Biology subjects

Parikh, A. N.

Publications and source records attributed to Parikh, A. N..

5 recordsLinked to original sources

bioRxiv2026

Small molecule ensembles reshape amyloid aggregation landscapes

Proteins in living systems are highly dynamic, continuously populating heterogeneous ensembles of functionally distinct conformational and aggregation states whose relative populations and interconversion rates are governed by an underlying free-energy landscape. Perturbations such as ligand binding, chemical modification, or changes in the environment remodel these assemblies, thereby reshaping protein behavior and function. Understanding how such protein networks are dynamically remodeled is a fundamental challenge in biophysics. Here, we utilize the A{beta}42 aggregation landscape as a model to demonstrate that remodeling can occur without detectable changes in the apparent activation free-energy barrier, instead arising from system-level redistribution of species along a conserved kinetic pathway. Using EPPS (4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid) as a model modulator, temperature-dependent kinetic analysis reveals an invariant apparent activation free energy, suggesting that the underlying energetic framework remains unchanged even as the system is reshaped. We find that EPPS modulates A{beta}42 disaggregation in a concentration-dependent manner. At intermediate concentrations, enhanced redistribution toward soluble species is observed, whereas at higher concentrations, modulator self-association into supramolecular clusters is associated with reduced net disaggregation and partial recovery of aggregation signatures. Thermal disruption of these assemblies restores activity, consistent with a role of modulator self-association in governing the observed behavior. Furthermore, our experiments indicate that this disaggregation process is reduced in crowded environments compared to dilute conditions. Together, these results support a biophysical framework in which amyloid remodeling is driven by species redistribution along a conserved kinetic landscape, where the extent of disaggregation is determined by modulator concentration-dependent partitioning of protein species, modulator self-association, and environmental constraints. SignificanceAn emerging view of protein function recognizes that proteins exist as dynamic networks of interconverting conformational and aggregation states. Binding interactions and environmental perturbations remodel these networks, thereby altering protein behavior. Amyloid aggregates associated with Alzheimers disease exemplify such dynamic systems, yet how small molecules remodel them remains poorly understood. Using A{beta}42 as a model, we show that small molecules remodel amyloid networks by redistributing protein populations in a concentration-dependent manner. This redistribution is modulated by self-association of the small molecule, molecular crowding, and temperature. These findings establish population redistribution within dynamic amyloid networks as a mechanism for remodeling protein assemblies, offering new insights into controlling pathological aggregation.

molecular biology↗

bioRxiv2025

Apolipoprotein interaction induces shape remodeling and lipid phase separation in giant unilamellar vesicles

Apolipoprotein A-I (ApoA-I) - a 243-residue amphipathic protein containing an N-terminal globular domain and a primarily helical C-terminal lipid binding domain - is a principal protein component of high-density lipoprotein (HDL) or "good" cholesterol, which is an essential component of lipid homeostasis in humans. Synthesized in the liver and intestine and excreted in the blood, ApoA-I undergoes complex, cooperative, and dynamic self-assembly with membrane lipids, producing unlipi-dated (or weakly lipidated), nascent discoidal, and mature HDL states. In vitro studies demonstrate that the reconstitution of purified protein and lipids restores this cooperative self-assembly. However, the kinetic pathways by which these mesoscopic, proteolipidic assemblies form remain incompletely understood. Here, we monitor the dynamics of ApoA-I-membrane interactions through real-time monitoring of morphological changes, which ensue when ApoA-I is incubated with minimal giant unilamellar vesicles (GUVs) composed of single phospholipids or phase-separating phospholipid-cholesterol mixtures. Our fluorescence microscopy measurements reveal that the interaction initiates a gross, morphological remodeling of the parent vesicle proceeding through discrete stages involving membrane poration, solute leakage, vesiculation, and lipid-lipid phase separation. Our atomic force microscopy measurements confirm that the outcome includes discoidal nanoparticles. This qualitative phenomenology is robust and fully reproducible for different protein mutants and alleles (WT APOA-1, {Delta}49ApoA-I, ApoE-3, and ApoE-4) and other lipid mixtures (including mixtures containing phosphoserine lipids). Our molecular simulations recapitulate the essential shape changes and further reveal the composition dependence of the interactions. Together, these findings outline key steps in protein-lipid interactions that facilitate the assembly of mesoscopic reconstituted lipoproteins and nanodiscs.

biophysics↗

bioRxiv2024

Regulating biocondensates within synthetic cells via segregative phase separation

