Data from: programming co-assembled peptide nanofiber morphology via anionic amino acid type: insights from molecular dynamics simulations
Data files
Nov 28, 2023 version files 27.68 GB
Abstract
Co-assembling peptides can be crafted into supramolecular biomaterials for use in biotechnological applications, such as cell culture scaffolds, drug delivery, biosensors, and tissue engineering. Peptide co-assembly refers to the spontaneous organization of two different peptides into a supramolecular architecture. Here we use molecular dynamics simulations to quantify the effect of anionic amino acid type on co-assembly dynamics and nanofiber structure in binary CATCH(+/-) peptide systems. CATCH peptide sequences follow a general pattern: CQCFCFCFCQC, where all C’s are either a positively charged or a negatively charged amino acid. Specifically, we investigate the effect of substituting aspartic acid residues for the glutamic acid residues in the established CATCH(6E-) molecule, while keeping CATCH(6K+) unchanged. Our results show that structures consisting of CATCH(6K+) and CATCH(6D-) form flatter β-sheets, have stronger interactions between charged residues on opposing β-sheet faces, and have slower co-assembly kinetics than structures consisting of CATCH(6K+) and CATCH(6E-). Knowledge of the effect of sidechain type on assembly dynamics and fibrillar structure can help guide the development of advanced biomaterials and grant insight into sequence-to-structure relationships.
README: Dataset from Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations Dataset
Dong X, Liu R, Seroski DT, Hudalla GA, Hall CK. Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations. PLOS Computational Biology.
This directory contains the results and the analysis from atomistic molecular dynamics simulations (AMBER/MD) and coarse-grained discontinuous molecular dynamics (PRIME20/DMD) simulations for the investigation of amino acid type on co-assembled peptide nanofiber morphology.
Table of Contents
- General overview of data included
- Description of output simulation data files used for analysis
- Description of scripts and software used for simulation analysis and the resulting output data analysis files
- File tree and general description of subdirectories and file organization for each tarball
- Code/Software Availability
General overview of data included <a name="general-overview"></a>
Coordinate files and analysis outputs from simulations are archived and compressed using tar and gzip. Files are organized in a similar structure to the manuscript. Parameter and topology files are included for MD simulations.
| tarball name | description |
|---|---|
| annealing-catch-repo.tar.gz | contains results and files relating to MD single bilayer and two stacked bilayer simulations |
| catch-remd-repo.tar.gz | contains results and files relating to REMD simulations of single CATCH peptide |
| catch-stacking-repo.tar.gz | contains results and files relating to MD two separated bilayer simulations |
| CATCH.DMD.tar.gz | contains results and files relating to PRIME20/DMD simulations |
To preview the files within each tarball use the following command: tar -tf tarball.tar.gz. A file tree has been created for each tarball. These can be recreated using the tree command: tar -tf tarball.tar.gz | tree --fromfile ..
Description of output simulation data files used for analysis <a name="output"></a>
AMBER molecular dynamics (MD) simulations
Each AMBER MD simulation produces a final coordinate file necessary for analysis. The coordinate files have a mdcrd file extension. For traditional MD simulations, the files are labeled equil40.mdcrd, signifying the 40th equilibration run, corresponding to 200 ns. For REMD (replica exchange molecular dynamics), the files are labeled remd.310K.mdcrd corresponding to the system at T = 310 K. Paired with each coordinate file is a parameter-topology file with a prmtop file extension. Both coordinate and parameter-topology files are contained in the same directory for each peptide system.
PRIME20 discontinous molecular dynamics (DMD) simulations <a name="simulation-output-data"></a>
PRIME20/DMD simulations produce two main files used for analysis: coordinate files with a pdb file extensions, and data files specifying hydrogen bonding partners with a bptnr file extension.
Coordinate files follow the standard Protein Data Bank file format.
Data files regarding hydrogen bonding partners with a bptnr extension contain a single column of integers. The first row corresponds to the collision number, the following rows corresponds to the index of the hydrogen bonding partner. As an example, consider the following snippet:
run0509.bptnr
100
30
62
...
In this data file, we are given the hydrogen bonding information for collision number 100. The 1st coarse-grained bead is hydrogen bonded to the 30th coarse-grained bead. The 2nd coarse-grained bead is hydrogen bonded to the 62nd coarse-grained bead, and so forth. Hydrogen bonding information is automatically calculated and outputed as part of the PRIME20/DMD software package.
