Biology subjects

Haimov, E.

Publications and source records attributed to Haimov, E..

4 recordsLinked to original sources

bioRxiv2026

Seipin and perilipin 3 promote distinct early steps of nascent lipid droplet biogenesis

Lipid droplets (LDs) are lipid storage organelles with critical roles in metabolism. Cells form LDs in response to various metabolic stresses (1). LD biogenesis occurs in the endoplasmic reticulum (ER) membrane and begins when triglyceride (TG) in the membrane phase separates (2-4). After nucleation, nascent LDs grow by absorbing TG from the membrane (5,6). How cells determine when TG in the ER membrane is added to existing LDs or is used to form new LDs or is not known. Here, we developed the first LD formation assay that allows the synthesis of TG in membranes, mimicking what occurs in cells. LDs arise stochastically after TG production begins. LD nucleation is affected by TG production rate and membrane phospholipid composition. Membrane-embedded LDs suppress nascent LD formation by sequestering TG and destabilizing nascent LDs by Ostwald ripening. We show that cells overcome this suppression in two ways. The ER membrane protein seipin accelerates LD nucleation where it localizes in a membrane, probably by increasing the kinetics of TG phase separation. The LD coat perilipin 3 inhibits nascent droplet dissipation by ripening. Together, our findings reveal a minimal LD formation machinery, and the mechanisms cells use to control whether TG in the ER drives new LD formation.

cell biology↗

bioRxiv2026

Recognition in Confinement: The Dynamics of Homologous Gene Pairing

How can protein-independent, side-by-side alignment of homologous double-stranded DNA (ds-DNA) arise as an early step in genome repair and genetic exchange, and what determines their kinetics under confinement? Although recombination proteins are known to facilitate this process, experiments indicate that an initial side-by-side arrangement of homologs can occur even in their absence. Helical Coherence Theory (HCT) proposes that sequence-dependent distortions of the double helix lead to commensurate charge patterns between interacting dsDNAs, favouring homologous over non-homologous alignment. However, HCT has largely been developed for straight, rigid dsDNA rods, an approximation limited to roughly one persistence length ({ell}B {approx} 50 nm), leaving the question open as to how recognition manifests in longer, fluctuating chains. Moreover, the dynamics and timescales of homolog searching under confinement, and the internal dynamics of the paired state, such as transient formation of local unpaired regions ("bubbles") and end fraying, remain unexplored. Here we extend HCT to dsDNA chains of multiple persistence lengths under confinement using coarse-grained simulations with a custom HCT-based force field, in order to come closer to understanding how homologous genes pair in vivo. We simulate two homologous chains within spherical cavities of radii 0.3-1 times their free-space gyration radius under two limiting ionic conditions. We found that confinement warrants homologous pairing; it occurs on microsecond timescales and depends non-monotonically on confinement size, with an optimal confinement that accelerates pairing while avoiding tangled states and metastable trapping in an ion-dependent manner. To resolve pairing dynamics, we develop a kinetic theory and fit it to simulation trajectories, distinguishing rates of independent pairing modes underlying bubble formation and fraying. Together, these results support a physical mechanism for homologous pairing beyond the rigid-rod limit and suggest how confinement can promote both encounter and stabilisation within the HCT framework.

biophysics↗

bioRxiv2021

An engineered nanocomplex with Photodynamic and Photothermal synergistic properties for cancer treatment

Photodynamic therapy (PDT) and photothermal therapy (PTT) are promising therapeutic methods for cancer treatment; however, as single modality therapies, either PDT or PTT are still limited in their success rate. A dual application of both PDT and PTT, in a combined protocol, has gained immense interest. In this study, gold nanoparticles (AuNPs) are conjugated with a PDT agent, meso-tetrahydroxyphenylchlorin (mTHPC) photosensitizer, designed as nanotherapeutic agents that can activate a dual photodynamic/photothermal therapy. The AuNP-mTHPC complex is biocompatible, soluable, and photostable. PDT efficiency is high because of immediate reactive oxygen species (ROS) production upon mTHPC activation by the 650 nm laser which decreased mitochondrial membrane potential ({Delta}{Psi}m). Likewise, the AuNP-mTHPC complex is used as a photoabsorbing (PTA) agent for PTT, due to efficient plasmon absorption and excellent photothermal conversion characteristics of AuNPs under laser irradiation at 532 nm. Under the laser irradiation of a PDT/PTT combination, a twofold phototoxicity outcome follows, compared to PDT-only or PTT-only treatment. This indicates that PDT and PTT have synergistic effects together as a combined therapeutic method. Hence, applying our AuNP-mTHPC may be a potential treatment of cancer in the biomedical field. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/471725v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@55fe3corg.highwire.dtl.DTLVardef@1a6468dorg.highwire.dtl.DTLVardef@161ea64org.highwire.dtl.DTLVardef@1638c91_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

Structural basis for long-chain isoprenoids synthesis by cis-prenyltransferases

Isoprenoids are the largest group of natural products, found in all living organisms and play an essential role in numerous cellular processes. These compounds are synthesized by prenyltransferases, catalyzing the condensation reaction between an allylic diphosphate primer and a variable number of isopentenyl diphosphate (C5) units. This superfamily of enzymes can be subdivided into trans- or cis-prenyltransferases according to the stereoisomerism of the product. The cis branch can be further classified according to product length. While the active site volume was suggested to determine the final length in enzymes synthesizing short- and medium-chain products (up to C60), long-chain enzymes (up to C120) and rubber synthases (>C10,000) fail to conform to this paradigm. Here, to resolve the structural basis for long-chain isoprenoid synthesis, we focused on the human cis-prenyltransferase complex (hcis-PT). This enzyme, peripheral to the endoplasmic reticulum membrane, produces the precursor for dolichol phosphate, a membrane residing glycosyl carrier. In line with its crucial role in the cellular protein glycosylation machinery, disease-causing mutations in hcis-PT were shown to result in a wide spectrum of clinical phenotypes. The crystallographic structures of hcis-PT in four different substrate/product-bound conformations revealed an outlet enabling product elongation into the bulk solvent. Moreover, hydrogen-deuterium exchange mass spectrometry analysis in solution showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Finally, using a fluorescent substrate analog and a fluorescently-labeled lipid nanodiscs, we show that product elongation and membrane association are closely correlated. Together, our results support directional product synthesis in long-chain enzymes and rubber synthases, with a distinct substrate inlet and product outlet, allowing direct membrane insertion of the elongating isoprenoid during catalysis. This mechanism uncouples active site volume from product length and circumvents the need to expulse hydrophobic product into a polar environment prior to membrane insertion.

biochemistry↗