Biology subjects

Abdul, W.

Publications and source records attributed to Abdul, W..

7 recordsLinked to original sources

bioRxiv2024

Enantiomeric histidine-rich peptide coacervates enhance antigen delivery to T cells

Peptides and peptidomimetics that self-assemble via LLPS have recently emerged as building blocks for fabricating functional biomaterials due to their unique physicochemical properties and dynamic nature. One of lifes most distinctive signatures is its selectivity for chiral molecules and, to date, coacervates comprised of D-amino acids have not been reported. Here, we demonstrate that histidine-rich repeats of (GHGXY)4 (X=L/V/P) and their enantiomers undergo LLPS opening new avenues for enhancing coacervate stability. Through a series of biophysical studies, we find that LLPS kinetics, droplet size, fusion, and encapsulation efficiency are dictated by the primary sequence. Further, these coacervates can encapsulate therapeutic cargo which are then internalized via endocytic mechanisms. Finally, we show that the coacervates enhance antigen presentation to CD4+ and CD8+ T cells resulting in robust proliferation and production of functional cytokines. Collectively, our study describes the development and characterization of enantiomeric peptide coacervates as attractive vaccine delivery vehicles with tunable physicochemical properties. HIGHLIGHTSO_LID amino acid-peptides were used for the first time to construct phase separating coacervates C_LIO_LIChirality does not restrict LLPS or modulate other coacervate properties C_LIO_LIAntigen delivery using chiral coacervates enhances and prolongs presentation to T cells C_LI PROGRESS AND POTENTIALPeptides can undergo self-assembly via liquid-liquid phase separation (LLPS) to result in solute-rich coacervates that can serve as biomaterials. Using histidine-rich peptide repeats, this work demonstrates that peptides composed of entirely D-amino acids can form functional coaceravtes. The kinetics of LLPS and bulk properties of the droplets can be controlled through simple amino acid substitutions. The coacervates, while immunologically inert, exert an adjuvanting effect and enhance antigen presentation to T cells leading to proliferation and functional cytokine production. The materials showcased here possess high translational potential for combined delivery of immunomodulators and antigens for vaccine delivery against infectious diseases or cancer. The deliverables from this study will also inspire the development of chiral systems that will contribute to the knowledge of cellular processes associated with phase changes integral to both physiology and pathology.

bioengineering↗

bioRxiv2024

A reaction-diffusion model captures the essence of liquid-liquid phase separation

In this work we propose the formulation of a continuum model for liquid-liquid phase separation (LLPS) using reaction diffusion framework. We consider a well mixed liquid consisting of three phases, the dense droplet phase, the dilute phase and the remaining part to be solvent phase. As a key feature, the model includes both the spatial and temporal aspects and a free energy functional between dense and dilute phase that is physically motivated by reference molecular simulation. The exhaustive numerical simulations of model captures the dynamical formation of droplets and existence of LLPS. As the time progresses, simulation reveal that smaller droplets gradually vanish, and a single droplet undergoes continuous growth until it reaches a stable size. The model predicts that that extent of diffusivity of dense and dilute phase as well as their mutual interaction would modulate the kinetics of droplet formation. Finally we show that introduction of fluctuation in the model accelerate the phase separation process.

biophysics↗

bioRxiv2024

Discovery of dynamic changes in 3D chromatin architecture through polymer physics model

The 3D organisation of the genome provides an intricate relationship between the chromatin architecture and its effects on the functional state of the cell. Recent advances in high-throughput sequencing and chromosome conformation capture technologies elucidated a comprehensive view of chromatin interactions on a genome-wide scale but provides only a 2D representation of how the chromatin is organised inside the cell nucleus. To quantitatively understand the structural alterations and dynamics of chromatin in 3D, we have developed a computational model that not only captures the hierarchical structural organisation but also provides mechanistic insights into the dynamics of spatial rearrangements of chromatin in developing lymphoid lineage cells. From the combination of approaches of polymer physics representing chromatin as a homopolymeric chain and incorporation of the biological information of chromosomal interactions inferred from the Hi-C data, we generated a coarse grained bead-on-a-string polymer model of chromatin to comprehend the mechanisms underlying the differential chromatin architecture. Our study showed that our simulated chromatin structure recapitulates the intrinsic features of chromatin organisation, including the fractal globule nature, compartmentalization, presence of topologically associating domains (TADs), phase separation and spatial preferences of genomic regions in the chromosomal territories. Comparative analyses of these simulated chromatin structures of differentiating B cell stages revealed compartmental switching and changes in the spatial positioning of lineage specific genomic regions. Analysis of the compactness of the switched regions showed insights into their acquired open-closed states for gene regulation and hence governing the cell fate through consequent structural rearrangement. Based on the remarkable performance of our model, we emphasise on its predictive potential by identifying switching of novel regions that demonstrated undergoing structural rearrangement which was subsequently validated through their differential expression patterns in vitro. These results reveal that although the chromatin organisation seems similar in most cell types, it undergoes distinct structural changes for the regulatory role of chromatin in sustaining cell specificity.