Description of scripts and software used for simulation analysis and the resulting output data analysis files <a name="scripts"></a>
Here we describe the scripts and software used to analyze the outputs of molecular dyanamics simulations. All molecular dynamics simulations are run using AMBER (Assisted Model Building with Energy Refinement) software. CPPTRAJ is a program within AMBER used to proccess coordinate trajectories and data files. CPPTRAJ is the main tool used to analyze our simulation outputs.
Generally, the AMBER20 package was used for MD simulation and analysis. Tools and packages availaible within CPPTRAJ and AMBER are dependent on the system administrator and the installation process chosen for the AMBER package. Instructions for installing AMBER is beyond the scope of this README file.
Each analysis/calculation is done independently of one another. As such, a general workflow for each analysis can be described as follows:
- Data Preparation - i.e. running the desired simulation
- Running CPPTRAJ or MM/GBSA
- Results
- Interpretation
For ease of reading and comprehension, the following subsections are organized as follows:
- subtitle describing calcuation or analyis
- a manual page link for commands used, provided as a reference for the user's curiosity, and to properly cite where variable descriptions are quoted from
- a generic example of an input script used for calculation
- command used to submit a script
- an example and description of the resulting output file
Ellipses ... are used to indicate that a section of text has been omitted for conciseness.
Contact map calculation <a name="contact"></a>
nativecontacts manual page\
input: contacts.in
parm 6K6D-01/6K6D.prmtop # loading parameter-topology file
trajin 6K6D-01/equil40.mdcrd # loading coordinate file
nativecontacts name 6K6D-01 !(:NME,ACE,WAT) byresidue # calling nativecontacts
run # running command
The nativecontacts command has the following syntax:
nativecontacts [name <dsname>] [<mask1>] [byresidue]
where:\
[name <dsname>] Data set name.\
<mask1> First mask to calculate contacts for.\
[byresidue] Write out the contact map by residue instead of by atom.
cpptraj < contacts.in
output: native.6K6D-01, nonnative.6K6D-01 for native and nonnative contacts, respectively
#Residue Residue Contacts
2.000 2.000 0.0000
3.000 2.000 23.5760
4.000 2.000 15.1536
5.000 2.000 68.7520
6.000 2.000 1.0392
7.000 2.000 0.0608
8.000 2.000 0.0000
9.000 2.000 0.0000
10.000 2.000 0.0000
Where the first two columns are the first and second residue number, and Contacts is the total number of contacts involved with the residue pair.
DSSP (Define Secondary Structure of Proteins) analysis <a name="dssp"></a>
secstruct manual page\
input: sec.in
parm 6D.prmtop # loading parameter-topology file
trajin remd.310K.mdcrd # loading coordinate file
secstruct dssp out dssp.out # calling secstruct command
run # running command
The secstruct command has the following syntax:
secstruct [name <dsname>] [out <filename>]
where:\
[name <dsname>] Data set name.\
[out <filename>] Output file name for secondary structure vs time.
cpptraj < sec.in
output: dssp.out.sum
#Residue Extended Bridge 3-10 Alpha Pi Turn Bend
1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 0.0000 0.0008 0.1359 0.0627 0.0000 0.1930 0.0000
3 0.0001 0.0003 0.1987 0.1758 0.0001 0.2521 0.0000
4 0.0000 0.0002 0.2674 0.2691 0.0002 0.2407 0.0978
5 0.0000 0.0010 0.2312 0.3669 0.0003 0.2470 0.0895
6 0.0001 0.0003 0.2033 0.4286 0.0004 0.2069 0.0851
7 0.0001 0.0003 0.1797 0.4604 0.0005 0.2190 0.0901
8 0.0000 0.0003 0.1653 0.4666 0.0005 0.2095 0.0682
9 0.0000 0.0001 0.1695 0.4298 0.0004 0.2475 0.1008
10 0.0001 0.0001 0.1689 0.3286 0.0003 0.2957 0.0911
11 0.0001 0.0008 0.1297 0.2081 0.0002 0.3507 0.0000
12 0.0001 0.0006 0.0722 0.1153 0.0001 0.2881 0.0000
13 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Where #Residue is the residue number, Extended is the total fraction of extended structure vs time, Bridge is the total fraction of bridge structure vs time, and so forth.
