Biology subjects

Hanna, S.

Publications and source records attributed to Hanna, S..

8 recordsLinked to original sources

bioRxiv2026

De novo design of a macrocycle induced dimerization system for cellular control

Investigating and manipulating cellular events requires precise control of protein function. To enable control over cellular processes, we set out to design a chemically induced dimerization (CID) system consisting of a de novo designed ligand and protein pair. Here we describe the design of a C2 symmetric membrane permeable macrocyclic peptide and a cognate protein homodimer which binds the macrocycle through a large interface with both chains. The designed homodimer binds the macrocycle with a KD of 36 nM, and the x-ray crystal structure of the protein homodimer-macrocycle complex is very close to the computational design model, with the C2 axis of the macrocycle aligned with the homodimer C2 axis. Transcriptional and split luciferase assays in mammalian cells demonstrates conditional control over both a reporter gene expression and luciferase reconstitution.

biochemistry↗

bioRxiv2022

Rapid Single-Shot Synthesis of the 217 Amino Acid-Long N-Terminal Domain of Pyocin S2

The impermeable outer membrane of Pseudomonas aeruginosa is bypassed by antibacterial proteins known as S-type pyocins. Because of their properties, pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections. Their production and modification, however, remains challenging. To address this limitation, we employed automated fast-flow peptide synthesis (AFPS) for the rapid production of a pyocin S2 import domain. The N-terminal domain sequence (PyS2NTD) was synthesized in under 10 hours and purified to yield milligrams quantities of the desired product. To our knowledge, the 217 amino acid sequence of PyS2NTD is among the longest peptides produced from a "single-shot" synthesis, i.e., made in a single stepwise route without the use of ligation techniques. Biophysical characterization of the PyS2NTD with circular dichroism was consistent with the literature reports. Fluorescently labeled PyS2NTD binds to P. aeruginosa expressing the cognate ferripyoverdine receptor (FpvA) and is taken up into the periplasm. This selective uptake was validated with confocal and super resolution microscopy, flow cytometry, and fluorescence recovery after photobleaching (FRAP). These modified, synthetic S-type pyocins domains can be used to probe import mechanisms of P. aeruginosa and leveraged to develop selective antimicrobial agents that bypass the outer membrane.

synthetic biology↗

bioRxiv2020

Optical Tweezer Stretching of Miniature Coarse-Grained Red Blood Cells

Due to the high computational cost of full-cell coarse-grained molecular dynamics modelling, being able to simulate "miniature" cells that effectively represent their full-sized counterparts would be highly advantageous. To accurately represent the morphological and elastic properties of a human red blood cell in silico, such a model is employed utilising the molecular dynamics package LAMMPS. The scale invariance of the model is first tested qualitatively by following the shape evolution of red blood cells of various diameters, then quantitatively by evaluating the membrane shear modulus from simulations of optical tweezer-style stretching. Cells of physical diameter of at least 0.5{micro}m were able to form the characteristic biconcave shape of human red blood cells, though smaller cells instead equilibrated to bowl-shaped stomatocytes. A positive correlation was found between the cell size and both magnitude of deformation from optical tweezer stretching and scaled shear modulus, indicating a lack of scale invariance in the models elastic response. However, the stable morphology and measured shear modulus of the 0.5 - 1.0{micro}m diameter cells are deemed close enough to past in vitro studies on human red blood cells for them to still offer valuable use in making simplified predictions of whole-cell mechanics. SIGNIFICANCEThe study tests the invariance of a coarse-grained molecular dynamics red blood cell (RBC) model to system scale, asking whether it is qualitatively and quantitatively viable to perform whole-cell simulations in "miniature". Simulating cells at a reduced scale greatly improves computational speed, making possible computational experiments that would otherwise be too computationally demanding. This facilitates the simulation of larger systems, both in number of whole-cells, and cells of greater structural complexity than the RBC. More generally, the accurate and efficient modelling of biological cells allows computational experimentation of real-world systems that would be very challenging or impossible to perform in vitro. Therefore, miniature-cell modelling could help both direct development in whole-cell modelling, and also developments in more widespread bio-physical studies.

biophysics↗

bioRxiv2020

De Novo Discovery of High Affinity Peptide Binders for the SARS-CoV-2 Spike Protein

