Biology subjects

Ahmed, Y.

Publications and source records attributed to Ahmed, Y..

18 recordsLinked to original sources

bioRxiv2026

A new class of lipid transfer proteins is required for the recycling of lipids from the P. falciparum digestive vacuole

Malaria parasites endocytose large quantities of hemoglobin from the host erythrocyte, a process critical for parasite survival, leading to extensive membrane internalization. While hemoglobin degradation in the digestive vacuole (DV) is well studied, how the parasite deals with the membranes arriving within the DV is unknown. Here we identified PfTUPA, a previously uncharacterized lipid transfer protein in the DV membrane that is needed for this function. PfTUPA contains a soluble TULIP-like lipid transport domain exposed to the DV lumen and a transmembrane lipid transfer domain of bacterial origin (PqiA) in the DV membrane. Structural comparisons revealed proteins with various PqiA and TULIP-like domain combinations across distant eukaryotic clades, indicating this is a frequent functional partnership. Hence, PfTUPA belongs to a new class of eukaryotic lipid transfer proteins that in malaria parasites is needed for a key function of its biology.

microbiology↗

bioRxiv2026

Optical Spectral Fingerprinting Enables Sensitive Detection of Anthracycline Chemotherapeutics in Synthetic Clinical Biofluids

Anthracycline chemotherapeutics are commonly used as frontline treatments for a wide array of cancers. However, their administration to patients results in substantial side effects, primarily cardiotoxicity, as well as myelosuppression and gastrointestinal toxicity. Current clinical management of such side effects is solely based on a lifetime dosage limit, which inhibits their anti-tumor efficacy. Many individualized factors, including age, family history of cardiovascular disease, treatment regimen, and other co-morbidities influence drug pharmacology. Despite this heterogeneity, there is no method for determining actual organ or tumor exposure to the treatment in an individual. Here, we developed an optical nanosensor array for four anthracyclines--doxorubicin, daunorubicin, epirubicin, and idarubicin. We used single-walled carbon nanotubes as the signal transducer due to their tunable near-infrared fluorescence. We screened twelve distinct ssDNA sequences paired with seven SWCNT (n,m) species at increasing concentrations of each of the four anthracyclines. The spectral responses were then used to develop machine learning-based classification models to identify different anthracycline types and concentrations. The optimized extreme gradient boosting model was able to classify high levels of each anthracycline with 100% accuracy. Concentration-based classification by PCA was performed for each anthracycline, distinguishing low ([≤] 5 {micro}M) and high (> 5 {micro}M) concentrations. Finally, we validated the sensor performance using synthetic urine and sweat. Our findings demonstrate the potential of carbon nanotube-based sensor array to measure the pharmacokinetics of anthracyclines in patients with the goal of enhancing anti-tumor efficacy and monitoring off-target toxicities.

bioengineering↗

bioRxiv2026

Leveraging Unified Sequence-Structure Representations for Enhanced Protein Stability Prediction

Protein thermal stability, quantified by the change in Gibbs free energy ({Delta}{Delta}G) upon mutation, is critical for drug design and enzyme engineering. Current multi-modal deep learning models, despite integrating sequence, often struggle with indirect information fusion and incomplete capture of sequence-structure interactions. We introduce ProStab-Former, addressing these limitations by establishing a unified sequence-structure representation space for protein stability prediction. It leverages a frozen, multi-modal protein foundation encoder for residue-level feature extraction. Fine-tuned modules include Stability-Aware Attention Layers (SAAL) with structural prior bias and mutation-aware gating, and an Epistatic Interaction Module for multi-point mutation prediction. The model achieves superior or competitive performance, surpassing a state-of-the-art baseline. Ablation confirms SAALs critical role; strong generalization is shown across tasks including melting temperature prediction and pathogenic mutation classification. Its exceptional efficiency, predicting numerous single-point mutations in a single pass, positions it as a practical tool for high-throughput protein engineering and variant effect analysis.

bioinformatics↗

bioRxiv2025

A Shared Amyloid Architecture in Cardiac Fibrils from Three Neuropathy-Associated ATTR Variants

