Biology subjects

Ohi, M. D.

Publications and source records attributed to Ohi, M. D..

15 recordsLinked to original sources

bioRxiv2026

Structural analyses of a heterodimeric SusCD complex captures intermediate states of maltooligosaccharide transport

Bacteroides are abundant gut bacteria with diverse polysaccharide metabolizing capabilities encoded by co-transcribed polysaccharide utilization loci (PULs). The starch utilization system (Sus) is required for starch and a-glucan metabolism in Bacteroides thetaiotaomicron and has served as a model for PUL studies. However, the mechanism of maltooligosaccharide (MOS) transport and the architecture of the SusCD complex remain incompletely understood. Here, we used cryo-electron microscopy to capture multiple transport-relevant conformations of the SusD lipoprotein and the TonB-dependent transporter SusC in both unliganded and ligand-bound states. In the absence of ligand, SusCD adopts three conformations including an open state in which SusD is displaced from SusC, a state containing the SusC plug, and a state lacking density for the SusC plug. Three-dimensional variability analysis of the structure where SusD is displaced from SusC reveals continuous SusD mobility coupled to movement of the SusC N-terminus. The maltoheptaose-bound SusCD structure reveals two binding sites, one at the SusD-SusC interface and a second within SusC, indicating how MOS stabilizes a closed SusCD assembly. Notably, all structures show that SusCD is a heterodimer, unlike other Sus-like transporters that assemble into SusCD heterotetramers. Native mass spectrometry confirms this heterodimeric stoichiometry, and comparisons with other SusCD-like complexes suggest a structural basis for this distinct assembly of SusCD. Together, these data define substrate binding and intermediate transport states in a canonical PUL system and reveal architectural divergence among Sus-like carbohydrate transport complexes in Bacteroides.

microbiology↗

bioRxiv2026

ResiRuler: A Toolkit for Visualizing Residue-Residue Distances and Structural Changes in Biomolecular Models

Proteins and their associated complexes often adopt multiple conformations, with the transitions between these states playing a critical role in biological function. However, the resulting structural heterogeneity can be challenging to visualize and communicate, often requiring manual inspection and time-consuming annotation of biomolecular structures. To address this, we developed ResiRuler, a local, browser-based tool that uses inter-residue distance measurements to quickly quantify atomic displacements and map changes in internal geometry across ensembles of related protein structures. By converting structural differences into residue-pair distance changes, ResiRuler enables rapid identification of regions undergoing coordinated motion, local rearrangement, or large-scale conformational change. The resulting visualizations can be exported as scripts for PyMOL and ChimeraX, allowing users to explore conformational differences and generate publication-quality molecular figures in their preferred visualization environment. Using atomic models in Macromolecular Crystallographic Information File (mmCIF) file format, ResiRuler aligns multiple structures and measures structural variation across models facilitating visualization and presentation of these differences. This allows for rapid visualization of which regions of proteins change among ensembles of structures. The program is available for download at https://github.com/tbaker67/ResiRuler on macOS and Linux operating systems.

bioinformatics↗

bioRxiv2026

The structural mechanism of eukaryotic fluoride channel activation and inhibition by monovalent cations

Fluoride is an environmentally prevalent inhibitor of fungi, plants, and other eukaryotes. The fluoride exporter (FEX) is the major resistance mechanism that prevents intracellular fluoride accumulation in eukaryotes. FEX activity is sodium-dependent, but the mechanism for Na+ activation and the impact of other cations on FEX function remain poorly understood. Here, we show that sodium and lithium have different effects on channel activity. We leverage these differences to understand how monovalent cations regulate FEX. Functional assays in a reconstituted system show that lithium acts as a competitive antagonist of channel activation by competing with sodium for the central cation binding site. We further demonstrate that FEX inhibition by lithium has consequences in vivo, as lithium markedly reduces fluoride tolerance of yeast. A cryo-EM structure of Candida albicans FEX with Li+, together with molecular dynamics (MD) simulations, reveals the structural mechanism underlying cation-dependent FEX activity. Whereas sodium binding supports a dynamic structure with a broader pore radius, lithium coordination causes a more rigid conformation that is more compact in the channels vestibule. These changes perturb the tilt angle of a pore lining helix, and the alter the rotamer of a key phenylalanine in the pore, which together constrict the permeation pathway. In addition to providing general insight into the mechanism of fluoride channel regulation by monovalent cations, these results identify lithium as a previously unknown environmental antagonist of eukaryotic fluoride export and tie cellular fluoride stress tolerance to the abundance of additional ions in the cellular milieu.

