Biology subjects

Prasad, A. K.

Publications and source records attributed to Prasad, A. K..

4 recordsLinked to original sources

bioRxiv2026

Generative Deep Learning and Molecular Dynamics Reveal Design Principles for Amyloid-Like Antimicrobial Peptides

Antimicrobial peptides (AMPs) are emerging as promising alternatives to conventional antibiotics, and growing evidence indicates a fundamental link between antimicrobial activity and amyloid-like self-assembly. Many AMPs are known to form amyloid-like fibrils, while several amyloidogenic peptides exhibit intrinsic antimicrobial properties, suggesting shared underlying physicochemical determinants such as amphipathicity, {beta}-sheet propensity, and charge distribution. However, the rational design of peptides that simultaneously encode these dual functionalities remains a significant challenge. Here, we present amyAMP, a generative deep-learning framework based on a Wasserstein generative adversarial network with gradient penalty (WGAN-GP), designed to learn and generate peptides with integrated antimicrobial and amyloidogenic properties. Trained on curated datasets of antimicrobial and amyloid-forming peptides, amyAMP captures the latent sequence-property relationships governing dual functionality. Statistical and latent-space analyses demonstrate that the generated peptides closely overlap with biologically relevant peptide space while remaining distinct from random sequences, indicating successful learning of key biochemical features. To validate functional behavior, we performed extensive coarse-grained molecular dynamics simulations to probe membrane interaction, peptide self-assembly, and membrane disruption. The simulations reveal rapid membrane adsorption, stable amphipathic insertion, and strong peptide-peptide aggregation. Notably, cooperative clustering of peptides on membrane surfaces induces membrane thinning and curvature perturbations, highlighting a mechanistic coupling between aggregation and antimicrobial activity. Collectively, these results establish that amyAMP effectively captures the shared physicochemical principles underlying antimicrobial action and amyloid-like self-assembly. This work provides a generalizable framework for the AI-guided design of multifunctional peptides to advance the development of next-generation therapeutics targeting antimicrobial resistance.

biophysics↗

bioRxiv2025

C-Terminal Amidation: Structural Insights into Enhanced Antimicrobial Peptide Efficacy and Amyloidogenesis

Post-translational modifications, such as C-terminal amidation, are energetically costly but critical for membrane-active antimicrobial peptides (AMPs). This study examined the impact of C-terminal amidation on uperin 3.5 (U3.5, an amyloid-forming AMP) interactions with POPE:DOPG (3:1) lipid bilayers using molecular simulations. Whereas, monomeric U3.5-NH2 rapidly attached to the lipid bilayer surface, forming a stable -helix, U3.5-OH exhibited weaker interactions. Simulations of U3.5 tetramers, derived from the amyloid cryo-electron microscopy structure, revealed that amidation enhanced peptide-bilayer and peptide-peptide interactions, initially stabilising {beta}-sheet structures and facilitating embedding into the bilayer. The {beta}-sheet tetramer gradually dissociated into monomeric U3.5-NH2 peptides on the bilayer surface. Following dissociation, the monomers formed stable, amphipathic -helices that were strongly embedded in the bilayer, consistent with a carpet-like antimicrobial mechanism. Enhanced peptide-lipid interactions resulted in lipid redistribution and changes to membrane curvature, potentially leading to membrane rupture. These findings highlight the role of U3.5-NH2 amyloid as a "carrier vehicle" for antimicrobial action at the bilayer interface, emphasizing the crucial function of C-terminal amidation in stabilising peptide structure and promoting antimicrobial activity.

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↗

bioRxiv2023

Helical Intermediate Formation and Its Role in Amyloid of an Amphibian Antimicrobial Peptide

Helical intermediates appear to be crucial in amyloid formation of several amyloidogenic peptides, including A{beta}, that are implicated in different neurodegenerative diseases. Intermediate species have been reported to be more toxic than mature amyloid fibrils. Hence, the focus of the current work is to understand both structural and mechanistic role of intermediates in the early stages of amyloid self-assembly in amyloidogenic peptides. Molecular dynamics (MD) simulations and the adaptive biasing force (ABF) method were utilized to investigate structural changes that lead to amyloid formation in amphibian peptide uperin-3.5 (U3.5), an antimicrobial and amyloidogenic peptide. Microsecond time-scale MD simulations revealed that peptide aggregation, into {beta}-sheet dominated aggregates, is centred on two important factors; evolution of -helical intermediates and the critical role of local peptide concentration inside these aggregates. Electrostatic attraction between the oppositely charged aspartate (D) and arginine (R) residues located near the N-terminus induced hydrogen bonding resulting in formation of precursor 310-helices close to the N-terminus. The 310-helices transitioned into -helices, thereby imparting partial helical conformations to the peptides. In the initial stages of aggregation, U3.5 peptides with amphipathic, partial helices aggregated to form small clusters of helical intermediates directed via hydrophobic interactions. These helices imparted stability to the helical intermediates, which promoted growth of clusters by further addition of peptides. This led to an increase in the local peptide concentration which enabled stronger peptide-peptide interactions and triggered a {beta}-sheet transition in these aggregates. Thus, the study emphasized that stabilisation of peptide helical content may be crucial to the evolution of {beta}-sheet-rich amyloid structures.

biophysics↗