ATTR amyloidosis results from the systemic accumulation of wild-type (ATTRwt) or mutant (ATTRv) transthyretin amyloids, leading to multi-organ dysfunction and death. The disease exhibits variable pathology and penetrance, and its relationship with the amyloid structure remains unclear. Patients carrying the neuropathy-associated variants ATTRvI84S and ATTRv-V122{Delta} present polymorphic ATTR fibrils, in contrast to the consistent morphology reported for most ATTR fibrils to date. Here, we aim to elucidate a potential link between neuropathic symptomatology, distinct mutations, and amyloid structural diversity, using cryo-EM. We determined the ex-vivo fibril structures from the variants ATTRv-P24S, ATTRv-A25S, and ATTRv-D38A, whose patients presented variable clinical manifestations, including neuropathy. Our findings revealed that, despite differences in mutations and diverse clinical phenotypes, these variants share a common amyloid core previously identified in ATTRwt and several other cardiac ATTRv. This structural consistency is significant for the development of structure-guided diagnostic tools capable of addressing the diverse spectrum of ATTR amyloidosis. HighlightsO_LIDetermines transthyretin amyloid structures of three human ATTRv by cryo-EM C_LIO_LIDetermines the structure of three ex-vivo ATTRv fibrils linked to polyneuropathy. C_LIO_LIReveals structural similarities of ATTRv amyloid cores. C_LIO_LIReveals a common fold despite the different mutations and symptomatology. C_LIO_LIContributes to the understanding of transthyretin aggregation in patients with diverse phenotypes C_LI

biophysics↗

bioRxiv2025

Structural polymorphism of ex-vivo ALECT2 amyloid fibrils revealed by cryo-EM

ALECT2 amyloidosis is a rare systemic disease characterized by the pathological deposition of leukocyte cell-derived chemotaxin-2 (LECT2) as amyloid fibrils, primarily affecting the kidneys and liver. The molecular mechanisms underlying LECT2 aggregation remain poorly defined, hindering diagnostic and therapeutic development. Here, we present cryo-electron microscopy structures of ex-vivo ALECT2 fibrils extracted from a patients kidney. We identified three fibril polymorphs: a predominant single-protofilament morphology and two minor double-protofilament morphologies. The dominant single-protofilament morphology comprises the full-length 133-residue LECT2 protein and retains all three native disulfide bonds. Low-resolution reconstructions of double-protofilament morphologies suggest they adopt a similar fold to the single protofilament morphology, but form paired assemblies with different inter-filament interfaces. Mass spectrometry also reveals acetylation within the fibrils. These findings offer critical insights into the structural basis of ALECT2 amyloid formation and identify molecular features that could inform future diagnostic and therapeutic approaches.

biophysics↗

bioRxiv2025

Structural variability of apolipoprotein A-I amyloid fibrils across organs, mutations, and clinical presentations, revealed by cryo-EM

Hereditary apolipoprotein A-I (AapoA-I) amyloidosis is a rare systemic disease caused by the deposition of amyloid fibrils formed by apolipoprotein A-I in multiple organs, leading to severe clinical outcomes. With no available therapies or diagnostic tools, defining the structure of AApoA-I fibrils is crucial to understanding disease mechanisms and guiding intervention. Using cryo-electron microscopy, we analyzed AApoA-I fibrils from the heart, kidney, liver, and spleen of patients carrying G26R, L90P, and R173P mutations. G26R fibrils, regardless of organ, exhibited untwisted morphologies and could not be resolved structurally. Conversely, L90P and R173P fibrils displayed a compact diabolo-shaped conformation in all organs analyzed. Their high-resolution maps enabled visualization of cis-Proline 66, which may represent a potential conformational switch during fibril formation. Our findings suggest that mutation-driven polymorphism may influence organ tropism and clinical presentation. This work advances our understanding of AapoA-I fibril assembly and provides insights toward developing targeted clinical tools.

biophysics↗

bioRxiv2025

Pex30-dependent membrane contacts sites maintain ER lipid homeostasis

In eukaryotic cells, communication between organelles and the coordination of their activities depend on membrane contact sites (MCS). How MCS are regulated under the dynamic cellular environment remains poorly understood. Here, we investigate how Pex30, a membrane protein localized to the endoplasmic reticulum (ER), regulates multiple MCS in budding yeast. We show that Pex30 is critical for the integrity of ER MCS with peroxisomes and vacuoles. This requires the Dysferlin domain (DysF) on Pex30 cytosolic tail. This domain binds to phosphatidic acid (PA) both in vitro and in silico, and it is important for normal PA metabolism in vivo . The DysF domain is evolutionarily conserved and may play a general role in PA homeostasis across eukaryotes. We further show that ER-Vacuole MCS requires Pex30 C-terminal Domain of Unknown Function and that its activity is controlled by phosphorylation in response to metabolic cues. These findings provide new insights into the dynamic nature of MCS and their coordination with cellular metabolism.

cell biology↗

bioRxiv2024

ATTRv-V30M Type A amyloid fibrils from the heart and nerves exhibit structural homogeneity.

