Samajdar, R. | bioRxiv Science

bioRxiv2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, non-equilibrium Greens function-density functional theory (NEGF-DFT) calculations, and unsupervised machine learning to understand the role of primary amino acid sequence and secondary structure on charge transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn) and a low-conductance state occurring for extended peptide structures. Conformer selection for the peptide structures is rationalized using principal component analysis (PCA) of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonably good agreement with experiments. Projected density of states (PDOS) calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides new avenues for understanding the electronic properties of longer peptides or proteins. Significance StatementElectron transport in proteins serves as a biological power line that fuels cellular activities such as respiration and photosynthesis. Within cells, proteins act as conduits, shuttling electrons through a series of reactions and pathways to generate proton gradients and to fuel ATP synthesis. Despite recent progress, the mechanisms underlying the flow of energy in protein complexes are not fully understood. Here, we study electron transport in peptides at the single-molecule level by combining experiments and molecular modeling. Our results reveal two distinct molecular sub-populations underlying electron transport that arise due to the flexibility of peptide backbones and the ability to fold into compact structures. This work provides a basis for understanding energy flow in larger proteins or biomolecular assemblies.

biophysics↗

bioRxiv2023

The origin of secondary structure transitions and peptide self-assembly propensity in trifluoroethanol-water mixtures

The formation of transient helical intermediates, implicated in the early-stages of amyloid formation in amyloidogenic peptides, is thought to be enhanced by membrane-peptide interactions. Uperin 3.5 is a seventeen-residue antimicrobial, amyloidogenic peptide that forms amyloid in phosphate buffered saline (PBS). The role of 2,2,2-trifluoroethanol (TFE) concentration, a known -helical stabiliser, in modulating aggregation of Uperin 3.5 peptide in membrane-mimetic TFE:water mixtures was investigated. Thioflavin T (ThT) fluorescence assays showed complete inhibition of aggregation at higher concentrations of TFE ([≥] 20% TFE:water v/v). However, a five-to-seven-fold increase in fibrillation kinetics was observed at 10% TFE:water mixtures in comparison to aggregation in a buffer. Further, aggregation in TFE:water mixtures was only observed upon addition of buffer. Interestingly, circular dichroism (CD) spectra showed the appearance of partial helical structures in 10% TFE:water, which transitioned to {beta}-sheet rich structures only after addition of buffer. Microsecond time-scale molecular dynamics (MD) simulations of multiple U3.5 peptides in both salt-free and salt-containing TFE:water mixtures showed that changes in the local environment of peptide residues determined the structural transition and aggregation trajectories for U3.5. Consistent with experiments, the greatest extent of aggregation was observed for low TFE concentration (10% TFE:water simulations), characterised by faster formation of helical intermediates (oligomers). While the presence of 10% TFE efficiently induced partial helical structure in individual U3.5 peptides, it did not impede peptide-peptide interactions, thus enabling peptide aggregation. Addition of salt, screened like-charge repulsion between positively charged residues of different peptides, leading to stronger inter-peptide interactions. Significantly, the presence of salt determined subsequent structural transitions in the helical intermediates; either forming a predominantly -helical oligomer in salt-free solutions or a {beta}-sheet-rich oligomer in salt-containing solutions.

biophysics↗