DOI: 10.5061/dryad.6wwpzgn70
title: Data from: Modulating peptide co-assembly via macromolecular crowding: Recipes for co-assembled structures

description: Peptide-based biomaterials are commonly found in applications such as
 tissue engineering, wound healing, and drug delivery. Control over the
 size and morphology of the peptide supramolecular structure remains a
 challenge. One way to influence peptide assembly is through macromolecular
 crowding. Here we use discontinuous molecular dynamics simulation combined
 with the PRIME20 force field to investigate the effect of hydrophobic
 crowders on the architecture of co-assembled peptide aggregates. The
 peptide system used in this work is a mixture of oppositely-charged
 synthetic peptides: “CATCH(6K+)” (KQKFKFKFKQK) and “CATCH(6E-)”
 (EQEFEFEFEQE). The systems explored contained a mixture of 50 CATCH(6K+)
 and 50 CATCH (6E-) peptides at peptide concentrations of 5 mM and 20 mM,
 and crowders with diameters of 10, 20, 40 and 80 Å. Crowders were modeled
 as spheres with either hard-sphere or square-well/square-shoulder
 interactions. At low concentrations where CATCH co-assembly typically does
 not occur, the crowders were effective chaperones to trigger co-assembly.
 Small hard-sphere crowders promoted formation of multilayer fibrils. Large
 highly hydrophobic crowders promoted the formation of monolayer β-sheet
 structures and suppressed the formation of fibril structures. Overall, the
 simulations demonstrate that the crowder size and crowder-sidechain
 interaction strength govern the supramolecular architecture of peptide
 co-assemblies.   
description: # Dataset from Modulating peptide co-assembly via macromolecular crowding:
 Recipes for co-assembled structures --- Modulating peptide co-assembly via
 macromolecular crowding: Recipes for co-assembled structures. *Nanoscale*
 This directory contains the results from coarse-grained discontinuous
 molecular dynamics (PRIME20/DMD) simulations for the investigating the
 impact of macromolecular crowding on peptide co-assembly. ## General
 overview of data included Coordinate files from simulations are archived
 and compressed using tar and gzip. | tarball name | description | |
 ------------------- |
 --------------------------------------------------------------------------------------------------------------------------------- | | 6K6E\_DMD.tar.gz | contains results and files relating to PRIME20/DMD simulations for systems of CATCH(6K/6E) peptides in the *absence* of crowders | | crowder\_DMD.tar.gz | contains results and files relating to PRIME20/DMD simulations for systems of CATCH(6K/6E) peptides in the *presence* of crowders | 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 .`. Additionally, a python script, *read_bptnr.py*, is included to open read files with a .bptnr extension. These files are described in the next section. ## PRIME20 discontinuous molecular dynamics (DMD) simulations 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 with a .bptnr extension contain information regarding hydrogen bonding partners. However, the very first file *run0000.bptnr* is empty as no assembly is present at the beginning of the simulation. Files that are generated during the simulation start at *run0001.bptnr* and 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. ## 6K6E\_DMD.tar.gz The **6K6E_DMD.tar.gz** contains the final results relating to PRIME20/DMD simulations of systems containing CATCH(6K+) and (6E-) peptides. The directory names describe the system. For example, the directory "c05cr00-1": "c05" indicates a peptide concentration of 5 mM, "cr00" indicates no crowders are present, and "-1" is the simulation number (each system was simulated in triplicate). 