Hydrogen bonding analysis <a name="hbcalc"></a>
hbond manual page\
avg manual page\
input: hbond_calc.in
parm 6K6E-01/6K6E.prmtop # loading parameter-topology file
trajin 6K6E-01/equil40.mdcrd # loading coordinate file
hbond 6K6E-01 donormask :157-468&:LYS acceptormask :157-468&:GLU,ASP nointramol # calling hbond command
run # running command
avg 6K6E-01[UU] out hb_avg_summary.out # calculating average of 6K6E-01[UU] dataset and writing average to hb_avg_summary.out
The hbond command has the following syntax:
hbond [name <dsname>] [donormask <dmask> [acceptormask <amask>] [nointramol]
where:\
[name <dsname>] Data set name.\
[donormask <dmask>] Use atoms in <dmask> as solute donor heavy atoms.\
[acceptormask <amask>] Use atoms in <amask> as solute acceptor atoms.\
[nointramol] Ignore intramolecular hydrogen bonds.
cpptraj < hbond_calc.in
output: hb_avg_summary.out
#Set <name>[avg] <name>[sd] <name>[ymin] <name>[ymax] <name>[yminidx] <name>[ymaxidx] <name>[names]
1 133.4 7.493 111 156 814 1046 "6K6E-01[UU]"
where:\
<name>[avg] Average of each set.\
<name>[sd] Standard deviation of each set.\
<name>[ymin] Y minimum of each set.\
<name>[ymax] Y maximum of each set.\
<name>[yminidx] Index of minimum Y value.\
<name>[ymaxidx] Index of maximum Y value.\
<name>[names] Name of each set.
For salt bridge calculations, the hbond command is also used, and the results are written to the file sb_avg_summary.out.
LIE (Linear interaction energy) analysis <a name="lie"></a>
lie manual page\
input: lie.in
parm 6K6D-01/6K6D.prmtop # loading parameter-topology file
trajin 6K6D-01/equil40.mdcrd # loading coordinate file
lie 6K6D-01 :LYS&!(@CA,C,O,N,H) :ASP&!(@CA,C,O,N,H) out 6K6D-01alie.out
run
avg 6K6D-01[EVDW] out lie_avg.out
The lie command has the following syntax:
lie [<name>] <Ligand mask> <Surroundings mask> [out <filename>]
where:\
<name> Data set name.\
<Ligand mask> Use atoms in <Ligand mask> as ligand atoms.\
<Surroundings mask> Use atoms in <Surroundings mask> as receptor atoms.
cpptraj < lie.in
output: 6K6D-01alie.out
#Frame [EELEC] [EVDW]
1 -1784.8048 -35.2083
2 -1731.6592 -61.9032
3 -1702.1564 -64.1674
4 -1570.4323 -73.3063
5 -1627.9084 -53.4717
6 -1641.7948 -66.5225
7 -1670.8649 -64.5885
8 -1740.3879 -51.1118
9 -1811.9532 -51.9266
...
Where #Frame is the frame number, [EELEC] is the electrostatic energy (kcal/mol), and [EVDW] is the van der Waals energy (kcal/mol).
MM/GBSA (Molecular mechanics with generalised Born and surface area solvation) analysis <a name="mmgbsa"></a>
MM/GBSA tutorial\
input: mmgbsa.in, pep.prmtop, pep_nowater.prmtop, rec.prmtop, lig.prmtop
where:\
pep.prmtop is the solvated complex parameter-topology file.\
pep_nowater.prmtop is the complex parameter-topology file.\
rec.prmtop is the receptor parameter-topology file.\
lig.prmtop is the ligand parameter-topology file.
mmgbsa.in
&general
endframe=1250
/
&gb
igb=2, saltcon=0.00
/
This input file is divided into two sections: general and gb. The 'endframe' variable sets which frame of the mdcrd to stop on. The presence of the '&gb' lets the script know to perform MM-GBSA calculations with the given input values. Where igb=2 specifies the Generalized Born method used and saltcon=0.00 specifies the salt concentration of the system.
Calling the MMPBSA.py provided in the AMBER package:
$AMBERHOME/bin/MMPBSA.py -O -i mmgbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp pep.prmtop -cp pep_nowater.prmtop -rp rec.prmtop -lp lig.prmtop -y equil40.mdcrd
output: FINAL_RESULTS_MMPBSA.dat
...
