Biology subjects

Ashaduzzaman, M.

Publications and source records attributed to Ashaduzzaman, M..

5 recordsLinked to original sources

bioRxiv2026

Structure-Activity Mapping of Intraperitoneal mRNA-LNPs: Decoupling Tumor and Liver Biodistribution in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) remains difficult to treat with nucleic acid therapeutics because efficient intratumoral delivery is limited and off-target liver accumulation is common. Here, we developed a structure-activity map for intraperitoneally administered mRNA lipid nanoparticles (mRNA-LNPs) to identify formulation features that improve delivery to pancreatic tumors while reducing liver expression. A full-factorial library of 48 mRNA-LNP formulations was generated by varying ionizable lipid, sterol, phospholipid, and PEG-lipid components. Formulations were characterized for size, polydispersity, zeta potential, and encapsulation, then evaluated in an orthotopic KPC8060 pancreatic tumor model after intraperitoneal administration of firefly luciferase mRNA-loaded LNPs. Biodistribution was assessed by Rhodamine B fluorescence and functional delivery by luciferase expression 12 h after dosing. Lipid composition strongly influenced both physicochemical properties and in vivo performance. G0-C14-based formulations produced the smallest and most homogeneous particles, whereas FTT5-containing formulations were generally larger. Across the 48-formulation library, mRNA expression and nanoparticle biodistribution varied significantly among tumor, pancreas, liver, and spleen. Statistical, decision-tree, and predictive modeling analyses identified composition rules associated with organ-selective delivery. High tumor expression was associated primarily with G0-C14 combined with DSPC and {beta}-sitosterol, whereas liver expression was favored by C12-200 or DLin-MC3-DMA with DOPE and DSPE-PEG. Notably, a G0-C14/DSPC/DSPE-PEG formulation emerged as a lead candidate, producing a greater than 6-fold increase in tumor luciferase signal relative to the library median while reducing liver exposure by approximately 60%. Histopathology showed no treatment-related liver or lung toxicity. These findings define actionable formulation rules for tuning intraperitoneal mRNA-LNP delivery in PDAC and support further development of tumor-selective mRNA therapeutics for pancreatic cancer.

bioengineering↗

bioRxiv2025

The Structural Basis of alpha/beta-tubulin Assembly and Disassembly by Tubulin Cofactors

Microtubules polymerize from cytoplasmic pools of soluble {beta}-tubulin heterodimers that support diverse cellular functions. The tubulin cofactors, TBCC, TBCD, TBCE, and the Arl2 GTPase, form TBC-DEG assemblies that regulate {beta}-tubulin assembly and disassembly from - and {beta}-tubulins, yet their underlying mechanisms remain incompletely understood. Here, we reconstitute the human TBC-DE and TBC-DEG assemblies from eukaryotic cells co-purified with monomeric {beta}-tubulin intermediates and determine their cryo-EM structures. The structures reveal that TBC-DEG disassembles {beta}-tubulin by releasing -tubulin through a lever-arm-like rotation in TBCE coupled to major conformational change in Arl2 upon its nucleotide release, while TBCD tightly holds {beta}-tubulin. TBCD dissociates -tubulin by refolding the {beta}-tubulin H10-S8 loop at its intradimer interface. The TBC-DEG-{beta}-tubulin or TBC-DE-{beta}-tubulin assemblies undergo extensive back-to-back dimerization mediated by {beta}-{beta}-tubulin homodimers, formed through their dissociated H8 helices at unoccupied intradimer interfaces. Structural comparisons demonstrate that the TBCE mechanical rotation, driven by the Arl2 GTPase cycle, either delivers -tubulin or removes it from beneath the TBCD-bound {beta}-tubulin and is directionally regulated by TBCC stabilizing {beta}-tubulin interfaces. Our findings suggest that TBC-DEG/TBCC catalyzing heterodimerization of -tubulin with {beta}-tubulin may have evolved to counteract the {beta}-tubulin intrinsic tendency to form off-pathway toxic homodimers through its exposed -tubulin-binding intradimer interface.

biochemistry↗

bioRxiv2025

Structural Basis of Kinesin-1 Autoinhibition and Its Control of Microtubule-Based Motility

Kinesin-1 was the first identified microtubule-based motor protein that drives anterograde intracellular transport of diverse cargoes in eukaryotic cells. Improper regulation and kinesin-1 defects are implicated in multiple neurological disorders as well as pathogens hijacks kinesin-1 to deliver their cargoes. Despite its importance, the molecular mechanisms governing kinesin-1 regulation and activation remains poorly understood. Here, we report the cryo-EM structure of the autoinhibited kinesin-1 heterotetramer and validate it using crosslinking mass spectrometry. The structure reveals a 36-nm particle in which the kinesin heavy chains (KHCs) adopt a head to tail configuration, stabilized by asymmetrically arranged kinesin light chain (KLC) tetratricopeptide repeat (TPR) domains that bind across folded KHC coiled-coils and wedge in between the KHC motor domains. This architecture inhibits kinesin motility by constraining the dimeric motor domains in a configuration that is incompatible with processive movement. In addition, the structure shows that the KLC C-terminal helices occlude the TPR cargo binding interfaces, revealing a second layer of autoinhibition that directly blocks cargo engagement. Functional studies and structural modeling suggest that binding of regulatory factors, such as MAP7D3, compete with intramolecular KHC coiled-coil interactions, resulting in the unfurling of the autoinhibited structure and activating motor motility. These findings provide a molecular framework for understanding kinesin-1 regulation and its implications for intracellular transport.

biochemistry↗

bioRxiv2023

Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH

The flavin-dependent halogenase AbeH produces 5-chlorotryptophan in the biosynthetic pathway of the chlorinated bisindole alkaloid BE-54017. We report that in vitro, AbeH (assisted by the flavin reductase AbeF) can chlorinate and brominate tryptophan as well as other indole derivatives and substrates with phenyl and quinoline groups. We solved the X-ray crystal structures of AbeH alone and complexed with FAD, as well as crystal structures of the tryptophan-6-halogenase BorH alone, in complex with 6-chlorotryptophan, and in complex with FAD and tryptophan. Partitioning of FAD and tryptophan into different chains of BorH and failure to incorporate tryptophan into AbeH/FAD crystals suggested that flavin and tryptophan binding are negatively coupled in both proteins. ITC and fluorescence quenching experiments confirmed the ability of both AbeH and BorH to form binary complexes with FAD or tryptophan and the inability of tryptophan to bind to AbeH/FAD or BorH/FAD complexes. FAD could not bind to BorH/tryptophan complexes, but FAD appears to displace tryptophan from AbeH/tryptophan complexes in an endothermic entropically-driven process.

biochemistry↗

bioRxiv2020

Utilization and prospectus of non-timber forest products as livelihood materials

A study was conducted to find out the present utilization of non-timber forest products of the Sundarbans and tries to find out the alternative uses of these resources. The Sundarbans is the largest mangrove forest in the world and proper utilization of all resources can get a chance to manage this forest in sustainable way. A questionnaire survey was conducted to get information about the utilization of non-timber forest products. It has been found that about 87% of the people are fully dependent and 13% of the people are partially dependent on the Sundarbans. Among minor forest products, golpata, honey and fish were used by 92%, 93% and 82% of people, respectively. Most of the people are unknown about the alternative use of minor forest products but there is a great chance to use them for better purposes. Alternative uses of these products will help to improve the forest conditions as well as the socio-economic conditions of the people adjacent to the Sundarbans.

bioengineering↗