biochemistry↗

bioRxiv2026

Structural basis of caveolin-driven membrane bending

Caveolins are monotopic membrane proteins essential for caveolae formation and have key roles in signaling and lipid regulation. Caveolins assemble into amphipathic discs with a central {beta}-barrel, an architecture distinct from other membrane-remodeling proteins. These discs embed in the membrane inducing membrane curvature. However, the mechanism of disc-driven bending remains unresolved. Using cryo-electron tomography, structure-guided mutagenesis, and mammalian cell studies, we show that evolutionarily distinct caveolins differ dramatically in their ability to curve membranes despite their conserved architecture. Through computational and theoretical analyses, we demonstrate that patterning of hydrophobic residues along the rim of the disc of human Caveolin-1 induces the deformation of the surrounding leaflet, dictating membrane bending. Finally, we determine a 4.1[A] resolution structure of Caveolin-1 within heterologous caveolae in situ, showing the disc adopts a funnel-like conformation, further shaping membrane architecture. Together, these findings reveal fundamental structural principles that empower caveolins to sculpt and remodel cellular membranes.

cell biology↗

bioRxiv2025

The molecular basis of sodium-dependent fluoride export by the eukaryotic fluoride channel FEX

Much of life on Earth, including plants, fungi, and bacteria, evolved to resist toxic environmental fluoride. In eukaryotes, the major resistance mechanism is fluoride export by FEX proteins. Using electrophysiology and transport assays, we establish that FEX from plants and yeasts are fluoride channels whose activity depends on reversible sodium ion binding. A cryo-EM structure of FEX from Candida albicans, together with mutagenesis studies, reveals a fluoride permeation route through a single phenylalanine-lined pore. Molecular dynamics simulations demonstrate that a cation binding motif adjacent to the pore provides a stable sodium binding site that is accessible from the external aqueous solution. We propose that sodium gating resolves a major conundrum of channel-based fluoride efflux by preventing fluoride permeation under conditions of membrane depolarization. Comparison to bacterial fluoride channels (Flucs) provides a unique glimpse of the evolution of structural and mechanistic complexity in a membrane protein family with inverted repeat architecture.

biophysics↗

bioRxiv2025

Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA

The Rev Response Element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 infection. However, our structural understanding of this crucial virological process remains limited. In this study, we determined several crystal structures of an intact RRE stem-loop II in two distinct conformations, performed negative-staining electron microscopy and molecular dynamics simulations, and revealed that this three-way junction RNA exhibits remarkable structural plasticity. Through in vitro Rev-binding and in vivo Rev-activity assays using various stem-loop II mutants designed to favor one of the conformers, we demonstrated that the structural plasticity of stem-loop II modulates Rev binding and oligomerization. Our findings illuminate emerging perspectives on RRE dynamics-based regulation of HIV-1 RNA nuclear export and provide a framework for developing anti-HIV drugs that target specific RRE conformations.

biophysics↗

bioRxiv2024

Structural basis for catalysis and selectivity of phospholipid synthesis by eukaryotic choline-phosphotransferase

Phospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily synthesized de novo through the Kennedy pathway that involves multiple enzymatic processes. The terminal reaction is mediated by a group of cytidine-5-diphosphate (CDP)-choline /CDP-ethanolamine-phosphotransferases (CPT/EPT) that use 1,2-diacylglycerol (DAG) and CDP-choline or CDP-ethanolamine to produce phosphatidylcholine (PC) or phosphatidylethanolamine (PE) those are the main phospholipids in eukaryotic cells. Here we present the structure of the yeast CPT1 in multiple substrate-bound states. Structural and functional analysis of these binding-sites reveal the critical residues for the DAG acyl-chain preference and the choline/ethanolamine selectivity. Additionally, we present the structure in complex with a potent inhibitor characterized in this study. The ensemble of structures allows us to propose the reaction mechanism for phospholipid biosynthesis by the family of CDP-alcohol phosphatidyltransferases (CDP-APs).

biochemistry↗

bioRxiv2023

A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase

The mechanism by which polymerase -primase (pol-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of pol-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to pol and increases pol processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of pol and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by pol-primase.