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](https://github.com/CarolHall-NCSU-CBE/Serial-DMD-PRIME20). ``` . └── . ├── c05cr00-1 │   └── results │   ├── run0000.bptnr │   ├── run0001.bptnr │   ├── run0001.pdb │   ├── run0002.bptnr │   ├── run0002.pdb │   ├── run0003.bptnr │   ├── run0003.pdb │   ├── run0004.bptnr │   ├── run0004.pdb │   ├── run0005.bptnr │   ├── run0005.pdb │   ├── run0006.bptnr │   ├── run0006.pdb │   ├── run0007.bptnr │   ├── run0007.pdb │   ├── run0008.bptnr │   ├── run0008.pdb │   ├── run0009.bptnr │   ├── run0009.pdb │   ├── run0010.bptnr │   ├── run0010.pdb ├── c05cr00-2 │   └── results ├── c05cr00-3 │   └── results ├── c20cr00-1 │   └── results ├── c20cr00-2 │   └── results └── c20cr00-3 └── results ``` ## crowder\_DMD.tar.gz The **crowder_DMD.tar.gz** contains the final results relating to PRIME20/DMD simulations simulations of systems containing CATCH(6K+) and (6E-) peptides in the presence of crowders. The directory names describe the system. For example, the directory "c05cr10e00-1": "c05" indicates a peptide concentration of 5 mM, "cr10" indicates a crowder diameter of 10 Å, "e00" indicates a crowder-peptide interaction strength of 0ε (see manuscript for more detail), and "-1" is the simulation number (each system was simulated in triplicate). 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](https://github.com/CarolHall-NCSU-CBE/Serial-DMD-PRIME20). ``` . └── . ├── c05cr10e00-1 │   └── results │   ├── run0000.bptnr │   ├── run0001.bptnr │   ├── run0001.pdb │   ├── run0002.bptnr │   ├── run0002.pdb │   ├── run0003.bptnr │   ├── run0003.pdb │   ├── run0004.bptnr │   ├── run0004.pdb │   ├── run0005.bptnr │   ├── run0005.pdb │   ├── run0006.bptnr │   ├── run0006.pdb │   ├── run0007.bptnr │   ├── run0007.pdb │   ├── run0008.bptnr │   ├── run0008.pdb │   ├── run0009.bptnr │   ├── run0009.pdb │   ├── run0010.bptnr │   ├── run0010.pdb ├── c05cr10e00-2 ├── c05cr10e00-3 ├── c05cr10e01-1 ├── c05cr10e01-2 ├── c05cr10e01-3 ├── c05cr10e02-1 ├── c05cr10e02-2 ├── c05cr10e02-3 ├── c05cr10e05-1 ├── c05cr10e05-2 ├── c05cr10e05-3 ├── c05cr10ehf-1 ├── c05cr10ehf-2 ├── c05cr10ehf-3 ├── c05cr20e00-1 ├── c05cr20e00-2 ├── c05cr20e00-3 ├── c05cr20e01-1 ├── c05cr20e01-2 ├── c05cr20e01-3 ├── c05cr20e02-1 ├── c05cr20e02-2 ├── c05cr20e02-3 ├── c05cr20e05-1 ├── c05cr20e05-2 ├── c05cr20e05-3 ├── c05cr20ehf-1 ├── c05cr20ehf-2 ├── c05cr20ehf-3 ├── c05cr40e00-1 ├── c05cr40e00-2 ├── c05cr40e00-3 ├── c05cr40e01-1 ├── c05cr40e01-2 ├── c05cr40e01-3 ├── c05cr40e02-1 ├── c05cr40e02-2 ├── c05cr40e02-3 ├── c05cr40e05-1 ├── c05cr40e05-2 ├── c05cr40e05-3 ├── c05cr40ehf-1 ├── c05cr40ehf-2 ├── c05cr40ehf-3 ├── c05cr80e00-1 ├── c05cr80e00-2 ├── c05cr80e00-3 ├── c05cr80e01-1 ├── c05cr80e01-2 ├── c05cr80e01-3 ├── c05cr80e02-1 ├── c05cr80e02-2 ├── c05cr80e02-3 ├── c05cr80e05-1 ├── c05cr80e05-2 ├── c05cr80e05-3 ├── c05cr80ehf-1 ├── c05cr80ehf-2 ├── c05cr80ehf-3 ├── c20cr10e00-1 ├── c20cr10e00-2 ├── c20cr10e00-3 ├── c20cr10e01-1 ├── c20cr10e01-2 ├── c20cr10e01-3 ├── c20cr10e02-1 ├── c20cr10e02-2 ├── c20cr10e02-3 ├── c20cr10e05-1 ├── c20cr10e05-2 ├── c20cr10e05-3 ├── c20cr10ehf-1 ├── c20cr10ehf-2 ├── c20cr10ehf-3 ├── c20cr20e00-1 ├── c20cr20e00-2 ├── c20cr20e00-3 ├── c20cr20e01-1 ├── c20cr20e01-2 ├── c20cr20e01-3 ├── c20cr20e02-1 ├── c20cr20e02-2 ├── c20cr20e02-3 ├── c20cr20e05-1 ├── c20cr20e05-2 ├── c20cr20e05-3 ├── c20cr20ehf-1 ├── c20cr20ehf-2 ├── c20cr20ehf-3 ├── c20cr40e00-1 ├── c20cr40e00-2 ├── c20cr40e00-3 ├── c20cr40e01-1 ├── c20cr40e01-2 ├── c20cr40e01-3 ├── c20cr40e02-1 ├── c20cr40e02-2 ├── c20cr40e02-3 ├── c20cr40e05-1 ├── c20cr40e05-2 ├── c20cr40e05-3 ├── c20cr40ehf-1 ├── c20cr40ehf-2 ├── c20cr40ehf-3 ├── c20cr80e00-1 ├── c20cr80e00-2 ├── c20cr80e00-3 ├── c20cr80e01-1 ├── c20cr80e01-2 ├── c20cr80e01-3 ├── c20cr80e02-1 ├── c20cr80e02-2 ├── c20cr80e02-3 ├── c20cr80e05-1 ├── c20cr80e05-2 ├── c20cr80e05-3 ├── c20cr80ehf-1 ├── c20cr80ehf-2 └── c20cr80ehf-3 ``` ## Usage Notes ### Reading files with a .pdb extension The .pdb files are human readable. The content of the .pdb files can be viewed with any text editor such as Sublime Text, Notepad++, TextEdit, etc. The .pdb file can also be loaded into a visualization software such as Visual Molecular Dynamics (VMD) or Chimera to produce a visual representation of the coordinates. ### Reading files with a .bptnr extension The .bptnr files are unformatted. These files can be read by using the format edit descriptor `(i8,Ni4)` where `i8` is an integer that describes the collision number and `N` is the total of number of beads in the system. The format edit descriptor can be used to write a Fortran or Python program (using [FortranFile)](https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.FortranFile.html) to read in the file. A python script *read_bptnr.py* has been provided in this repository to aid in opening and reading these files. The script takes in two arguments: (1) the path of the .bptnr file to be read and (2) the total number of coarse-grained beads in the system. Each system contains 100 CATCH peptides. Each peptide is represented by 44 coarse-grained beads. For considering only the peptides, this is a total of 4400 beads. Each crowder is represented by 1 coarse-grained bead. The number of crowders and total number of coarse-grained beads in each system considered is summarized in the table below. | Peptide Concentration (mM) | Crowder Diameter (Å) | # of crowder beads | total # of beads | | -------------------------- | -------------------- | ------------------ | ---------------- | | 5 | 10 | 12634 | 17034 | | | 20 | 1579 | 5979 | | | 40 | 197 | 4597 | | | 80 | 25 | 4425 | | 20 | 10 | 3148 | 7548 | | | 20 | 394 | 4794 | | | 40 | 49 | 4449 | | | 80 | 6 | 4406 | The script returns the final hydrogen bonding partners in the snapshot. This information is represented using two columns of integers. The first column is the bead number. The second column is the hydrogen bonding partner. When the second column contains a value of 0, this indicates that the coarse-grained bead in the first column does not have a hydrogen bonding partner. #### *read_bptnr.py* usage example For example, to read the 'run0020.bptnr' from the simulation with the directory name c20cr10e00-1, we would use the following command ```python read_bptnr.py run0020.bptnr 7548 ``` This would return the following: ``` 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 0 10 0 11 0 12 4123 13 3462 14 4121 15 3460 16 4119 17 3458 18 4117 19 3456 20 4115 21 0 22 0 23 4112 24 3451 25 4110 26 3449 27 4108 28 3447 ... ``` The output indicates that beads 1-11, 21, and 22 do not have hydrogen bonds. While bead 12 is hydrogen bonding to bead 4123, and so forth. ## Code/Software Availability [PRIME20/DMD code](https://github.com/CarolHall-NCSU-CBE/Serial-DMD-PRIME20)