Biology subjects

Baratam, K.

Publications and source records attributed to Baratam, K..

6 recordsLinked to original sources

bioRxiv2026

Phosphoinositides protonation states dictate AKT1 binding with membrane

Phosphoinositides are key regulators of membrane-associated signaling, yet their electrostatic properties are commonly represented by a single nominal charge in molecular simulations and structural models. Using the essential protein kinase AKT1 as a model system, we show that phosphoinositide protonation microstates, both the degree and positional placement of protons, govern peripheral membrane-protein recognition. By integrating quantum-mechanics-derived headgroup parameters, microsecond-scale all-atom molecular dynamics, and umbrella-sampling free-energy calculations with the available solid-state NMR-derived lipid populations via Bayesian/Maximum Entropy reweighting, we account explicitly for the thermodynamic ensemble of phosphoinositide proto-nation states. This population-weighted free-energy framework provides a quantitative mechanistic rationale for the strict specificity of wild-type AKT1 toward PI(3, 4, 5)P3 and elucidates how the oncogenic sentry mutation (E17K) alters this specificity to enable high-affinity PIP2 binding. Furthermore, Proximity-based Labeling of Membrane Associated Proteins (PLiMAP) assays experimentally confirm that AKT1 pleckstrin homology domain binding to distinct phosphoinositide species is differentially sensitive to pH. Together, our findings establish a direct connection between phosphoinositide protonation equilibria, binding energetics, and AKT1 lipid specificity. Beyond AKT1, these results demonstrate that the dynamic protonation microstates of anionic phospholipids act as a functional regulatory layer governing peripheral membrane-protein recruitment across diverse cellular microenvironments.

biophysics↗

bioRxiv2026

Dose-Dependent Softening of Bacterial Model Membranes by Structurally Distinct Antimicrobial Peptides: A Coarse-Grained Molecular Dynamics Study

Antimicrobial peptides (AMPs) act at the membrane interface, where they remodel lipid packing defects and redistribute lateral stresses, yet a quantitative, dose-dependent understanding of how they alter membrane mechanical properties remains incomplete. We use coarse-grained MARTINI 3 molecular dynamics simulations to systematically characterize the mechanical and microstructural response of a 70:30 POPE:POPG bilayer to three AMPs spanning distinct structural classes: aedesin (alpha-helical, 2MMM), arenicin-1 (beta-hairpin, 2JSB), and indolicidin (disordered, 1G89). For each peptide we vary the surface loading from one to four peptides per leaflet and extract the bending modulus Kc, the area compressibility modulus KA, peptide localization depth, bilayer thickness, peptide-lipid and peptide-peptide spatial organization, and leaflet-resolved lipid packing defect distributions. All three peptides soften Kc monotonically with loading, but at per-peptide rates that span a threefold range and order systematically by structural class: - 1.39 {+/-} 0.09, - 0.66 {+/-} 0.04, and - 0.44 {+/-} 0.01 kBT per peptide for aedesin, arenicin-1, and indolicidin, respectively. The tilt and twist moduli remain invariant across all conditions, indicating that the perturbation operates selectively on long-wavelength collective deformation modes. KA softens for the two structured peptides but is statistically indistinguishable from the control for indolicidin, a dissociation we trace to a supraphosphate adsorption versus interfacial insertion dichotomy: structured peptides sit above the phosphate plane and act as supraphosphate wedges, while the disordered peptide threads into the interface without coherently displacing lipids. Independent geometric, spatial-organization, and microstructural observables corroborate this framework, with the deep versus shallow defect remodeling asymmetry providing a clean microstructural counterpart to the Kc-KA dichotomy. Acyl chain order parameters resolve the per-lipid splay from the bilayer-averaged response and show that the per-lipid perturbation tracks conformational state rather than peptide length: the two structured peptides impose comparable per-lipid chain disordering despite differing in length, while the disordered peptide imposes far less. These findings establish a quantitative connection between peptide-induced defect remodeling and the elastic response of the bilayer, and suggest a design principle in which conformational restriction maximizes the per-peptide membrane perturbation, motivating experimental tests on stapled-peptide AMP analogs.

