ###################################################################################################################################### REAMDE decribes the steps need to be followed to perform "Electron Transfer (ET) Rate" Calculations using Solvaccess, Pathways (VMD plugin), and SDA7. This tutorial describes the "Electron Transfer Rate Calculation Study" on proteins Cytochrome_f and Plastocyanine. Proteins are taken from protein data bank. PDB ID: 1TU2 which is the Complex of Nostoc Cytochrome F and Plastocyanin detremined with paramagnetic NMR experiment. For more info: Please read the research paper "R. Gabdouilline, R. Wade, JACS 2009, 131, 9230-9238". Date: 28 June 2016 Mentioned below is 3 steps procedure as follows: ###################################################################################################################################### ----------------------------------------------------- STEP 1 ------------------------------------------------------------------- ###################################################################################################################################### ####### PROCEDURE for Calculation of "Electron Transfer Couplings (T_DA)" and generation of "Reaction_Criteria_Files (.rxnac)" ####### ###################################################################################################################################### - define SDA_HOME as SDA software directory. COMMAND: export SDA_HOME="/path/to/SDA/installation/directory" - Go to your SDA example directory. COMMAND: cd $SDA_HOME/examples/cytf_pc_et - For running electron transfer couplings (T_DA). COMMAND: cd et_calc/ - Here, two proteins are Cytochrome_f and Plastocyanin for this example run. Consider two proteins p1 (Cytochrome_f.pdb) and p2 (Plastocyanin.pdb)." - p1 (Cytochrome_f.pdb) has a cofactor with electron donor (e.g. FE of HEC 254) - p2 (Plastocyanin.pdb) has a cofactor with electron acceptor (e.g. CU of CU2 106). - Make copy of two proteins as p1.pdb and p2.pdb COMMAND: cp Cytochrome_f.pdb p1.pdb COMMAND: cp Plastocyanin.pdb p2.pdb In this folder (~/et_calc/), electron transfer couplings (T_DA) are precomputed for SDA7 electron transfer rate calculation. First, the electron coupling (T_DA) from donor to the surface atoms of p1, as well as the T_DA from surface atoms of p2 to the acceptor atom, are calculated. This is done in this folder, PRIOR to the actual SDA7 simulation, because the proteins are considered as rigid bodies and those T_DA values won't change during the simulation. The rest of the ET pathway (interaction of surface atoms of p1 and p2) is computed during the SDA7 run, because it depends on the relative position of p1 and p2 during BD simulation. ------------------------------------------------------------ What you need to have: - two input pdb files (donor and acceptor) "!!!! CAUTION: Remove the "*" from atom names, if present in PDB files !!!!!" - vmd version 1.9.1 or later (must include the plugin "topotools") - the plugin "PATHWAYS" for VMD: http://people.chem.duke.edu/~ilya/Software/Pathways/docs/pathways.html -- follow the downloading and installing instructions, most notably: -- give user execution rights for pathcore program (chmod u+x pathcore) -- link plugin folder to PATH of your system (in .bashrc or .bashrc_user) -- if your pathways plugin crashes with error "cannot parse selection segid {}....", then use a adapted pathways.tcl to force segid = "0". This can be found here: /hits/fast/mcm/buelowsn/plug_vmd/pathways.tcl - python 2.7 ------------------------------------------------------------ What you need to do: - read [R. Gabdouilline, R. Wade, JACS 2009, 131, 9230-9238] for an explanation of the method - edit "et_prep_sda.sh" Script -- define location of "Solvaccess" and vmd "pathways" plugin -- define your protein name "prefixes" (without the .pdb) -- define donor "atom name" and "residue number" (resid) -- define acceptor "atom name" and "residue number" (resid) -- define the minimum solvent accessibility (s.a.). The higher the s.a., the more "surfacy" the atom is. JACS paper value is "1.0". -- define the minimum T_DA (JACS paper value = -8.0) of a surface atom pair from p1 and p2 to be considered for calculation during SDA7 run from the formula: ln (T_DA (1)) + ln (T_DA (2)) >= tda_limit, where 1 is a surface atom of p1 and 2 is a surface atom of p2 !! - make the following scripts executable: -- et_prep_sda.sh ### It will run all scripts one-by-one and generate final outputs as reaction_criteria files (.rxnac) ### -- topo_prep_sda.tcl ### Create .psf file with bond information, guessed from distances ### -- sc_prep_sda.tcl ### Script to calculate T_DA's between a central atom (donor/acceptor) and surface atoms, taken from input file ..._tda.dat ### -- asa_to_pw.py ### Read the list {...}_tda.dat and store together with solvent accessibility into file {...}_acc_TDA.dat ### -- create_inp_sda.py ### Read the files of solvent accessibility and T_DA for p1 and p2, Calculate, ### ### if ln(T_DA [1]) + ln(T_DA [2]) >= tda_limit , If yes: write the respective atoms in {...