ATTR amyloidosis is a systemic disease characterized by the deposition of amyloid fibrils made of transthyretin, a protein integral to transporting retinol and thyroid hormones. Transthyretin is primarily produced by the liver and circulates in blood as a tetramer. The retinal epithelium also secretes transthyretin, which is secreted to the vitreous humor of the eye. Because of mutations or aging, transthyretin can dissociate into amyloidogenic monomers triggering amyloid fibril formation. The deposition of transthyretin amyloid fibrils in the myocardium and peripheral nerves causes cardiomyopathies and neuropathies, respectively. Using cryo-electron microscopy, here we determined the structures of amyloid fibrils extracted from cardiac and nerve tissues of an ATTRv-V30M patient. We found that fibrils from both tissues share a consistent structural conformation, similar to the previously described structure of cardiac fibrils from an individual with the same genotype, but different from the fibril structure obtained from the vitreous humor. Our study hints to a uniform fibrillar architecture across different tissues within the same individual, only when the source of transthyretin is the liver. Moreover, this study provides the first description of ATTR fibrils from the nerves of a patient and enhances our understanding of the role of deposition site and protein production site in shaping the fibril structure in ATTRv-V30M amyloidosis.

biophysics↗

bioRxiv2024

Multi-organ structural homogeneity of amyloid fibrils in ATTRv-T60A amyloidosis patients, revealed by Cryo-EM

ATTR amyloidosis is a degenerative disorder characterized by the systemic deposition of the protein transthyretin. These amyloid aggregates of transthyretin (ATTR) can deposit in different parts of the body causing diverse clinical manifestations. Our laboratory aims to investigate a potential relationship between the different genotypes, organ of deposition, clinical phenotypes, and the structure of ATTR fibrils. Using cryo-electron microscopy, we have recently described how the neuropathic related mutations ATTRv-I84S and ATTRv-V122{Delta} can drive structural polymorphism in ex vivo fibrils. Here we question whether the mutation ATTRv-T60A, that commonly triggers cardiac and neuropathic symptoms, has a similar effect. To address this question, we extracted and determined the structure of ATTR-T60A fibrils from multiple organs (heart, thyroid, kidney, and liver) from the same patient and from the heart of two additional patients. We have found a consistent conformation among all the fibril structures, acquiring the "closed-gate morphology" previously found in ATTRwt and others ATTRv related to cardiac or mixed manifestations. The closed-gate morphology is composed by two segments of the protein that interact together forming a polar channel, where the residues glycine 57 to isoleucine 68 act as a gate of the polar cavity. Our study indicates that ATTR-T60A fibrils present in peripheral organs adopt the same structural conformation in all patients, regardless of the organ of deposition.

molecular biology↗

bioRxiv2024

Amyloid fibril polymorphism in the heart of an ATTR amyloidosis patient with polyneuropathy attributed to the V122Δ variant

ATTR amyloidosis is a phenotypically heterogeneous disease characterized by the pathological deposition of transthyretin in the form of amyloid fibrils into various organs. ATTR amyloidosis may result from mutations in variant (ATTRv) amyloidosis, or aging in wild-type (ATTRwt) amyloidosis. ATTRwt generally manifests as cardiomyopathy, whereas ATTRv may present as polyneuropathy, cardiomyopathy, or mixed, in combination with many other symptoms deriving from multisystem organ involvement. Over 220 different mutational variants of transthyretin have been identified, many of them being linked to specific disease symptoms. Yet, the role of these mutations in explaining differential disease manifestations remains unclear. Using cryo-electron microscopy, here we structurally characterized fibrils from the heart and the liver of an ATTRv patient carrying the V122{Delta} mutation, which is predominantly associated with polyneuropathy. Our results show that these fibrils are polymorphic, presenting as both single and double filaments. Our study alludes to a structural connection contributing to phenotypic variation in ATTR amyloidosis, as polymorphism in ATTR fibrils may manifest in patients with predominantly polyneuropathic phenotypes. SignificanceATTR amyloidosis is a systemic, clinically diverse disease that results in organ failure due to the accumulation of transthyretin amyloid fibrils. ATTR patients present with varied symptoms, yet the root of this phenotypic heterogeneity remains unclear. Previous studies suggest an association between phenotype and fibril structure polymorphism. Here we describe the cryo-electron microscopy structure of variant transthyretin amyloid fibrils associated with a predominantly polyneuropathy phenotype. We have found polymorphism within these fibrils, a phenomenon we have thus far only observed in polyneuropathic associated transthyretin mutations. Our results signify an association between fibril structure and phenotype in ATTR amyloidosis.

