LassoHTP: a High-throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

13 July 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Lasso peptides are a sub-class of ribosomally synthesized and post-translationally modified peptides with a slipknot conformation. Often with superior thermal stability, protease resistance, and antimicrobial activity, lasso peptides are promising candidates for bioengineering and pharmseutical applications. To enable high-throughput computational prediction and design of lasso peptides, we developed software, LassoHTP, for automatic lasso peptide structure construction and modeling. LassoHTP consists of three modules, including: scaffold constructor, mutant generator, and molecular dynamics (MD) simulator. Based on a user-provided sequence and conformational annotation, LassoHTP can either generate the structure and conformational ensemble as is or conduct random mutagenesis. We used LassoHTP to construct eight known lasso peptide structures de novo and to simulate their conformational ensembles from 100 ns MD simulations. For benchmarking, we calculated the root mean square deviation (RMSD) of these ensembles with reference to their experimental crystal or NMR PDB structures; we also compared these RMSD values against those of the MD ensembles that are initiated from the PDB structures. The results show that the RMSD values of the LassoHTP-initiated ensembles are highly similar to those of the PDB-initiated ensembles with the ∆RMSD ranging from 0.0 to 1.2 Å and averaging at 0.5 Å. LassoHTP offers a computational platform to develop strategies for lasso peptide prediction and design.

Keywords

High-throughput Modeling
RiPPs
Lasso Peptides

Supplementary materials

Title
Description
Actions
Title
SI pdf
Description
Sample codes; scaffold structure models; force field parameters; steered MD simulation protocol; sample input files; RMSD values for tested lasso peptides and their substructures (PDF)
Actions

Supplementary weblinks

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.