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -242.4318 17.1318 1.0835
EEL -2110.0628 479.1307 30.3029
...
Where VDWAALS is van der Waals contribution from MM and EEL is the electrostatic energy as calculated by the MM force field.
File tree and general description of subdirectories and file organization for each tarball <a name="file-tree"></a>
Calculations and analysis are done using scripts from the AMBER package as previously described. Please refer to the AMBER manual for more details. In the descriptions the "*" is used as a wildcard character to be interpreted as a possible string of characters.
annealing-catch-repo.tar.gz <a name="annealing-catch-repo-tree"></a>
The annealing-catch-repo.tar.gz tarball contains files pertaining to atomistic MD simulations (using the AMBER forcefield) of single bilayer and two stacked bilayer structures of CATCH peptides. Each simulation had an annealing stage prior to equilibration.
The directory annealing-catchff14SB contains the subdirectories n12L2 and n12L4 which correspond to the single bilayer result files and stacked bilayer result files, respectively. The subdirectory structures contains the starting structures for each simulation.
Within n12L2 and n12L4 are subdirectories that are labeled systematically based on the CATCH system and the simulation run number, for example "4K4D-01" refers to the CATCH(4K+/4D-) system and is the 1st in a triplicate of simulations. Each directory that is labeled by a CATCH system name contains generally the following: the topology file (.prmtop extension), the input coordinates (.rst7 extension), along with the final simulation coordinates (equil*.mdcrd and equil*.pdb). For more information regarding these files, please refer to the AMBER manual.
Within n12L2 are subdirectories regarding analysis of the results. n12L2analysis contains outputs from MMGBSA (FINAL_RESULTS_MMPBSA.dat), LIE analysis (*lie.out), results for calculating the number of salt bridges (sb), and results for calculating the number of backbone (bb) and intramolecular (intra) hydrogen bonds (hb). The *n12L2contacts directory contains results for calculating the number of native and nonnative contacts within each simulation system.
Within n12L4 are subdirectories regarding analysis of the results. The n12L4/hb_analysis contains results for calculating the number of hydrogen bonds. The n12L4/contacts directory contains results for calculating the number of native and nonnative contacts within each simulation system. The n12L4/results directy contains results of MMGBSA analysis. The n12L4/sb_analysis contains results of calculating the number of salt bridges within a system.
Inputs for MMGBSA and LIE analysis can be found in the n12L2 and n12L4 and are labeled mmgbsa.in and lie.in, respectively.
.
└── annealing-catchff14SB
├── n12L2
│ ├── 4K4D-01
│ │ ├── 4K4D.prmtop
│ │ ├── 4K4D.rst7
│ │ ├── 4K4D_nowater.prmtop
│ │ ├── 4K4D_nowater.rst7
│ │ ├── CATCH4K4Dn24.inp
│ │ ├── CATCH4K4Dn24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ ├── 4K4D-02