}_sda_et_inp.rxnac ### -- sort_asa.py ### Sorts Solvaccess output and only keeps atoms with solvent accessibility > threshold sac ### - run COMMAND: ./et_prep_sda.sh Note: "For more details: Please check inside the Scripts" -------------------------------------------------------------------- What you get: Aside from some intermediate/debugging output you should end up with two files: - {your_p1_name}_sda_et_inp.rxnac - {your_p2_name}_sda_et_inp.rxnac These two files should contain the same number of lines !! The first line of the p1 file defines the surface partner atom of the first line of the p2 file, and so on. The second last row are solvent accessibilities. The last row are natural log of T_DA between the cofactor and the surface atom. SDA7 reads the lines of the two files simultaneously, calculates the distance between all the pairs, and calculates an overall ET transfer rate. The two files have to be specified in SDA7 input: GROUP = ReactionCriteria et_sol1 = {your_p1_name}_sda_et_inp.rxnac et_sol2 = {your_p2_name}_sda_et_inp.rxnac computation = electron_transfer *** NOTE: Result of this example performed at HITS: *** *** You can compare the results with the ones provided in the "../et_calc_hits/" directory. *** ###################################################################################################################################### ----------------------------------------------------- STEP 2 ----------------------------------------------------------------- ###################################################### GRIDS GENERATION ############################################################ ###################################################################################################################################### Generate the Grids as per procedure given in Barnase-Barstar (Tutorial_SDA7) : Example script for preparing desolvation and hydrophobic grids and effective charges need to be run first to generate grids and effective charges. Script: "../../../examples/bnbs/prepare_grids_and_ecm/run_ed_hd_ecm.sh" "CAUTION: DO NOT RUN THIS SCRIPT AS IT IS !!! YOU NEED TO FOLLOW THESE STEPS ON YOUR PDBs TO GENERATE GRIDS." For the ET Rate Calculation exercise: Normally, you have to generate GRIDS for the proteins of your interest. Here, we have created the GRID files for you which are used in this example. Check the grid files here: - Go to the directory COMMAND: cd ../data_grid *** NOTE: If you want to gererate the GRID files for the proteins of your interest: *** *** FOLLOW THE STEPS, as per procedure given in Barnase-Barstar, ON YOUR PDBs TO GENERATE GRIDS *** The protein PDBs and generated grids have to be specified in SDA7 input. "!!!!!! CAUTION: Make sure the "input PDBs" used here are same as in "STEP 1" !!!!!" ###################################################################################################################################### ----------------------------------------------------- STEP 3 ----------------------------------------------------------------- ################################################## RUN SDA CALCULATIONS ############################################################ ###################################################################################################################################### SDA Simulations need to be run on order to calculate Electron Transfer Rate using the file generated from above exercise. For the ET Rate Calculation exercise: - Go to the directory COMMAND: cd ../run What you need to have: Input files: -- sda_et.in ### SDA input file. ### -- run_cytf_pc_et.sh ### RUN Script ### What you need to do: -- sda_et.in ### SDA input file. (Here, we run simulation for 50 runs 'nrun=50') ### edit "sda_et.in" Check for the required input files and parameters. Make sure the input files specified are present at mentioned path. -- run_cytf_pc_et.sh ### RUN Script ### edit "run_cytf_pc_et.sh" Provide the correct path of SDA binaries and input/output files. - run COMMAND: ./run_cytf_pc_et.sh What you get: Output generated as specified in "sda_et.in" file: -- sda_out_et ### Output of SDA run ### -- electron_transfer.log ### Output file containing Rate constant data ### After running SDA7, bootstrap: -- elect_boot.out ### Contains the rate k_ET dependent on factor W (see R. Gabdouilline, R. Wade, JACS 2009, 131, 9230-9238). ### Plot the data in Xmgrace using Script "xmgrace_plot_kET_data_SDA.xvg". Note: Result of this example performed at HITS: You can compare the results with the ones provided in the "$SDA_RUN/run_hits/" directory ###################################################################################################################################### ####################################################### END ##################################################################### ######################################################################################################################################