molecular biology↗

bioRxiv2024

Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis

ATTR amyloidosis results from the conversion of transthyretin into amyloid fibrils that deposit in tissues causing organ failure and death. This conversion is facilitated by mutations in ATTRv amyloidosis, or aging in ATTRwt amyloidosis. ATTRv amyloidosis exhibits extreme phenotypic variability, whereas ATTRwt amyloidosis presentation is consistent and predictable. Previously, we found an unprecedented structural variability in cardiac amyloid fibrils from polyneuropathic ATTRv-I84S patients. In contrast, cardiac fibrils from five genotypically-different patients with cardiomyopathy or mixed phenotypes are structurally homogeneous. To understand fibril structures impact on phenotype, it is necessary to study the fibrils from multiple patients sharing genotype and phenotype. Here we show the cryo-electron microscopy structures of fibrils extracted from four cardiomyopathic ATTRwt amyloidosis patients. Our study confirms that they share identical conformations with minimal structural variability, consistent with their homogenous clinical presentation. Our study contributes to the understanding of ATTR amyloidosis biopathology and calls for further studies. One-Sentence Summary: Wild-type cardiac ATTR fibrils are structurally homogeneous.

biophysics↗

bioRxiv2023

Caltubin regulates microtubule stability via Ca2+-dependent mechanisms favouring neurite regrowth

Microtubule regulation is highly controlled in nerve regeneration. Caltubin, a novel Lymnaea stagnalis protein, contains putative EF-hand calcium-binding motifs and promotes neuronal outgrowth in Lymnaea and mouse. Here, we generated cell-permeable caltubin proteins to investigate mechanisms underlying this effect. We observed increased neurite extension and outgrowth following injury in caltubin-treated mouse neurons compared to vehicle controls. Purified caltubin bound -tubulin between its L391-V405 amino acids and promoted microtubule assembly. Caltubin competitively inhibited binding of tubulin tyrosine ligase, which catalyzes tubulin retyrosination, and increased the ratio of detyrosinated to tyrosinated tubulin. Our crystal structure analysis confirmed that caltubin has four Ca2+-binding EF-hand motifs, like calmodulin but has distinct peptide binding domains. Our work suggests a unique Ca2+-dependent regulatory mechanism of microtubule assembly by caltubin. This may represent an essential mechanism of axonal regulation, which may optimize its activity in response to various calcium states, both physiological and following injury.

cell biology↗

bioRxiv2022

Structural polymorphism of amyloid fibrils in cardiac ATTR amyloidosis revealed by cryo-electron microscopy

The deposition of amyloidogenic transthyretin (ATTR) in ATTR amyloidosis leads to an unexplained variety of clinical phenotypes, including cardiomyopathy. In brain amyloid conditions, there is an apparent association between the clinical phenotype and the amyloid fibril structure. Here, we question this phenotype-structure association in cardiac amyloidoses by determining the cryo-electron microscopy structures of fibrils extracted from the hearts of seven ATTR amyloidosis patients. We found that, in contrast to brain fibrils, cardiac ATTR fibrils display a structural polymorphism that is not genotype-specific, can co-exist within the same individual, and is independent of the cardiac phenotype. This polymorphism challenges the current paradigm of "one disease equals one fibril fold" proposed in tauopathies and synucleinopathies, and questions whether a similar structural heterogeneity occurs in other amyloidoses. One-Sentence SummaryUnlike brain amyloid fibrils, cardiac ATTR fibrils are polymorphic independent of genotype and even within the same patient.

molecular biology↗

bioRxiv2022

Feedback in the β-catenin destruction complex imparts bistability and cellular memory

Wnt ligands are considered classical morphogens, for which the strength of the cellular response is proportional to the concentration of the ligand. Herein, we show an emergent property of bistability arising from feedback among the Wnt destruction complex proteins that target the key transcriptional co-activator {beta}-catenin for degradation. Using biochemical reconstitution, we identified positive feedback between the scaffold protein Axin and the kinase GSK3. Theoretical modeling of this feedback between Axin and GSK3 predicted that the activity of the destruction complex exhibits bistable behavior. We experimentally confirmed these predictions by demonstrating that cellular cytoplasmic {beta}-catenin concentrations exhibit an "all-or-none" response with sustained memory (hysteresis) of the signaling input. This bistable behavior was transformed into a graded response and memory was lost through inhibition of GSK3. These findings provide a mechanism for establishing decisive, switch-like cellular response and memory upon Wnt pathway stimulation. One Sentence SummaryPositive feedback within the {beta}-catenin destruction complex gives rise to bistability and memory in response to Wnt stimulation, imparting signal transduction accuracy and insulation.