The {beta}-coronavirus SARS-CoV-2 has caused a global pandemic. Affinity reagents targeting the SARS-CoV-2 spike protein, the most exposed surface structure of the virus, are of interest for the development of therapeutics and diagnostics. We used affinity selection-mass spectrometry for the rapid discovery of synthetic high affinity peptide binders for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. From library screening with 800 million synthetic peptides, we identified three sequences with nanomolar affinities (dissociation constants Kd = 80 to 970 nM) for RBD and selectivity over human serum proteins. Picomolar RBD concentrations in biological matrix could be detected using the biotinylated lead peptide in ELISA format. These peptides might associate with the SARS-CoV-2-spike-RBD at a site unrelated to ACE2 binding, making them potential orthogonal reagents for sandwich immunoassays. We envision our discovery as a robust starting point for the development of SARS-CoV-2 diagnostics or conjugates for virus directed delivery of therapeutics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/317131v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@803e9borg.highwire.dtl.DTLVardef@18e5d74org.highwire.dtl.DTLVardef@1998310org.highwire.dtl.DTLVardef@16ba5cc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2020

Tripartite Inhibition of SRC-WNT-PKC Signalling Consolidates Human Naive Pluripotency

Different conditions have been devised to isolate MEK/ERK signalling independent human naive pluripotent stem cells (PSCs) that are distinct from conventional primed PSCs and better correspond to pre-implantation developmental stages. While the naive conditions described thus far endow human PSCs with different extents of naivety features, isolating human pluripotent cells that retain characteristics of ground state pluripotency while maintaining differentiation potential and genetic integrity, remains a major challenge. Here we engineer reporter systems that allow functional screening for conditions that can endow both the molecular and functional features expected from human naive pluripotency. We establish that simultaneous inhibition of SRC-NF{kappa}B, WNT/{beta}CATENIN and PKC signalling pathways is essential for enabling expansion of teratoma competent fully naive human PSCs in defined or xeno-free conditions. Divergent signalling and transcriptional requirements for maintaining naive pluripotency were found between mouse and human. Finally, we establish alternative naive conditions in which MEK/ERK inhibition is substituted with inhibition for NOTCH/RBPj signalling, which allow obtaining alternative human naive PSCs with diminished risk for loss of imprinting and deleterious global DNA hypomethylation. Our findings set a framework for the signalling foundations of human naive pluripotency and may advance its utilization in future translational applications. Highlights of key findingsO_LICombined inhibition of SRC, WNT and PKC signaling consolidates human naive pluripotency C_LIO_LIStable expansion of DNA/RNA methylation-independent and TGF/ACTIVIN-independent human naive PSCs C_LIO_LIOpposing roles for ACTIVIN and WNT/{beta}CATENIN signaling on mouse vs. human naive pluripotency C_LIO_LI2i and MEK/ERKi independent alternative human naive PSC conditions via inhibiting NOTCH/RBPj signaling C_LI

developmental biology↗

bioRxiv2018

Imaging of sub-cellular fluctuations provides a rapid way to observe bacterial viability and response to antibiotics

Determining the viability of bacteria in a sample is an essential microbiological technique used in healthcare, industrial bioprocesses and research. Increasingly, attention has been focussing on antimicrobial susceptibility tests (AST), allowing rapid and appropriate prescribing of antibiotics. Current AST are limited in speed as they rely on detecting growth of microorganisms. Faster AST could be enabled by the recent discovery that living bacteria manifest nano-scale fluctuations, which reduce when the bacteria die. Here, we demonstrate a direct method of visualising fluctuations within bacterial cells using Sub-Cellular Fluctuation Imaging (SCFI), which is based on Total Internal Reflection Microscopy (TIRM). We show that SCFI can measure the viability of bacterial samples within minutes, distinguishing not only between live and dead bacteria but also live bacteria in different metabolic states. Importantly, we subsequently show that SCFI can rapidly distinguish antibiotic-treated resistant and susceptible bacteria, and therefore has particular application as a rapid AST.

