Biology subjects

Merzaban, J.

Publications and source records attributed to Merzaban, J..

4 recordsLinked to original sources

bioRxiv2025

Combined TIRF and 3D Super-Resolution Microscopy for Nanoscopic Spatiotemporal Characterization of Adhesion Molecules on Microvilli

The homing of hematopoietic stem/progenitor cells (HSPCs) and leukemic cells is a multistep process governed by complex spatiotemporal interactions between adhesion molecules under shear stress. While the molecular and biological mechanisms of this process have been extensively studied, the precise spatial and temporal organization of adhesion molecules that influences homing efficiency remains relatively poorly understood. In particular, the roles of the cell surface topography and its morphological changes during homing in shaping the spatial organization of adhesion molecules remain elusive. This is partly due to the lack of imaging techniques that simultaneously capture both nanoscopic cell surface morphology and the spatial distribution of the adhesion molecules. Here, we develop a microfluidics-based super-resolution (SR) imaging platform that enables the three-dimensional (3D) mapping of the cell surface morphology and the spatial distribution of the adhesion molecules during HSPC and leukemic cell rolling by integrating total internal reflection fluorescence microscopy (TIRFM) with single-molecule localization microscopy (SMLM). We reconstruct the cell surface morphology, which is critical to the homing, using TIRFM, and precisely overlay the spatial distribution of adhesion molecules, including CD44, PSGL-1, and actin cytoskeleton, determined by 3D-SMLM, on the topographic map. We show distinct nanoscopic localizations of adhesion molecules on the microvilli of HSPCs/leukemic cells and their reorganization under shear stress during cell rolling, at a spatial resolution of approximately 30 nm. The approach offers a powerful means to elucidate the complicated interplay between cell surface morphology and ligand-receptor interactions. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/672391v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@19e513eorg.highwire.dtl.DTLVardef@e7dd0corg.highwire.dtl.DTLVardef@617295org.highwire.dtl.DTLVardef@1a9ae0a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages

Malaria pathogenicity results from the parasites ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in{Delta} pfap2-mrp parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the{Delta} pfap2-mrp parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.

genomics↗

bioRxiv2022

The purified recombinant FAT domain of the Focal Adhesion Kinase does not bind directly to recombinant Talin or MBD2 in vitro

Controlled localization and activation of the focal adhesion kinase (FAK) functionally links adhesion, migration and survival of the cell. The C-terminal focal adhesion targeting (FAT) domain of FAK is an important regulator of the localization, activation and molecular associations of FAK. Here, we aimed to investigate the structural basis for how FAK FAT binds to Talin and MBD2, which were previously reported to be cytoplasmic and nuclear ligands, respectively. Using several biophysical methods with purified recombinantly expressed protein constructs, we failed to observe measurable interactions between FAT and either the Talin FERM domain or MBD2. We conclude that the association of FAT with these proteins requires additional factors or post-translational modifications not present in bacterially produced purified proteins.

biophysics↗

bioRxiv2018

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

bioinformatics↗