biophysics↗

bioRxiv2026

Exploring the Energy Landscape of Hairpin Folding using the TIS-DNA model

Coarse-grained (CG) modeling of DNA has been gathering steam in recent years due to the limitations imposed by current computer hardware, and deficiencies of atomistic force-fields. Specifically, CG simulations have emerged as a potent tool for exploring complex energy landscapes underlying biochemical processes, such as DNA transcription, as well as material design based on programmable self-assembly. In this chapter, we illustrate how the Three Interaction Site (TIS) model for DNA, a robust coarse-graining framework, can be used to study the folding landscape of DNA hairpins. We show that despite its simplicity, the TIS-DNA model quantitatively describes the hairpin folding thermodynamics and recapitulates many features of the kinetics, including the multiplicity of pathways. The free energy landscape exhibits single-funnel character with a distinct bias towards the folded state. It is likely that folding initiates through non-specific collapse of the DNA chain, involving multiple excursions on the energy landscape, until the opposing strands are approximately aligned. Subsequently, the loop region becomes more ordered, and after the first native-contact nucleates, the rest of the process becomes essentially downhill.

biophysics↗

bioRxiv2025

Division of labor in cargo and membrane recognition by SNX1-SNX5: Insights from multiscale modelling

Sorting Nexins (SNXs) are a large group of diverse cellular trafficking proteins that play essential roles in membrane remodeling and cargo sorting between organelles. SNX proteins comprise a banana-shaped BAR domain that acts as a curvature-inducing scaffold and a phosphoinositide lipids sensitive Phox-Homology Domain (PXD) that interacts with the membrane to ensure specific and efficient organelle binding. In concert with the larger retromer machinery, these proteins traffic and recycle cargo between the endosomal membrane, trans-Golgi network, and plasma membrane. Interestingly, the SNX1-SNX5 heterodimeric construct forms a part of the newly discovered pathway where cargo sorting and membrane remodeling can take place in a retromer-independent fashion. In this work, we use molecular dynamics and continuum mechanics simulations to understand the features of SNX1-SNX5 heterodimer, especially the molecular determinants at PXDs, which impart organelle membrane specificity and retromer-independent cargo recognition ability to these proteins. Our all-atom molecular dynamics simulations with isolated PXDs and full-length SNX1-SNX5 on bilayers show that SNX1-PXD has robust membrane-binding features that are largely insensitive to single or double mutation of the basic residues on its surface. Comparing the simulation-based binding poses against the recently solved cryo-EM structures of tubular membrane-bound SNX1 homodimer and SNX1-SNX5 heterodimer also provided interesting insights into the association profile of isolated PXDs when they have the freedom to explore different membrane-binding poses. Our protein-protein simulations of SNX5-PXD with the tail region of the CI-MPR transmembrane cargo protein using metadynamics simulations reveal aromatic residue-rich{pi} - {pi} interactions between the two proteins, and a favorable and kinetically accessible binding free energy profile for SNX5. To model the emergent behavior of cargo sequestration and endosomal tube formation by SNX1-SNX5 heterodimer, we also performed Dynamically Triangulated Surface (DTS) based mesoscopic simulations by developing an augmented Helfrich-like continuum-mechanics Hamiltonian to incorporate transmembrane proteins in DTS models. SIGNIFICANCESorting Nexins (SNXs) are a conserved family of endosomal coat proteins that drive cargo-rich tubule formation for receptor transport and recycling within the cell. The cargo-recognition and sorting in these pathways are mediated by the associated retromer complex. SNX1-SNX5 heterodimer is unique to the SNXs family as it has been shown to sequester cargo for trafficking in a retromer-independent manner. The canonical membrane adaptor Phox-homology domain of SNX5 has evolved to carry out this special function. Using molecular dynamics and advanced sampling metadynamics calculations as well as Helfrich-like Hamiltonian-based mesoscopic modelling, we explore the molecular and thermodynamic driving forces that makes the SNX1-SNX5 heterodimeric constructs multifunctional in character.

biophysics↗

bioRxiv2024

SOP-MULTI: A self-organized polymer based coarse-grained model for multi-domain and intrinsically disordered proteins with conformation ensemble consistent with experimental scattering data

