LysinebasedTrypsinActSite. A computer application for modeling Chymotrypsin

Transcription

1 LysinebasedTrypsinActSite A computer application for modeling Chymotrypsin Version.2 May 2006

2 LysTAS A computer application for modeling chymotrypsin Version.2 May 2006 Table of Contents Page. Introduction to the LysTAS 2 2. Requirements 2 3. Installing LysTAS on your Computer 2 4. Running LysTAS 3 5. Example (test runs) using the LysTAS application Amber99/SASA Charmm27/SASA Amber99/ASP Charmm27/ASP Amber99/HCT 5.6. Charmm27/HCT 2 6. Index of modules & Subroutine Calls 4 7. Contact Info 6

3 TrypsinActSite A tool for modelling chymotrypsin The application is based upon a molecular template which is comprised of a cyclic hexapeptide (Lys-Xaa-Lys-Asp-Lys-Xbb) with branches (Ace-Gly-Ala-Ser, Ace-Hid, Ace-Asp). It offers quite a lot of choices inside the framework hexapeptide and Lysine. Figure. Requirements We need to have installed the following:. A UNIX operating system. 2. TINKER molecular modeling software ( 3. Perl. Installation In order to install the program you just simply unzip it in the folder of your choice by typing the following command in the shell: 2

4 $shell: tar -zxvf tas.tar.gz Running. Input file (Recommended): $shell:./simtrypsin < input.file > output.file & Example of an input File: Comments /opt # Installation path of TINKER # Version of TINKER (4.) Gly # Xaa peptide (Fig. ) Gly # Xbb peptide (Fig. ) # Choice (specific D/L chirality) L L D L L D L D D # Peptide (Y - -Y 9 ) (Fig. ) L D L L D L L D D # Peptide 2 (Y - -Y 9 ) (Fig. ) D L L D L L L L L # Peptide 3 (Y - -Y 9 ) (Fig. ) D L D D L D D D L # Peptide 4 (Y - -Y 9 ) (Fig. ) # Leave this line blank to continue # The total time of MD (fs) # Time step length (fs) 2 # Time between dumps (ps) 300 # Temperature (K) SASA amber99 # Implicit Solvation model # Force Field 3

5 2. Command Prompt: $shell:./simtrypsin.pl By typing the previous command in the shell the following command prompts appear: ###################################### ## ## ## TrypsinActSite - A Tool For Modeling ChymoTrypsin ## ## ## ## Version.2 December 2006 ## ## ## ## ## ##################################### Enter the full path where the parameter directory of TINKER For instance if /usr/tinker enter /usr Path: /opt # If TINKER is installed at /opt/tinker/ the user just types /opt. Enter the version of TINKER you have installed (4. or 4.2) If you have 4.2 press 2 otherwise press [ 2 ]: # The user enters from the keyboard the version of the TINKER which is installed. Enter AminoAcid: Ala Enter AminoAcid2: Ala # AminoAcid is the Xaa depicted in the Figure. # AminoAcid2 is the Xbb depicted in the Figure. 4

6 Choose an option. Specific Sequence of Chiralities D/L 2. A symmetrical changes of D/L 3. All combinations of D/L) Enter ( or 2 or 3) [2]: # Option : The user enters a specific sequence. For example Y Y 2 Y 3 Y 4 Y 5 Y 6 Y 7 Y 8 Y 9 D L D D L D L L L Table. Y, Y 2, Y 3, Y 4, Y 5, Y 6, Y 7, Y 8, Y 9 see figure. # IF the user wants to continue entering another #sequence of chiralities types Y, otherwise he presses ENTER #(Carriage Return) to start the simulation. Enter a specific sequence of chiralities: D D D D D D D Enter another one, or <enter> to continue: D D D D D D L Enter another one, or <enter> to continue: L L L L L L L Enter another one, or <enter> to continue: # Press ENTER (Carriage Return) to continue. #Option 2: Symmetrical changes of D/L. # # The chirality of the residues into cycle positions i and i+3 are #substituted simultaneously each time. Therefore, Lys...Asp4, Xaa2... #Lys5, Lys3... Xaa6 make three pairs. Xaa2 and Xaa6 are simultaneously #substituted with the same residue. This operation is necessary in #order to retain symmetry in the molecule. These changes produce #2 3 = 8 combinations. The chiralities of Asp, His and Ser of the #catalytic triad changed independently and produced 2 3 = 8 new #combinations, so that the total number of combinations was #8 Χ 8 = 64. # # Option 3: All possible combinations of D/L. 5

7 # # The program creates input files for all the possible combinations of # D/L (Y, Y 2, Y 3, Y 4, Y 5, Y 6, Y 7, Y 8, Y 9 ). Enter the Number of Dynamics Steps to be Taken (fs) : Enter the Time Step Length in Femtoseconds [.0] : Enter Time between Dumps in Picoseconds [0.] : 2 Enter the Desired Temperature in Degrees K [298] : 300 Enter the Implicit Solvation Model [ASP/SASA/ONION/STILL/HCT/ACE/GBSA] : SASA 6

8 TEST RUNS The machine used for running the following tests constists of an AMD ATHLON.8 Ghz and 52 Mb RAM with RED HAT installed and running. ) AMBER99/SASA (Estimated run time ~ 3 hrs) INPUT /opt Gly Gly L L L L L L L L D SASA amber99 OUTPUT Peptide RMSd(%) d(%) d2(%) d3(%)

