Biology subjects

Pantelopulos, G. A.

Publications and source records attributed to Pantelopulos, G. A..

5 recordsLinked to original sources

bioRxiv2026

Cryo-EM reveals patient- versus organ-specific structural diversity and bound ligands in lambda-6 light chain amyloids

Immunoglobulin light chain (LC) amyloidosis is a debilitating multiorgan disease with limited treatment options. Sequence and structural variability make LC amyloids particularly challenging for therapeutic targeting. We report four cryo-EM structures of lambda6-LC amyloid fibrils from four organs of two patients. Fibrils from different patients show different N-terminal conformations expanding known repertoire of lambda6-LC amyloid folds. These folds contain a planar beta-arch with a flexible linker containing the complementarity-determining region 2, flanked by N- and C-terminal segments in variable patient-specific conformations. The surface location of the structurally frustrated charged segment may contribute to the overrepresentation of the lambda6-LC family in amyloidosis. These and other lambda6-LC amyloid structures from different patients show different side chain packing. Conversely, cardiac, renal and splenic amyloids from the same patient exhibit similar structures with small peripheral organ-specific variations. Moreover, they show similar orphan densities, suggesting collagen-like triple helices bound to a tyrosine ladder along the fibril spine. Mass spectrometry detects collagen type-VI in tissue-extracted amyloids. Molecular dynamics simulations suggest amyloid binds collagen-VI triple helices via mixed interactions facilitated by the geometric complementarity between the layered amyloid structure and the triple helix. Similar interactions may drive formation of other amyloid-collagen complexes, influencing biological properties of amyloids.

biophysics↗

bioRxiv2025

Accurate determination of the preferred aggregation number of a micelle-encapsulated membrane protein dimer

The preferred aggregation number of dodeclyphoshocholine (DPC) micelles [Formula] encapsulating dimeric and higher order protein assemblies is difficult to determine via experimental techniques due to uncertainty in dimer geometry and heterogeneity in the conformational ensemble. Dimerization of the Amyloid Precursor Protein transmembrane domain (C99) is a particular step of importance in the production of amyloid-{beta} protein and the amyloid cascade. Molecular dynamics simulations of the C99 dimer and other transmembrane proteins have been performed to compliment micelle-phase protein structure studies. It has often been assumed that the value of [Formula] is the same as that of the pure, empty micelle. Here, we provide a convenient method for testing that assumption, while also accounting for the finite-size effects inherent in computer simulations of micelle self-assembly. Employing large, unbiased, coarsegrained molecular dynamics simulations of DPC and C99 dimer self-assembly, we determined the radius of gyration to be 21.6 {+/-} 2.0 [A] for the micelle-encapsulated dimer, and 16.0 {+/-} 1.0 [A] for the pure DPC micelle. Using these radii of gyration, we performed all-atom simulations of DPC-encapsulated C99 dimers with preferred aggregation numbers of 100 and 54 DPC to test the effect of using an expected versus a naive estimate of aggregation number on the structure of the transmembrane protein dimer. Through atomistic simulations, we determined that the transmembrane dimeric structure displays different characteristics depending on the aggregation number of the micelle, in addition to increased water penetration and micelle defects when the aggregation number is too small.

biophysics↗

bioRxiv2025

Exploring the kinetics and mechanism of phase separation in ternary lipid mixtures containing APP C99 using atomistic vs coarse-grained MD simulations

The phase separation of lipid bilayers, composed of mixtures of saturated and unsaturated lipids and cholesterol, is a topic of fundamental importance in membrane biophysics and cell biology. The formation of lipid domains, including liquid-disordered domains enriched in unsaturated lipids and liquid-ordered domains enriched in saturated lipids and cholesterol is believed to be essential to the function of many membrane proteins. Experiment, theory, and simulation have been used to develop a general understanding of the thermodynamic driving forces underlying phase separation in ternary and quaternary lipid mixtures. However, the kinetics of early events in lipid phase separation in the presence of transmembrane proteins remain relatively understudied. Using large-scale all-atom and coarse-grained simulations, we explore the kinetics and phase separation of ternary lipid mixtures of saturated lipid, unsaturated lipid, and cholesterol. Order parameters employed in the Cahn-Hilliard theory provide insight into the kinetics and mechanism of lipid phase separation. We observe three distinct time regimes in the phase separation process: a shorter time exponential phase followed by a power law phase followed by a longer time plateau phase. Comparison of lipid, protein and lipid-protein dynamics between all-atom and coarse-grained models identifies both quantitative and qualitative differences and similarities in the phase separation kinetics. Moreover, timescaling of dynamics of AA and CG simulation yields a similar kinetic mechanism of phase separation. The findings of this study elucidate fundamental aspects of membrane biophysics and the ongoing efforts to define the role of lipid rafts in the structure and function of cellular membrane.

biophysics↗

bioRxiv2018

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation.

Cholesterol is essential to the formation of phase separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition, and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using Molecular Dynamics simulations, employing a physiologically-relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior, I) miscible liquid disordered bulk, II) phase separated, domain registered coexistence of liquid disordered and liquid ordered and domains, and III) phase separated, domain-anti-registered coexistence of liquid-disordered and newly-identified nanoscopic gel domains composed of cholesterol threads we name \"cholesterolic gel\" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid mixture phase separation.

biophysics↗

bioRxiv2016

Bridging microscopic and macroscopic mechanisms of p53-MDM2 binding using molecular simulations and kinetic network models

Under normal cellular conditions, the tumor suppressor protein p53 is kept at a low levels in part due to ubiquitination by MDM2, a process initiated by binding of MDM2 to the intrinsically disordered transactivation domain (TAD) of p53. Although many experimental and simulation studies suggest that disordered domains such as p53 TAD bind their targets nonspecifically before folding to a tightly-associated conformation, the molecular details are unclear. Toward a detailed prediction of binding mechanism, pathways and rates, we have performed large-scale unbiased all-atom simulations of p53-MDM2 binding. Markov State Models (MSMs) constructed from the trajectory data predict p53 TAD peptide binding pathways and on-rates in good agreement with experiment. The MSM reveals that two key bound intermediates, each with a non-native arrangement of hydrophobic residues in the MDM2 binding cleft, control the overall on-rate. Using microscopic rate information from the MSM, we parameterize a simple four-state kinetic model to (1) determine that induced-fit pathways dominate the binding flux over a large range of concentrations, and (2) predict how modulation of residual p53 helicity affects binding, in good agreement with experiment. These results suggest new ways in which microscopic models of bound-state ensembles can be used to understand biological function on a macroscopic scale.\n\nAUTHOR SUMMARYMany cell signaling pathways involve protein-protein interactions in which an intrinsically disordered peptide folds upon binding its target. Determining the molecular mechanisms that control these binding rates is important for understanding how such systems are regulated. In this paper, we show how extensive all-atom simulations combined with kinetic network models provide a detailed mechanistic understanding of how tumor suppressor protein p53 binds to MDM2, an important target of new cancer therapeutics. A simple four-state model parameterized from the simulations shows a binding-then-folding mechanism, and recapitulates experiments in which residual helicity boosts binding. This work goes beyond previous simulations of small-molecule binding, to achieve pathways and binding rates for a large peptide, in good agreement with experiment.

biophysics↗