Biology subjects

Qureshi, B. M.

Publications and source records attributed to Qureshi, B. M..

4 recordsLinked to original sources

bioRxiv2026

Molecular determinants underlying substrate receptor specificity of human CRL4B E3 ubiquitin ligase

The vertebrate CRL4 family of Cullin-RING E3 ubiquitin ligases is distinguished from other cullin-based ligases by the presence of two highly homologous paralogs, CUL4A and CUL4B. Both CRL4 complexes use the DDB1 subunit to recruit dedicated and interchangeable substrate receptors called DCAFs, but the underlying mechanisms guiding DCAF specificity for CUL4B or CUL4A remain poorly understood. Here, we performed structural and biochemical analyses of the CRL4BLIS1 complex and identified two molecular determinants for CUL4B-specific DCAFs. First, we discovered that the unique CUL4B N-terminal extension directly binds CUL4B-specific DCAFs, enhancing their complex formation. This direct interaction can be modulated by phosphorylation, adding the possibility for spatiotemporal regulation. Second, the cryo-EM model of the CRL4BLIS1 complex identified a novel interface on the DDB1 subunit which promotes LIS1 recruitment. Quantitative affinity measurements and mutational analysis confirmed that this DDB1 interface is generally important for recruiting CUL4B-specific DCAFs including WDR1 and BRWD1, but not for CUL4A-specifc DCAFs, such as DCAF8. Together, our study identifies molecular determinants and unexpected interfaces on CRL4 components that dictate preference for DCAF recruitment. Graphical Abstract showing how the two CRL4 complexe s, namely CRL4A and CRL4B, recruit their DCAFs O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/711546v1_ufig1.gif" ALT="Figure 1000"> View larger version (39K): org.highwire.dtl.DTLVardef@10e476eorg.highwire.dtl.DTLVardef@73a405org.highwire.dtl.DTLVardef@1571a1org.highwire.dtl.DTLVardef@1d70946_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Plant-specific adaptations of the CDC48 unfoldase

Targeted protein degradation through the CDC48 unfoldase enables the maintenance and rapid adaptation of proteomes across eukaryotes. However, the profound differences between animals, fungi, and plants are expected to have led to a significant adaptation of the CDC48-mediated degradation. While animal and fungal CDC48 systems have shown structural and functional preservation, such analysis is lacking for plants. We determined the structural and functional characteristics of Arabidopsis thaliana CDC48A in various states and bound to the target-identifying cofactors UFD1 and NPL4. Our analysis reveals several features that distinguish AtCDC48 from its animal and yeast counterparts, despite an 80% sequence identity. Key features are that AtCDC48A displays distinct domain dynamics and interacts differently with AtNPL4. Moreover, AtNPL4 and AtUFD1 do not form an obligate heterodimer, but independently bind to AtCDC48A and mediate target degradation; however, their joint action is synergistic. An evolutionary analysis supports that these Arabidopsis features are conserved across plants and represent the ancestral state of eukaryotic CDC48 systems. Jointly, our findings support that plant CDC48 retains a greater modular and combinatorial cofactor usage, highlighting a specific adaptation of targeted protein degradation in plants.

plant biology↗

bioRxiv2024

Loading of extracellular vesicles with nucleic acids via hybridization with sponge-like lipid nanoparticles

The translation of cell-derived extracellular vesicles (EVs) into biogenic gene delivery systems is limited by relatively inefficient loading strategies. In this work, we describe the loading of various nucleic acids into small EVs via their spontaneous hybridization with preloaded non-lamellar liquid crystalline lipid nanoparticles (LCNPs) under physiological conditions, forming hybrid EVs (HEVs). We correlate LCNPs topological characteristics with their propensity to fuse/aggregate with EVs and found that sponge (L3) phases at pH 7.4 were particularly suitable to induce a controlled hybridization process. State-of-the-art single-particle analysis techniques revealed that L3-based LCNPs interact with various EV subpopulations and that around 40% of HEVs were loaded with the genetic cargo. Importantly, this study demonstrates that EV membrane proteins remain accessible on HEV surfaces, with their intrinsic enzymatic activity unaffected after the hybridization process. Finally, HEVs showed in vitro improved transfection efficiencies compared to unhybridized LCNPs. In summary, this versatile platform holds potential for loading various nucleic acid molecules into native EVs and may help developing EV-based therapeutics. TeaserTopology of lipid nanoparticles influences their hybridization behavior with extracellular vesicles and produces novel biogenic gene delivery systems.

bioengineering↗

bioRxiv2023

On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seeding experiments

The aggregation of the protein -synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the -synuclein fibrils hampers efforts in disease-relevant in vitro studies on -synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of -synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4 a pH- dependent selection between Types 1, 2 and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.

biophysics↗