Protocol to study the oligomeric organization of single-span transmembrane peptides using molecular dynamics simulations

Autor: Mauricio P. Sica, Micaela V. Kortsarz, Angelines A. Morillas, Cristian R. Smulski
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: STAR Protocols, Vol 3, Iss 3, Pp 101636- (2022)
Druh dokumentu: article
ISSN: 2666-1667
DOI: 10.1016/j.xpro.2022.101636
Popis: Summary: Herein, you will find detailed information for the preparation of a coarse-grained array of peptides embedded in a lipid membrane. It contains all the steps to set up and run a molecular dynamic simulation using a coarse-grained approach. We provide analytical tools and scripts for generating a residue-level contact matrix between multiple peptides, as well as geometric analysis of arrangements between multiple peptides. This protocol was designed to study the organization of transmembrane peptides in an unbiased manner using computational approaches.For complete details on the use and execution of this protocol, please refer to Smulski et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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