programming co-assembled peptide nanofiber morphology via anionic amino acid type: insights from molecular dynamics simulations

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,..., 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., , # Dataset from Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations Dataset

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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

1. [General overview of data included](#general-overview)
2. [Description of output simulation data files used for analysis](#output)
3. [Description of scripts and software used for simulation analysis and the resulting output data analysis files](#scripts)
* [Contact map calculation](#contact)
* [DSSP (Define Secondary S...