Multidomain proteins with long flexible linkers and full-length intrinsically disordered proteins (IDPs) are best defined as an ensemble of conformations rather than a single structure. Determining high-resolution ensemble structures of such proteins poses various challenges using tools from experimental structural biophysics. Integrative approaches combining available low-resolution ensemble-averaged experimental data and in silico biomolecular reconstructions are now often used for the purpose. However, an exhaustive Boltzmann weighted conformation sampling for large proteins, especially for ones where both the folded and disordered domains exist in the same polypeptide chain, remains a challenge. In this work, we present a 2-site per amino-acid resolution SOP-MULTI force field for simulating coarse-grained models of multidomain proteins. SOP-MULTI combines two well-established self-organized polymer (SOP) models --: (i) SOP-SC models for folded systems and (ii) SOP-IDP for IDPs. For the SOP-MULTI, we train the cross-interaction terms between the beads belonging to the folded and disordered regions to generate experimentally-consistent conformation ensembles for full-length multi-domain proteins such as hnRNPA1, TDP-43, G3BP1, hGHR-ECD, TIA1, HIV-1 Gag, Poly-Ubiquitin and FUS. When back-mapped to all-atom resolution, SOP-MULTI trajectories faithfully recapitulate the scattering data over the range of the reciprocal space. We also show that individual folded domains preserve native contacts with respect to solved folded structures, and root mean square fluctuations of residues in folded domains match those obtained from all-atom molecular dynamics simulations trajectories of the same folded systems. SOP-MULTI Force Field is made available as a LAMMPS-compatible user package along with setup codes for generating the required files for any full-length protein with folded and disordered regions.

biophysics↗

bioRxiv2019

Flexible pivoting of the pleckstrin domain domain in dynamin catalyzes fission by affecting membrane properties: Insights into the molecular degrees of freedom

The neuronal dynamin1 functions in the release of synaptic vesicles by orchestrating the process of GTPase-dependent membrane fission. Dynamin1 associates with the plasma membrane-localized phosphatidylinositol-4,5-bisphosphate (PIP2) with its centrally-located pleckstrin homology domain (PHD). The PHD is dispensable as fission can be managed, albeit at much slower rates, even when the PHD-PIP2 interaction is replaced by a generic polyhistidine- or polylysine-lipid interaction. However, even when the PHD is present, the length of the dynamin scaffold and in turn the membrane remodeling and fission rates are severely restricted with mutations such as I533A on membrane-interacting variable loop 1 (VL1) of PHD. These observations suggest that PIP2-containing membrane interactions of PHD could have evolved to expedite fission to fulfill the requirement of rapid kinetics of synaptic vesicle recycling. Here, we use a suite of multiscale modeling approaches that combine atomistic molecular dynamics simulations, mixed resolution membrane mimetic models, coarse-grained molecular simulations and advanced free-energy sampling methods (metadynamics and umbrella sampling) to explore PHD-membrane interactions. Our results reveal that: (a) the binding of PHD to PIP2-containing membranes modulates the lipids towards fission-favoring conformations and softens the membrane, (b) that PHD engages another loop (VL4) for membrane association, which acts as an auxiliary pivot and modulates the orientation flexibility of PHD on the membrane - a mechanism we believe may be important for high fidelity dynamin collar assembly on the membrane. (c) Through analyses of our trajectories data and free-energy calculations on membrane-bound WT and mutant systems, we also identify key residues on multiple VLs that stabilizes PHD membrane association. And we suggest experiments to explore the ability of PHD to associate with membrane in orientations that favors faster fission. Together, these insights provide a molecular-level understanding of the "catalytic" role of the PHD in dynamin-mediated membrane fission. SIGNIFICANCEDynamin, a large multi-domain GTPase, remodels the membrane by self-assembling onto the neck of a budding vesicle and induces fission by its energy driven conformational changes. In this work, we use multi-scale molecular simulations to probe the role of dynamins pleckstrin-homology domain (PHD), which facilitates membrane interactions. Notably, PHD is dispensable for fission as is the case with extant bacterial and mitochondrial dynamins. However, reconstitution experiments suggest that the functional role of PHD in neuronal-membrane goes beyond that of an adaptor domain as it possibly expedites the fission reaction during synaptic vesicle recycling. We provide a molecular-dynamics picture of how PHDs make membranes more pliable for fission and suggest new insights into the molecular-level processes driving the expedited fission behavior.

biophysics↗