Living cells orchestrate a myriad of biological reactions within a highly complex and crowded environment. A major factor responsible for such seamless assembly are the preferential interactions between the constituent macromolecules, either associative or segregative, that can drive de-mixing to produce co-existing phases, and thus provide a dynamic intracellular compartmentalization. But how these two types of interactions, occurring simultaneously within the cytoplasmic space, influence each other is still largely unknown. This makes understanding and applying the molecular interactions that interfere with each other in such crowded environments crucial when engineering increasingly complex synthetic cells. Here, we show that the interplay between segregative and associative phase separation within cell-mimicking vesicles can lead to rich dynamics between them. Using on-chip microfluidic systems, we encapsulate the associative and segregative components in cell-sized containers and trigger their phase separations to create hierarchical structures that act as molecular recruiters, membrane targeting agents, and initiators of condensation. The obtained multiphase architecture provides an isolated microenvironment for condensates, restricting their molecular communication as well as diffusive motion, and leading to budding-like behaviour at the lipid membrane. In conclusion, we propose segregative phase separation as a universal condensate regulation strategy in managing molecular distribution, condensate location, as well as membrane interaction. We believe our approach will facilitate controlling the behaviour of membraneless organelles within synthetic cells.

synthetic biology↗

bioRxiv2020

Coupling between lipid miscibility and phosphotyrosine driven protein condensation at the membrane

Lipid miscibility phase separation has long been considered to be a central element of cell membrane organization. More recently, protein condensation phase transitions, into three-dimensional droplets or in two-dimensional lattices on membrane surfaces, have emerged as another important organizational principle within cells. Here, we reconstitute the LAT:Grb2:SOS protein condensation on the surface of giant unilamellar vesicles capable of undergoing lipid phase separations. Our results indicate that assembly of the protein condensate on the membrane surface can drive lipid phase separation. This phase transition occurs isothermally and is governed by tyrosine phosphorylation on LAT. Furthermore, we observe that the induced lipid phase separation drives localization of the SOS substrate, K-Ras, into the LAT:Grb2:SOS protein condensate. Statement of SignificanceProtein condensation phase transitions are emerging as an important organizing principles in cells. One such condensate plays a key role in T cell receptor signaling. Immediately after receptor activation, multivalent phosphorylation of the adaptor protein LAT at the plasma membrane leads to networked assembly of a number of signaling proteins into a two-dimensional condensate on the membrane surface. In this study, we demonstrate that LAT condensates in reconstituted vesicles are sufficient to drive lipid phase separation. This lipid reorganization drives another key downstream signaling molecule, Ras, into the LAT condensates. These results show that the LAT condensation phase transition, which is actively controlled by phosphorylation reactions, extends its influence to control lipid phase separation in the underlying membrane.

biophysics↗

bioRxiv2020

Recurrent Dynamics of Rupture Transitions of Single Giant Vesicles at Solid Surfaces

Single giant vesicles (GVs) rupture spontaneously from their salt-laden suspension onto solid surfaces. At hydrophilic surfaces, they rupture via a recurrent burst-heal dynamics: during burst, single pores nucleate at the contact boundary of the adhering vesicles facilitating asymmetric spreading and producing a "heart" shaped membrane patch. During the healing phase, the competing pore closure produces a daughter vesicle. At hydrophobic surfaces, by contrast, the GVs rupture via a distinctly different, yet recurrent, bouncing ball rhythm: Rendered tense by the substrate interactions, GVs porate and spread monomolecular layer on the hydrophobic surface in a symmetric manner. Here too, the competition from pore closure produces a daughter vesicle, which re-engages with the substrate. In both cases, the pattern of burst-reseal events repeats multiple times splashing and spreading the vesicular fragments as bilayer patches at the solid surface in a pulsatory manner. These remarkable recurrent dynamics arise not because of the elastic properties of the solid surface but because the competition between membrane spreading and pore healing, prompted by the surface-energy dependent adhesion, determine the course of the topological transition. STATEMENT OF SIGNIFICANCEGiant lipid vesicles adhering to a solid surface experience strong mechanical stresses. The contacting membrane segment loses thermal fluctuations and accumulates mechanical tension, the equilibration of which can give rise to global shape changes, lipid phase separation, and traction forces. Beyond a threshold tension, vesicles porate, unravel, and spread. Here, we find that a competition from pore-healing can make rupture iterative, rather than a single all-or-nothing event. During burst, single pores expand, spreading a lipid bilayer on the hydrophilic surface and a monolayer on the hydrophobic one. During heal, pore-healing can produce daughter vesicles. This burst-reseal event reiterates "splashing" portions of single vesicles at the solid surface and "bouncing" the remainder as a secondary vesicle in multiple steps.

biophysics↗