│ │ ├── 4K4D.prmtop
│ │ ├── 4K4D.rst7
│ │ ├── 4K4D_nowater.prmtop
│ │ ├── 4K4D_nowater.rst7
│ │ ├── CATCH4K4Dn24.inp
│ │ ├── CATCH4K4Dn24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ ├── 4K4D-03
│ │ ├── 4K4D.prmtop
│ │ ├── 4K4D.rst7
│ │ ├── 4K4D_nowater.prmtop
│ │ ├── 4K4D_nowater.rst7
│ │ ├── CATCH4K4Dn24.inp
│ │ ├── CATCH4K4Dn24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ ├── 4K4E-01
│ │ ├── 4K4E.prmtop
│ │ ├── 4K4E.rst7
│ │ ├── 4K4E_nowater.prmtop
│ │ ├── 4K4E_nowater.rst7
│ │ ├── CATCH4K4En24.inp
│ │ ├── CATCH4K4En24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ ├── 4K4E-02
│ │ ├── 4K4E.prmtop
│ │ ├── 4K4E.rst7
│ │ ├── 4K4E_nowater.prmtop
│ │ ├── 4K4E_nowater.rst7
│ │ ├── CATCH4K4En24.inp
│ │ ├── CATCH4K4En24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ ├── 4K4E-03
│ │ ├── 4K4E.prmtop
│ │ ├── 4K4E.rst7
│ │ ├── 4K4E_nowater.prmtop
│ │ ├── 4K4E_nowater.rst7
│ │ ├── CATCH4K4En24.inp
│ │ ├── CATCH4K4En24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ ├── 6K6D-01
│ │ ├── 6K6D-01.out
│ │ ├── 6K6D.prmtop
│ │ ├── 6K6D.rst7
│ │ ├── 6K6D_nowater.prmtop
│ │ ├── 6K6D_nowater.rst7
│ │ ├── CATCH6K6Dn24.inp
│ │ ├── CATCH6K6Dn24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6D-02
│ │ ├── 6K6D-02.out
│ │ ├── 6K6D.prmtop
│ │ ├── 6K6D.rst7
│ │ ├── 6K6D_nowater.prmtop
│ │ ├── 6K6D_nowater.rst7
│ │ ├── CATCH6K6Dn24.inp
│ │ ├── CATCH6K6Dn24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6D-03
│ │ ├── 6K6D-03.out
│ │ ├── 6K6D.prmtop
│ │ ├── 6K6D.rst7
│ │ ├── 6K6D_nowater.prmtop
│ │ ├── 6K6D_nowater.rst7
│ │ ├── CATCH6K6Dn24.inp
│ │ ├── CATCH6K6Dn24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6E-01
│ │ ├── 6K6E-01.out
│ │ ├── 6K6E.prmtop
│ │ ├── 6K6E.rst7
│ │ ├── 6K6E_nowater.prmtop
│ │ ├── 6K6E_nowater.rst7
│ │ ├── CATCH6K6En24.inp
│ │ ├── CATCH6K6En24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6E-02
│ │ ├── 6K6E-02.out
│ │ ├── 6K6E.prmtop
│ │ ├── 6K6E.rst7
│ │ ├── 6K6E_nowater.prmtop
│ │ ├── 6K6E_nowater.rst7
│ │ ├── CATCH6K6En24.inp
│ │ ├── CATCH6K6En24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6E-03
│ │ ├── 6K6E-03.out
│ │ ├── 6K6E.prmtop
│ │ ├── 6K6E.rst7
│ │ ├── 6K6E_nowater.prmtop
│ │ ├── 6K6E_nowater.rst7
│ │ ├── CATCH6K6En24.inp
│ │ ├── CATCH6K6En24.pdb
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6Econtacts.in
│ ├── bb_hb_calc.in
│ ├── cpptraj.log
│ ├── intra_hb_calc.in
│ ├── lie.in
│ ├── mmgbsa.in
│ ├── mmgbsa_script.in
│ ├── n12L2analysis
│ │ ├── 6K6D-01alie.out
│ │ ├── 6K6D-02alie.out
│ │ ├── 6K6D-03alie.out
│ │ ├── 6K6E-01alie.out
│ │ ├── 6K6E-02alie.out
│ │ ├── 6K6E-03alie.out
│ │ ├── lie_avg.out
│ │ ├── n12L2_bb_avg.out
│ │ ├── n12L2_intra_hb.out
│ │ └── n12L2_sb_avg.out
│ ├── n12L2contacts
│ │ ├── 6K6D-01equil40.pdb
│ │ ├── 6K6E-01equil40.pdb
│ │ ├── 6K6Econtacts.in
│ │ ├── contacts.in
│ │ ├── native.6K6D-01
│ │ ├── native.6K6D-02
│ │ ├── native.6K6D-03
│ │ ├── native.6K6E-01
│ │ ├── native.6K6E-02
│ │ ├── native.6K6E-03
│ │ ├── nonnative.6K6D-01
│ │ ├── nonnative.6K6D-02