9 2) CHARMM27/SASA (Estimated run time ~ 3 hrs) INPUT /opt L L D L L D L D D SASA Charmm27 OUTPUT Peptide RMSd(%) d(%) d2(%) d3(%)

10 3) AMBER99/ASP (Estimated run time ~ 3 hrs) INPUT /opt L L L L L L L L D ASP amber99 OUTPUT Peptide RMSd(%) d(%) d2(%) d3(%)

11 4) CHARMM27/ASP (Estimated run time ~ 3 hrs) INPUT /opt L L L L L L L L D ASP charmm27 OUTPUT Peptide RMSd(%) d(%) d2(%) d3(%)

12 5) AMBER99/HCT (Estimated run time ~ 3 hrs) INPUT /opt L L L L L L L L D HCT amber99 OUTPUT Peptide RMSd(%) d(%) d2(%) d3(%)

13 6) CHARMM27/HCT (Estimated run time ~ 3 hours) INPUT /opt L L L L L L L L D HCT charmm27 OUTPUT Peptide RMSd(%) d(%) d2(%) d3(%)

14 Description of the test run. Input file o In the first line of the input file the user enters the path where is installed the TINKER molecular modeling software. o In the second line the user enters the version of the TINKER which is installed. For instance if it is 4.2 the user just types 2. o In the next two lines the user inputs the aminoacids which will be positioned in the Xaa and Xbb positions in the peptide (Figure ). o In the next line by entering you choose to build a peptide with a specific D/L chirality. o In the next lines the chiralities of the amino acids (Figure ) are entered. o otherwise press ENTER to continue (Carriage Return). o Then the total time of molecular dynamics is entered (fs). o The time interval(fs). o The interval between coordinate/trajectory(ps). o The implicit solvation model. o The temperature(k). Output file The output file shows in the second column the number of the peptide the percentage of the frames that have RMS 2 Å. In the second column the percentage of the frames that have RMS under 2 Å. In the third column the percentage of the frames that the distance between the atom of the hydrogen atom of the Histidine (HD) and the first oxygen atom of the Aspartic Acid (OD2) is 3 Å. In the fourth column the percentage of the frames that the distance between the atom of the hydrogen atom of the Histidine (HD) and the second oxygen atom of the Aspartic Acid (OD2) is 3 Å. In the fifth column the percentage of the frames that the distance between the hydrogen atom of the Serine (HG) and the nitrogen atom of the Histidine (NE2) is 3 Å. 3

15 Index of Perl scripts and modules amber99_to_charmm27: a program to convert amber94 to charmm27 force field in TINKER xyz format. Input file is in amber99 force field STDOUT gives charmm27. analyze.pl: "analyze.pl" accepts as input a ASCII file which contains the results. It outputs a ASCII file /results/results.txt where in the first column is the number of the peptide. In the second column the percentage of the frames that have RMS under 2. In the third column the percentage of the frames that the distance between the atom of the hydrogen atom of the Histidine (HD) and the first oxygen atom of the Aspartic Acid (OD2) is under 3 A. In the fourth column the percentage of the frames that the distance between the atom of the hydrogen atom of the Histidine (HD) and the second oxygen atom of the Aspartic Acid (OD2) is under 3 A. In the fifth column the percentage of the frames that the distance between the hydrogen atom of the Serine (HG) and the nitrogen atom of the Histidine (NE2) is under 3 A. atom_find.pm: finds the position of an atom in the xyz matrix and its used for connecting two atoms found in a xyz matrix. Accepts as input the ATOM TYPE, found in the amber99 parameter file and outputs the number (position) of the atom in the xyz matrix. Build_options.pm: "build_options.pm" creates the input files for building the peptides. The files are used as input for the TINKER executables => protein + xyzedit. Option 2: Symmetrical changes of D/L. The chirality of the residues into cycle positions i and i+3 are #substituted simultaneously each time. Therefore, Lys...Asp4, Xaa2... #Lys5, Lys3... Xaa6 make three pairs. Xaa2 and Xaa6 are simultaneously substituted with the same residue. This operation is necessary for retaining the symmetry in the molecule. These changes produce 2*2*2 = 8 combinations. 4

16 The chiralities of Asp, His and Ser of the catalytic triad changed independently and produced 2*2*2 = 8 new combinations, so that the total number of combinations was 8 * 8 = 64. Option 3: Builds 52 peptides with all the possible combinations of D/L s. connect_xyz.pm: "connect_xyz.pm" co-operating with atom_find.pm connects two atoms found in a XYZ matrix. Create_input.pm: This module creates the input files for building the sidechains aceaspnme, acealasernme, acehidnme, aceglnnme. data2sql.pl: Meazures the value of the a) RMS distance of the heavy atoms of the active site, b) the distance between the atom of the hydrogen atom of the Histidine (HD) and the first oxygen atom of the Aspartic Acid (OD2), c) the distance between the atom of the hydrogen atom of the Histidine (HD) and the second oxygen atom of the Aspartic Acid (OD2), d) the distance between the hydrogen atom of the Serine (HG) and the nitrogen atom of the Histidine (NE2) The script is executed internally by the simtrypsin.pl script geometry.pl: Finds the value of the interatomic distance, angle or dihedral angle defined by two to four input atoms. The subroutines that make the computations are modifications of the original tinker subroutine geometry.f. TINKER can be downloaded from 5

17 Contact info. For any comments, suggestions and bugs you can contact with the following Ioannis Demetropoulos : idimitr@cc.uoi.gr Vasileios Tatsis : btatsis@cc.uoi.gr 6