physiology↗

bioRxiv2018

Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

The Nucleosome Remodeling and Deacytelase (NuRD) complex is a co-repressive complex involved in many pathological and physiological processes in the cell. Previous studies have identified one of its components, Mbd3, as a potent inhibitor for reprogramming of somatic cells to pluripotency. Following OSKM induction, early and partial depletion of Mbd3 protein followed by applying naive ground-state pluripotency conditions, results in a highly efficient and near-deterministic generation of mouse iPS cells. Increasing evidence indicates that the NuRD complex assumes multiple mutually exclusive protein complexes, and it remains unclear whether the deterministic iPSC phenotype is the result of a specific NuRD sub complex. Since complete ablation of Mbd3 blocks somatic cell proliferation, here we aimed to identify alternative ways to block Mbd3-dependent NuRD activity by identifying additional functionally relevant components of the Mbd3/NuRD complex during early stages of reprogramming. We identified Gatad2a (also known as P66), a relatively uncharacterized NuRD-specific subunit, whose complete deletion does not impact somatic cell proliferation, yet specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuit during both stem cell differentiation and reprogramming to pluripotency. Complete ablation of Gatad2a in somatic cells, but not Gatad2b, results in a deterministic naive iPSC reprogramming where up to 100% of donor somatic cells successfully complete the process within 8 days. Genetic and biochemical analysis established a distinct sub-complex within the NuRD complex (Gatad2a-Chd4-Mbd3) as the functional and biochemical axis blocking reestablishment of murine naive pluripotency. Disassembly of this axis by depletion of Gatad2a, results in resistance to conditions promoting exit of naive pluripotency and delays differentiation. We further highlight context- and posttranslational dependent modifications of the NuRD complex affecting its interactions and assembly in different cell states. Collectively, our work unveils the distinct functionality, composition and interactions of Gatad2a-Chd4-Mbd3/NuRD subcomplex during the resolution and establishment of mouse naive pluripotency.

developmental biology↗

bioRxiv2017

High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency

The ability to reprogram somatic cells into induced pluripotent stem cells (iPSCs) with four transcription factors Oct4, Sox2, Klf4 and cMyc (abbreviated as OSKM)1 has provoked interest to define the molecular characteristics of this process2-7. Despite important progress, the dynamics of epigenetic reprogramming at high resolution in correctly reprogrammed iPSCs and throughout the entire process remain largely undefined. This gap in understanding results from the inefficiency of conventional reprogramming methods coupled with the difficulty of prospectively isolating the rare cells that eventually correctly reprogram into iPSCs. Here we characterize cell fate conversion from fibroblast to iPSC using a highly efficient deterministic murine reprogramming system engineered through optimized inhibition of Gatad2a-Mbd3/NuRD repressive sub-complex. This comprehensive characterization provides single-day resolution of dynamic changes in levels of gene expression, chromatin modifications, TF binding, DNA accessibility and DNA methylation. The integrative analysis identified two transcriptional modules that dominate successful reprogramming. One consists of genes whose transcription is regulated by on/off epigenetic switching of modifications in their promoters (abbreviated as ESPGs), and the second consists of genes with promoters in a constitutively active chromatin state, but a dynamic expression pattern (abbreviated as CAPGs). ESPGs are mainly regulated by OSK, rather than Myc, and are enriched for cell fate determinants and pluripotency factors. CAPGs are predominantly regulated by Myc, and are enriched for cell biosynthetic regulatory functions. We used the ESPG module to study the identity and temporal occurrence of activating and repressing epigenetic switching during reprogramming. Removal of repressive chromatin modifications precedes chromatin opening and binding of RNA polymerase II at enhancers and promoters, and the opposite dynamics occur during repression of enhancers and promoters. Genome wide DNA methylation analysis demonstrated that de novo DNA methylation is not required for highly efficient conducive iPSC reprogramming, and identified a group of super-enhancers targeted by OSK, whose early demethylation marks commitment to a successful reprogramming trajectory also in inefficient conventional reprogramming systems. CAPGs are distinctively regulated by multiple synergystic ways: 1) Myc activity, delivered either endogenously or exogenously, dominates CAPG expression changes and is indispensable for induction of pluripotency in somatic cells; 2) A change in tRNA codon usage which is specific to CAPGs, but not ESPGs, and favors their translation. In summary, our unbiased high-resolution mapping of epigenetic changes on somatic cells that are committed to undergo successful reprogramming reveals interleaved epigenetic and biosynthetic reconfigurations that rapidly commission and propel conducive reprogramming toward naive pluripotency.

developmental biology↗