Biology subjects

Saeed, H.

Publications and source records attributed to Saeed, H..

7 recordsLinked to original sources

bioRxiv2026

A conditional upper-bound design map for rhodopsin-augmented electro microbial CO2-to-biomass conversion

The value of rhodopsin proton pumps as light harvesters in electro-microbial CO2-to-biomass conversion depends on molecular photophysics, pathway energetics and reactor light delivery. We couple these scales for Cupriavidus necator, comparing Calvin-Benson-Bassham (CBB) and reductive glycine (rGlyP) assimilation. The model predicts a 17.9% dark rGlyP yield advantage, close to 16.5% measured in chemostats. At 568 nm, 100 PPFD and 45% membrane occupancy, light-derived ATP raises yield by 17% for rGlyP and 14% for CBB. Charging CO2 capture and formate electrosynthesis, a retinal-only reactor reaches 3.29% efficiency versus 2.56% in the dark. A carotenoid antenna raises this to 3.52% at the model-derived 70% transfer estimate and helps in 93.2% of uncertainty samples, but lowers efficiency at the thermodynamic limit by diverting photons from photovoltaics. Point-source CO2 cuts the relative light benefit from 38% to 8%. Rhodopsin is therefore most useful when upstream formate is energy-intensive, not as a general efficiency boost.

systems biology↗

bioRxiv2026

AI-enabled rhodopsin design for blue-light enhanced bacterial growth

We developed an AI-guided design pipeline that generated and validated non-natural microbial rhodopsins with spectral properties not yet known in nature. The pipeline comprised a three-stage in silico design, a genetic algorithm (GA) for sequence generation, a stacked LASSO and XGBoost machine-learning (ML) regressor for spectral prediction and fitness ranking, and a Markov-based sequence plausibility filter to enforce proton pumping like characteristics. Four candidate rhodopsins (APR1, APR2, APR6, and APR7) targeting blue light absorption were designed and AlphaFold3 structural modelling predicted retinal binding pocket architecture consistent with outward proton-pumping function. Experimental characterisation confirmed that all four variants absorbed light at [~]410 nm and significantly promoted the growth of Cupriavidus necator under blue light illumination. This study demonstrates that AI-enabled design can engineer proteins with no natural precedent, generating light-harvesting rhodopsins with novel spectral properties while preserving biological function, marking a significant advance in programmable synthetic biology.

Synthetic Biology↗

bioRxiv2025

Differences in the co-distribution of the Cannabinoid Receptor-1, FAAH, and MAGL in the human and mouse brain could be limiting clinical translation of endocannabinoid outcomes in mouse models of Alzheimer disease.

Endocannabinoid system (ECS) outcomes in mouse models of Alzheimer disease (AD) do not always align with the clinical disease course. We compared the distribution of the Cannabinoid Receptor-1 (CB1R) and the enzymes, FAAH and MAGL, in autopsy AD brain samples as well as in the J20 (hAPPSwe/Ind) mouse model of AD. Both sources revealed several anti-CB1R immunoreactive species, e.g. one at 47-kDa (corresponding to the protein-coding sequence) and a reported putative splice variant at 37 kDa. We did not observe any changes in the mean expression in CB1R, FAAH or MAGL in the human samples, but did observe sex- and genotype-specific changes in the mouse brain. Regression analysis revealed strong sex- and APOE {varepsilon}4-dependent associations among the CB1Rs as well as between CB1Rs and MAGL (but not FAAH) in human cortical (but not hippocampal) samples. In the J20 mouse, associations between CB1Rs were limited to hippocampal samples, whereas associations between CB1R and both MAGL and FAAH were observed in the cortex. A diagnosis of AD disrupted any associations in the human dataset, whereas in several instances, the associations were enhanced by the hAPPSwe/Ind transgene. This inferred species-dependent regulation of the ECS could impact the clinical translational of ECS outcomes in preclinical models of AD pathology.

neuroscience↗

bioRxiv2025

Decoupled Information Theoretic Feature Selection for Rapid Protein Key Tuning Residue Identification