biochemistry↗

bioRxiv2022

Structural characterization of a breast cancer-associated mutation in caveolin-1

Caveolin-1 (CAV1) is a membrane sculpting protein that oligomerizes to generate flask-shaped invaginations of the plasma membrane known as caveolae. Mutations in CAV1 have been linked to multiple diseases in humans. Such mutations often interfere with oligomerization and the intracellular trafficking processes required for successful caveolae assembly, but the molecular mechanisms underlying these defects have not been structurally explained. Here, we investigate how a breast cancer-associated mutation in one of the most highly conserved residues in CAV1, P132L, affects CAV1 structure and oligomerization. We show that P132 is positioned at a major site of protomer-protomer interactions within the CAV1 complex, providing a structural explanation for why the mutant protein fails to homo-oligomerize correctly. Using a combination of computational, structural, biochemical, and cell biological approaches, we find that despite its homo-oligomerization defects P132L is capable of forming mixed hetero-oligomeric complexes with wild type CAV1 and that these complexes can be incorporated into caveolae. These findings provide insights into the fundamental mechanisms that control the formation of homo- and hetero-oligomers of caveolins that are essential for caveolae biogenesis, as well as how these processes are disrupted in human disease.

biophysics↗

bioRxiv2022

Molecular architecture of the human caveolin-1 complex

Membrane sculpting proteins shape the morphology of cell membranes and facilitate remodeling in response to physiological and environmental cues. Complexes of the monotopic membrane protein caveolin function as essential curvature-generating components of caveolae, flask-shaped invaginations that sense and respond to plasma membrane tension. However, the structural basis for caveolins membrane remodeling activity is currently unknown. Here, we show, using cryo-electron microscopy, that the human caveolin-1 complex is composed of 11 protomers organized into a tightly packed disc with a flat membrane-embedded surface. The structural insights suggest a new mechanism for how membrane sculpting proteins interact with membranes and reveal how key regions of caveolin-1, including its scaffolding, oligomerization, and intramembrane domains, contribute to its function. One-Sentence SummaryCryo-electron microscopy reveals that Caveolin-1 oligomerizes into a tightly packed disc with a flat membrane-binding surface.

biophysics↗

bioRxiv2021

Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SS

Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires Disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 [A] resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure. We hypothesize this conformational flexibility is likely to facilitate the Dot/Icm T4SSs ability to translocate a remarkably large set of [~]300 putative substrates across the inner and outer membranes of the bacterial cell.

microbiology↗

bioRxiv2020

Cryo-EM reveals species-specific components within the Helicobacter pylori Cag type IV secretion system core complex

The pathogenesis of Helicobacter pylori-associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The H. pylori Cag T4SS includes a large membrane-spanning core complex containing 5 proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the H. pylori T4SS core complex is dependent on incorporation of interwoven species-specific components.

microbiology↗

bioRxiv2020

Structural analysis of the Legionella pneumophila Dot/Icm Type IV Secretion System Core Complex

Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine.

microbiology↗

bioRxiv2020

Structure and assembly of CAV1 8S complexes revealed by single particle electron microscopy

Highly stable oligomeric complexes of the monotopic membrane protein caveolin serve as fundamental building blocks of caveolae. Current evidence suggests these complexes are disc shaped, but the details of their structural organization and how they assemble are poorly understood. Here, we address these questions using single particle electron microscopy of negatively stained recombinant 8S complexes of human Caveolin-1. We show that 8S complexes are toroidal structures ~15 nm in diameter that consist of an outer ring, an inner ring, and central protruding stalk. Moreover, we map the position of the N- and C-termini and determine their role in complex assembly, and visualize the 8S complexes in heterologous caveolae. Our findings provide critical insights into the structural features of 8S complexes and allow us to propose a new model for how these highly stable membrane-embedded complexes are generated.

cell biology↗

bioRxiv2018

Microtubule minus-end aster organization is driven by processive HSET-tubulin clusters

Higher-order structures of the microtubule (MT) cytoskeleton are comprised of two architectures: bundles and asters. Although both architectures are critical for cellular function, the molecular pathways that drive aster formation are poorly understood. Here, we study aster formation by human minus-end directed kinesin-14 (HSET/KIFC1). We show that HSET is incapable of forming asters from pre-formed, non-growing MTs, but rapidly forms MT asters in the presence of soluble tubulin. HSET binds soluble (non-polymer) tubulin via its N-terminal tail domain to form heterogeneous HSET-tubulin \"clusters\" containing multiple motors. Cluster formation induces motor processivity and rescues the formation of asters from non-growing MTs. We then show that excess soluble tubulin stimulates aster formation in HeLa cells overexpressing HSET during mitosis. We propose a model where HSET can toggle between MT bundle and aster formation in a manner governed by the availability of soluble tubulin.

biophysics↗