│ │ ├── nonnative.6K6D-03
│ │ ├── nonnative.6K6E-01
│ │ ├── nonnative.6K6E-02
│ │ └── nonnative.6K6E-03
│ ├── nohup.out
│ ├── nohup2.out
│ └── salt_bridge_calc.in
├── n12L4
│ ├── 4K4D-01
│ │ ├── 4K4D.prmtop
│ │ ├── 4K4D.rst7
│ │ ├── 4K4D_nowater.prmtop
│ │ ├── 4K4D_nowater.rst7
│ │ ├── CATCH4K4Dn48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 4K4D-02
│ │ ├── 4K4D.prmtop
│ │ ├── 4K4D.rst7
│ │ ├── 4K4D_nowater.prmtop
│ │ ├── 4K4D_nowater.rst7
│ │ ├── CATCH4K4Dn48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 4K4D-03
│ │ ├── 4K4D.prmtop
│ │ ├── 4K4D.rst7
│ │ ├── 4K4D_nowater.prmtop
│ │ ├── 4K4D_nowater.rst7
│ │ ├── CATCH4K4Dn48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 4K4E-01
│ │ ├── 4K4E.prmtop
│ │ ├── 4K4E.rst7
│ │ ├── 4K4E_nowater.prmtop
│ │ ├── 4K4E_nowater.rst7
│ │ ├── CATCH4K4En48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 4K4E-02
│ │ ├── 4K4E.prmtop
│ │ ├── 4K4E.rst7
│ │ ├── 4K4E_nowater.prmtop
│ │ ├── 4K4E_nowater.rst7
│ │ ├── CATCH4K4En48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 4K4E-03
│ │ ├── 4K4E.prmtop
│ │ ├── 4K4E.rst7
│ │ ├── 4K4E_nowater.prmtop
│ │ ├── 4K4E_nowater.rst7
│ │ ├── CATCH4K4En48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6D-01
│ │ ├── 6K6D-01.out
│ │ ├── 6K6D.prmtop
│ │ ├── 6K6D.rst7
│ │ ├── 6K6D_nowater.prmtop
│ │ ├── 6K6D_nowater.rst7
│ │ ├── CATCH6K6Dn48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_run.out
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6D-02
│ │ ├── 6K6D-02.out
│ │ ├── 6K6D.prmtop
│ │ ├── 6K6D.rst7
│ │ ├── 6K6D_nowater.prmtop
│ │ ├── 6K6D_nowater.rst7
│ │ ├── CATCH6K6Dn48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_run.out
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6D-03
│ │ ├── 6K6D-03.out
│ │ ├── 6K6D.prmtop
│ │ ├── 6K6D.rst7
│ │ ├── 6K6D_nowater.prmtop
│ │ ├── 6K6D_nowater.rst7
│ │ ├── CATCH6K6Dn48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_run.out
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6E-01
│ │ ├── 6K6E-01.out
│ │ ├── 6K6E.prmtop
│ │ ├── 6K6E.rst7
│ │ ├── 6K6E_nowater.prmtop
│ │ ├── 6K6E_nowater.rst7
│ │ ├── CATCH6K6En48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_run.out
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6E-02
│ │ ├── 6K6E-02.out
│ │ ├── 6K6E.prmtop
│ │ ├── 6K6E.rst7
│ │ ├── 6K6E_nowater.prmtop
│ │ ├── 6K6E_nowater.rst7
│ │ ├── CATCH6K6En48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_run.out
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── 6K6E-03
│ │ ├── 6K6E-03.out
│ │ ├── 6K6E.prmtop
│ │ ├── 6K6E.rst7
│ │ ├── 6K6E_nowater.prmtop
│ │ ├── 6K6E_nowater.rst7
│ │ ├── CATCH6K6En48.pdb
│ │ ├── FINAL_RESULTS_MMPBSA.dat
│ │ ├── equil40.mdcrd
│ │ ├── equil40.pdb
│ │ ├── lig.prmtop
│ │ ├── mmgbsa.in
│ │ ├── mmgbsa_run.out
│ │ ├── mmgbsa_script.in
│ │ ├── rec.prmtop
│ ├── contacts
│ │ ├── 6K6Econtacts.in
│ │ ├── contacts.in
│ │ ├── native.6K6D-01
│ │ ├── native.6K6D-02
│ │ ├── native.6K6D-03
│ │ ├── native.6K6E-01
│ │ ├── native.6K6E-02
│ │ ├── native.6K6E-03
│ │ ├── nonnative.6K6D-01