Rational protein engineering requires identifying residues that modulate function without disrupting functionality, a key challenge in protein engineering. Existing computational methods struggle to distinguish genuine functional sites from positions coevolving due to structural constraints, leading to high false-discovery rates. Here we present an information-theoretic decoupling framework that, without machine learning, isolates key tuning residues by computationally "denoising" sequence data, iteratively removing confounding evolutionary signals to reveal underlying functional sites. We validated this framework across 10 datasets spanning enzymes, fluorescent proteins, and antibodies. In a nanobody-antigen binding case study, our method identified > 25% (6/20) of verified binding-critical residues (p = 0.031), while the best of five benchmarked tools found zero. Performance was consistent across all datasets, with supervised variants achieving large effect sizes (Hedges g > 0.7, p < 0.01) and unsupervised variants also showing gains (g > 0.2, p < 0.05) over benchmarks. This interpretable framework provides a generalizable method to accelerate protein design, from focusing antibody maturation to optimizing biocatalysts.

bioinformatics↗

bioRxiv2021

Structure and dynamics of a cold-active esterase reveals water entropy and active site accessibility as the likely drivers for cold-adaptation

Cold-active esterases hold great potential for undertaking useful biotransformations at low temperatures. Here, we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical /{beta} hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7s closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dynamics at different temperatures, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Comparison of B-factors with the closest related mesophilic and thermophilic esterases suggests the EstN7 cap region is proportionally less flexible. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are the main drivers of EstN7s cold adaptation rather than changes in dynamics.

biochemistry↗

bioRxiv2021

Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber

Cold active esterases represent an important class of enzymes capable of undertaking useful chemical transformations at low temperatures. EstN7 from Bacillus cohnii represents a true psychrophilic esterase with a temperature optimum below 20{degrees}C. We have recently determined the structure of EstN7 and have used this knowledge to understand substrate specificity and expands its substrate range through protein engineering. Substrate range is determined by a plug at the end of acyl binding pocket that blocks access to a buried water filled cavity, so limiting EstN7 to turnover of C2 and C4 substrates. Data mining revealed a potentially important commercial reaction, conversion of triacetin to only the 1,2-glyceryl diacetate isomer, which the EstN7 could achieve. Residues M187, N211 and W206 were identified as plug residues. M187 was identified as the key plug residue but mutation to alanine destabilised the structure as whole. Another plug mutation, N211A had a stabilising effect on EstN7 and suppressed the destabilising M187A mutation. The M187A-N211A variant had the broadest substrate range, capable of hydrolysing a C8 substrate. Thus, the structure of EstN7 together with focused engineering has provided new insights into the structural stability and substrate specificity that allowed expansion of substrate range.

biochemistry↗

bioRxiv2019

The Arabian camel, Camelus dromedarius interferon epsilon: functional expression, in vitro refolding, purification and cytotoxicity on breast cancer cell lines MDA-MB-231 and MCF-7

The current study highlights for the first time cloning, overexpression, purification, and assessing the cytotxcity of the novel interferon epsilon (IFN{varepsilon}), from the Arabian camel Camelus dromedarius, against two human breast cancer cell lines MDA-MB-231 and MCF-7. Full-length cDNA encoding interferon epsilon (IFN{varepsilon}) was isolated and cloned from the liver of the Arabian camel, C. dromedarius using reverse transcription-polymerase chain reaction. The sequence analysis of the camel IFN{varepsilon} cDNA showed a 582-bp open reading frame encoding a protein of 193 amino acids with an estimated molecular weight of 22.953 kDa. A BLAST search analysis revealed that the C. dromedarius IFN{varepsilon} shared high sequence identity with the IFN genes of other species, such as Camelus ferus, Vicugna pacos, and Homo sapiens. Expression of the camel IFN{varepsilon} cDNA in Escherichia coli gave a fusion protein band of 22.73 kDa after induction with either isopropyl {beta}-D-1-thiogalactopyranoside or lactose for 5 h. Recombinant IFN{varepsilon} protein was overexpressed in the form of inclusion bodies that were easily solubilized and refolded using SDS and KCl. The solubilized inclusion bodies were purified to apparent homogeneity using nickel affinity chromatography. We examined the effect of IFN{varepsilon} on two breast cancer cell lines MDA-MB-231 and MCF-7. In both cell lines, IFN{varepsilon} inhibited cell survival in a dose dependent manner as observed by MTT assay, morphological changes and apoptosis assay. Caspase-3 expression level was found to be increased in MDA-MB-231 treated cells as compared to untreated cells.

molecular biology↗