A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides. Issue 3 (23rd December 2021)

• Record Type: Journal Article
• Authors: Banerjee, Akash; Lu, Chien Yu; Dutt, Meenakshi
• Is Part Of: Physical chemistry chemical physics. Volume 24:Issue 3(2021)
• Page Start: 1553
• Page End: 1568
• Publication Date: 2021-12-23
• Subjects: Chemistry, Physical and theoretical -- Periodicals; 541.3
• DOI: 10.1039/d1cp04205j
• Languages: English
• ISSNs: 1463-9076

Abstract

Abstract : This hybrid coarse-grained model resolves the chemical structure of lipid-like peptides and their assembly. Atomistic resolution is reintroduced to study the relative organization of the peptides within an assembly. Abstract : Reconstituted photosynthetic proteins which are activated upon exposure to solar energy hold enormous potential for powering future solid state devices and solar cells. The functionality and integration of these proteins into such devices has been successfully enabled by lipid-like peptides. Yet, a fundamental understanding of the organization of these peptides with respect to the photosynthetic proteins and themselves remains unknown and is critical for guiding the design of such light-activated devices. This study investigates the relative organization of one such peptide sequence V6 K2 (V: valine and K: lysine) within assemblies. Given the expansive spatiotemporal scales associated with this study, a hybrid coarse-grained (CG) model which captures the structure, conformation and aggregation of the peptide is adopted. The CG model uses a combination of iterative Boltzmann inversion and force matching to provide insight into the relative organization of V6 K2 in assemblies. The CG model reproduces the structure of a V6 K2 peptide sequence along with its all atom (AA) solvation structure. The relative organization of multiple peptides in an assembly, as captured by CG simulations, is in agreement with corresponding results from AA simulations. Also, a backmapping procedure reintroduces the AA details of the peptides within the aggregates captured by the CG model to demonstrate the relative organization of the peptides. Furthermore, a large number of peptides self-assemble into an elongated micelle in the CG simulation, which is consistent with experimental findings. The coarse-graining procedure is tested for transferability to longer peptide sequences, and hence can be extended to other amphiphilic peptide sequences.