│ │ ├── nonnative.6K6D-02
│ │ ├── nonnative.6K6D-03
│ │ ├── nonnative.6K6E-01
│ │ ├── nonnative.6K6E-02
│ │ └── nonnative.6K6E-03
│ ├── hb_analysis
│ │ └── hb_avg_summary.out
│ ├── hbond_calc.in
│ ├── mmgbsa.in
│ ├── mmgbsa_script.in
│ ├── nohup.out
│ ├── nohup2.out
│ ├── results
│ │ ├── 6K6D-01FINAL_RESULTS_MMPBSA.dat
│ │ ├── 6K6D-01alie.out
│ │ ├── 6K6D-01equil40.pdb
│ │ ├── 6K6D-02FINAL_RESULTS_MMPBSA.dat
│ │ ├── 6K6D-02alie.out
│ │ ├── 6K6D-02equil40.pdb
│ │ ├── 6K6D-03FINAL_RESULTS_MMPBSA.dat
│ │ ├── 6K6D-03alie.out
│ │ ├── 6K6D-03equil40.pdb
│ │ ├── 6K6E-01FINAL_RESULTS_MMPBSA.dat
│ │ ├── 6K6E-01alie.out
│ │ ├── 6K6E-01equil40.pdb
│ │ ├── 6K6E-02FINAL_RESULTS_MMPBSA.dat
│ │ ├── 6K6E-02alie.out
│ │ ├── 6K6E-02equil40.pdb
│ │ ├── 6K6E-03FINAL_RESULTS_MMPBSA.dat
│ │ ├── 6K6E-03alie.out
│ │ ├── 6K6E-03equil40.pdb
│ ├── salt_bridge_calc.in
│ └── sb_analysis
│ └── sb_avg_summary.out
└── structures
├── CATCH4K4Dn48.pdb
├── CATCH4K4En48.pdb
├── CATCH6K6Dn48.pdb
└── CATCH6K6En48.pdb
catch-remd-repo.tar.gz <a name="catch-remd-repo-tree"></a>
The catch-remd-repo.tar.gz tarball contains file pertaining to the Replica Exchange Molecular Dynamics (REMD) simulations for single CATCH peptides. The remd-catchff14sb contains the subdirectories 6D, 6E, and 6K, which correspond to the CATCH(6D-), (6E-), and (6K+) peptide, respectively. Within each CATCH peptide subdirectory contains the necessary files to replicate the REMD simulations and the final results. For more information regarding REMD and the purpose of these files, please refer to the AMBER manual.
For each system, we analyzed the secondary structure content for each system using the Define Secondary Structure of Proteins (DSSP) algorithm. Output files are labeled as "dssp.out" and "dssp.out.sum".
.
└── remd-catchff14sb
├── 6D
│ ├── 6D.pdb
│ ├── 6D.prmtop
│ ├── dssp.out.sum
│ ├── remd.310K.mdcrd
├── 6E
│ ├── 6E.pdb
│ ├── 6E.prmtop
│ ├── dssp.out.sum
│ ├── remd.310K.mdcrd
└── 6K
├── 6K.pdb
├── 6K.prmtop
├── dssp.out.sum
└── remd.310K.mdcrd
catch-stacking-repo.tar.gz <a name="catch-stacking-repo-tree"></a>
The catch-stacking-repo.tar.gz tarball contains results and files relating to MD two separated bilayer simulations.
Within catch-stacking-10A-annealing are subdirectories that are labeled systematically based on the CATCH system and the simulation run number, for example "6K6D-01" refers to the CATCH(6K+/6D-) system and is the 1st in a triplicate of simulations. Each directory that is labeled by a CATCH system name contains generally the following: the topology file (.prmtop extension), the input coordinates (.rst7 extension), along with the final simulation coordinates (equil*.mdcrd and equil*.pdb). For more information regarding these files, please refer to the AMBER manual.
The subdirectory stacking-contacts contains results for calculating the number of contacts between the two bilayers for the two separated bilayer simulations.
The subdirectory structures contains a copy of the starting structures for each simulation system.
.