cell biology↗

bioRxiv2022

Context-aware information selection and model recommendation with ACCORDION

New discoveries and knowledge are summarized in thousands of published papers per year per scientific domain, making it incomprehensible for scientists to account for all available knowledge relevant for their studies. In this paper, we present ACCORDION (ACCelerating and Optimizing model RecommenDatIONs), a novel methodology and an expert system that retrieves and selects relevant knowledge from literature and databases to recommend models with correct structure and accurate behavior, enabling mechanistic explanations and predictions, and advancing understanding. ACCORDION introduces an approach that integrates knowledge retrieval, graph algorithms, clustering, simulation, and formal analysis. Here, we focus on biological systems, although the proposed methodology is applicable in other domains. We used ACCORDION in nine benchmark case studies and compared its performance with other previously published tools. We show that ACCORDION is: comprehensive, retrieving relevant knowledge from a range of literature sources; very effective, reducing the error of the initial baseline model by more than 80%, recommending models that closely recapitulate desired behavior, and outperforming previously published tools; selective, recommending only the most relevant, context-specific, and useful subset (15-20%) of candidate knowledge in literature; diverse, accounting for several distinct criteria to recommend more than one solution, thus enabling alternative explanations or intervention directions.

systems biology↗

bioRxiv2021

Classifying Literature Extracted Events for Automated Model Extension

1In this study, we investigate the integration of three previously developed tools: FLUTE, VIOLIN, and CLARINET. We show how using these tools together adds additional capabilities in extending models from relevant research literature. We illustrate how we plan to address current modeling pitfalls with these tools (such as machine reading errors and literature volume), and how we plan to use these tools as the foundation for an automated model extension framework. Documentation and links to our tools can be found at: violin-tool.readthedocs.io clarinet-docs.readthedocs.io flute.readthedocs.io

systems biology↗

bioRxiv2020

CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation

In this work, we describe the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. A key aim of CRIMSON is to create a software environment that makes powerful computational haemodynamics tools accessible to a wide audience, including clinicians and students, both within our research laboratories and throughout the community. The overall philosophy is to leverage best-in-class open source standards for medical image processing, parallel flow computation, geometric solid modelling, data assimilation, and mesh generation. It is actively used by researchers in Europe, North and South America, Asia, and Australia. It has been applied to numerous clinical problems; we illustrate applications of CRIMSON to real-world problems using examples ranging from pre-operative surgical planning to medical device design optimization. CRIMSON binaries for Microsoft Windows 10, documentation and example input files are freely available for download from www.crimson.software, and the source code with compilation instructions is available on GitHub https://github.com/carthurs/CRIMSONFlowsolver (CRIMSON Flowsolver) under the GPL v3.0 license, and https://github.com/carthurs/CRIMSONGUI (CRIMSON GUI), under the AGPL v3.0 license. Support is available on the CRIMSON Google Groups forum, located at https://groups.google.com/forum/#!forum/crimson-users.

bioengineering↗

bioRxiv2019

An Interscholastic Network to Generate LexA Enhancer Trap Lines in Drosophila

Binary expression systems like the LexA-LexAop system provide a powerful experimental tool kit to study gene and tissue function in developmental biology, neurobiology and physiology. However, the number of well-defined LexA enhancer trap insertions remains limited. In this study, we present the molecular characterization and initial tissue expression analysis of nearly 100 novel StanEx LexA enhancer traps, derived from the StonEx1 index line. This includes 76 insertions into novel, distinct gene loci not previously associated with enhancer traps or targeted LexA constructs. Additionally, our studies revealed evidence for selective transposase-dependent replacement of a previously-undetected KP element on chromosome III within the StanEx1 genetic background during hybrid dysgenesis, suggesting a molecular basis for the over-representation of LexA insertions at the NK7.1 locus in our screen. Production and characterization of novel fly lines were performed by students and teachers in experiment-based genetics classes within a geographically diverse network of public and independent high schools. Thus, unique partnerships between secondary schools and university-based programs have produced and characterized novel genetic and molecular resources in Drosophila for open-source distribution, and provide paradigms for development of science education through experience-based pedagogy.

genetics↗