bioinformatics↗

bioRxiv2024

Protein Translation Can Fluidize Bacterial Cytoplasm

The cytoplasm of bacterial cells is densely packed with highly polydisperse macromolecules that exhibit glassy dynamics. Research has revealed that metabolic activities in living cells can counteract the glassy nature of these macromolecules, allowing the cell to maintain critical fluidity for its growth and function. While it has been proposed that the crowded cytoplasm is responsible for this glassy behavior, a detailed explanation for how cellular activity induces fluidization remains elusive. In this study, we introduce and validate a novel hypothesis through computer simulations: protein synthesis in living cells contributes to the metabolism-dependent fluidization of the cytoplasm. The main protein synthesis machinery, ribosomes, frequently shift between fast and slow diffusive states. These states correspond to the independent movement of ribosomal subunits and the actively translating ribosome chains called polysomes, respectively. Our simulations demonstrate that the frequent transitions of the numerous ribosomes, which constitute a significant portion of the cell proteome, greatly enhance the mobility of other macromolecules within the bacterial cytoplasm. Considering that ribosomal protein synthesis is the largest consumer of ATP in growing bacterial cells, the translation process likely serves as the primary mechanism for fluidizing the cytoplasm in metabolically active cells.

biophysics↗

bioRxiv2023

On the Spatial Positioning of Ribosomes around chromosome in E. coli Cytoplasm

The spatial organization of ribosomes in the cytoplasm of Escherichia coli (E. coli) bacteria has been a subject of longstanding intrigue. Previous investigations suggested that ribosomes remain completely excluded from the chromosome-rich nucleoid region in a "poor solvent" like cytoplasm. Here, we present an integrated model of the bacterial cytoplasm, informed by experimental data, which updates this prevailing narrative. We demonstrate that ribosomes maintain a delicate balance of both attractive and repulsive interactions with the chromosome, contrary to the conventional notion of it acting as an inert crowder in cytoplasm. The multi-dimensional spatial distribution of free ribosomes (30S and 50S) and bound ribosomes (70S polysome) inside the cytoplasm reveals that the extent of mutual ribosome-chromosome segregation is relatively less pronounced due to the presence of non-negligible amount of ribosomes within the inner core of the cytoplasm. In particular, we identify a central void within the inner-most core of the nucleoid that lacks chromosomal DNA but can accommodate finite proportion of both free (11 %) and bound (18 %) ribosomes. Furthermore, our analysis of the chromosome mesh size and the conformation of bound ribosomes suggests that bound ribosomes remain elongated and would be able to navigate past the chromosome mesh to access the central void. Together by highlighting the dynamic nature of ribosome localization in E. coli, this investigation proposes that this segregation is crucial for maximizing the utilization of synthesized mRNA and facilitating efficient translation into proteins, which are essential for bacterial survival.

biophysics↗

bioRxiv2021

Mechanistic underpinning of nonuniform collective motions in swarming bacteria

Self-propelled bacteria can exhibit a large variety of non-equilibrium self-organized phenomena. Swarming is one such fascinating dynamical scenario where a number of motile individuals grouped into clusters and move in synchronized flows and vortices. While precedent investigations in rod-like particles confirm that increased aspect-ratio promotes alignment and order, recent experimental studies in bacteria Bacillus subtilis show a non-monotonic dependence of cell-aspect ratio on their swarming motion. Here, by computer simulations of an agent-based model of selfpropelled, mechanically interacting, rod-shaped bacteria in overdamped condition, we explore the collective dynamics of bacterial swarm subjected to a variation of cell-aspect ratio. When modeled with an identical self-propulsion speed across a diverse range of cell aspect ratio, simulations demonstrate that both shorter and longer bacteria exhibit slow dynamics whereas the fastest speed is obtained at an intermediate aspect ratio. Our investigation highlights that the origin of this observed non-monotonic trend of bacterial speed and vorticity with cell-aspect ratio is rooted in the cell-size dependence of motility force. The swarming features remain robust for a wide range of surface density of the cells, whereas asymmetry in friction attributes a distinct effect. Our analysis identifies that at an intermediate aspect ratio, an optimum cell size and motility force promote alignment, which reinforces the mechanical interactions among neighboring cells leading to the overall fastest motion. Mechanistic underpinning of the collective motions reveals that it is a joint venture of the short-range repulsive and the size-dependent motility forces, which determines the characteristics of swarming.

biophysics↗

bioRxiv2020

Nucleoid associated proteins and their effect on E. coli chromosome

A seemingly random and disorganized bacterial chromosome, in reality, is a well organized nucleus-like structure, called the nucleoid, which is maintained by several nucleoid associated proteins(NAPs). Here we present an application of a previously developed Hi-C based computational method to study the effects of some of these proteins on the E. coli chromosome. Simulations with encoded Hi-C data for mutant, hupAB deficient, E. coli cells, revealed a decondensed, axially expanded chromosome with enhanced short range and diminished long range interactions. Simulations for mutant cells deficient in FIS protein revealed that the effects are similar to that of the hupAB mutant, but the absence of FIS led to a greater disruption in chromosome organization. Absence of another NAP, MatP, known to mediate Ter macrodomain isolation, led to enhanced contacts between Ter and its flanking macrodomains but lacked any change in matS sites localization. Deficiency of MukBEF, the only SMC complex present in E. coli, led to disorganization of macrodomains. Upon further analysis, it was observed that the above mutations do not significantly impact the local chromosome organization (~ 100 Kb) but only affect the chromosome on a larger scale (>100 Kb). These observations shed more light on the sparsely explored effects of NAPs on the overall chromosome organization and helps us understand the myriad complex interactions NAPs have with the chromosome.

biophysics↗