└── catch-stacking-10A-annealing
├── 6K6D-01
│ ├── 6K6D.prmtop
│ ├── 6K6D.rst7
│ ├── 6K6D_nowater.prmtop
│ ├── 6K6D_nowater.rst7
│ ├── CATCH6K6Dn48.inp
│ ├── CATCH6K6Dn48.pdb
│ ├── equil1.mdcrd
│ ├── equil40.mdcrd
│ ├── equil40.pdb
├── 6K6D-02
│ ├── 6K6D.prmtop
│ ├── 6K6D.rst7
│ ├── 6K6D_nowater.prmtop
│ ├── 6K6D_nowater.rst7
│ ├── CATCH4K4Dn48.pdb
│ ├── CATCH4K4En48.pdb
│ ├── CATCH6K6Dn48.inp
│ ├── CATCH6K6Dn48.pdb
│ ├── CATCH6K6En48.pdb
│ ├── equil1.mdcrd
│ ├── equil40.mdcrd
│ ├── equil40.pdb
├── 6K6D-03
│ ├── 6K6D.prmtop
│ ├── 6K6D.rst7
│ ├── 6K6D_nowater.prmtop
│ ├── 6K6D_nowater.rst7
│ ├── CATCH6K6Dn48.inp
│ ├── CATCH6K6Dn48.pdb
│ ├── equil1.mdcrd
│ ├── equil40.mdcrd
│ ├── equil40.pdb
├── 6K6Dnohup.out
├── 6K6E-01
│ ├── 6K6E.prmtop
│ ├── 6K6E.rst7
│ ├── 6K6E_nowater.prmtop
│ ├── 6K6E_nowater.rst7
│ ├── CATCH6K6En48.inp
│ ├── CATCH6K6En48.pdb
│ ├── equil1.mdcrd
│ ├── equil40.mdcrd
│ ├── equil40.pdb
├── 6K6E-02
│ ├── 6K6E.prmtop
│ ├── 6K6E.rst7
│ ├── 6K6E_nowater.prmtop
│ ├── 6K6E_nowater.rst7
│ ├── CATCH6K6En48.inp
│ ├── CATCH6K6En48.pdb
│ ├── equil1.mdcrd
│ ├── equil40.mdcrd
│ ├── equil40.pdb
├── 6K6E-03
│ ├── 6K6E.prmtop
│ ├── 6K6E.rst7
│ ├── 6K6E_nowater.prmtop
│ ├── 6K6E_nowater.rst7
│ ├── CATCH6K6En48.inp
│ ├── CATCH6K6En48.pdb
│ ├── equil1.mdcrd
│ ├── equil40.mdcrd
│ ├── equil40.pdb
├── 6K6Enohup.out
── stacking-contacts
├── 6K6D-01contacts.out
├── 6K6D-01equil40.pdb
├── 6K6D-02contacts.out
├── 6K6D-02equil40.pdb
├── 6K6D-03contacts.out
├── 6K6D-03equil40.pdb
├── 6K6Dcontacts.in
├── 6K6Dcontacts.out
├── 6K6E-01contacts.out
├── 6K6E-01equil40.pdb
├── 6K6E-02contacts.out
├── 6K6E-02equil40.pdb
├── 6K6E-03contacts.out
├── 6K6E-03equil40.pdb
├── 6K6Econtacts.in
├── 6K6Econtacts.out
├── native.6K6D-01
├── native.6K6D-02
├── native.6K6D-03
├── native.6K6E-01
├── native.6K6E-02
├── native.6K6E-03
├── nonnative.6K6D-01
├── nonnative.6K6D-02
├── nonnative.6K6D-03
├── nonnative.6K6E-01
├── nonnative.6K6E-02
└── nonnative.6K6E-03
CATCH.DMD.tar.gz <a name="catch-dmd-tree"></a>
The CATCH.DMD.tar.gz contains the final results relating to PRIME20/DMD simulations. Provided are the coordinate files (.pdb extension) and files indicating the hydrogen bonding partners (.bptnr extension). More information regarding the simulations are provided in the associated manuscript and on the Hall group's GitHub.
.
└── CATCH.DMD
├── 6K6Dt018-01run0508.pdb
├── 6K6Dt018-01run0509.bptnr
├── 6K6Dt018-02n0509.bptnr
├── 6K6Dt018-02run0509.pdb
├── 6K6Dt018-03n0509.bptnr
├── 6K6Dt018-03run0509.pdb
├── 6K6Et018-01n0509.bptnr
├── 6K6Et018-01run0508.pdb
├── 6K6Et018-02n0509.bptnr
├── 6K6Et018-02run0509.pdb
├── 6K6Et018-03n0509.bptnr
└── 6K6Et018-03run0509.pdb
Code/Software Availability <a name="code-software-availability"></a>
Methods
Please refer to the manuscript for details.
Citation: Dong X, Liu R, Seroski DT, Hudalla GA, Hall CK. Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations. PLOS Computational Biology.