Biology subjects

Arifuzzaman, M.

Publications and source records attributed to Arifuzzaman, M..

4 recordsLinked to original sources

bioRxiv2025

Structural insights into autophosphorylation-mediated heat shock response by the protein-arginine kinase McsAB

McsAB is a protein-arginine kinase that activates heat shock genes by inhibiting the transcriptional repressor CtsR. However, the mechanism by which McsAB suppresses CtsR during heat shock remains unclear. Here, we present cryo-electron microscopy structures of Bacillus subtilis McsAZ2-McsB and its complex with CtsR. Our structural analyses reveal that McsAZ2-McsB forms a rod-shaped heterotetramer, with two of these heterotetramers assembling into an asymmetrically crossing shape through phosphorylated arginine residues (pArg194 and pArg333) of McsB. The CtsR dimer binds to the groove of the McsAZ2-McsB oligomer via pArg115 of McsA and pArg194 of McsB. Anisotropy experiments indicate that CtsR dissociates slowly from its operator during heat shock, and McsAB facilitates this process in an ATP-dependent manner. Furthermore, mutations in the arginine residues of McsAB reduce its ability to hijack CtsR during heat shock. These results demonstrate that autophosphorylation of McsAB is essential for a rapid and effective heat shock response.

biochemistry↗

bioRxiv2023

Morpho-physiobiochemical dissection reveals insight into salt-induced differential responses in genetically modified Solanum melongena L. (Bt Brinjal) varieties using an indigenous hydroponic system

Salinity is a major abiotic constraint of crop production in many countries, including Bangladesh, where a significant amount of cultivable areas are diversely affected by rising salt concentrations. Therefore, it is of paramount importance to figure out the possible solutions to cope with this abiotic stress. So, the development of tolerant genotypes of various crop species can be the best alternative to enhance crop production as well as to improve the livelihoods of poor marginal farmers. With this in mind, the impact of different NaCl levels (50 mM, 100 mM, and 150 mM) on four different Bt Brinjal (Bacillus thuringiensis) genotypes (BARI Bt Begun-1, BARI Bt Begun-2, BARI Bt Begun-3, and BARI Bt Begun-4) was evaluated using morpho-physicochemical analyses at growth, harvesting, and postharvest stages by establishing a new indigenous cost-effective hydroponic system. Our results show that excess salt (> 100 mM) has a detrimental effect on plant growth and development and most of the traits measured across different growth stages. Based on the different measured traits, BARI Bt Begun-1 and BARI Bt Begun-2 varieties outperformed in terms of better morpho-physiological, biochemical, photosynthetic, and antioxidant capacity under salt stress when compared to BARI Bt Begun-3 and BARI Bt Begun-4. Therefore, we conclude that BARI Bt Begun-1 and BARI Bt Begun-2 are moderately tolerant varieties, while BARI Bt Begun-3 and Begun-4 were susceptible varieties to salinity stress. The identified salt-responsive contrasting varieties can serve as valuable genetic materials in comparative genomics for breeding salt-tolerant Brinjal varieties and the newly established hydroponic system could be utilized in translational research programs.

plant biology↗

bioRxiv2020

Measuring Orthopedic Plate Strain to Track Bone Healing Using a Fluidic Sensor Read via Plain Radiography

We describe a fluidic X-ray visualized strain indicator under applied load (X-VISUAL) to quantify orthopedic plate strain and inform rehabilitative care. This sensor uses a liquid-level gauge with hydro-mechanical amplification and is visualized in plain radiographs which are routinely acquired during patient recovery to find pathologies but are usually insufficient to quantify fracture stiffness. The sensor has two components: a stainless-steel lever which attaches to the plate, and an acrylic fluidic component which sits between the plate and lever. The fluidic component has a reservoir filled with radio-dense solution and an adjoining capillary wherein the fluid level is measured. When the plate bends under load, the lever squeezes the reservoir, which pushes the fluid along the channel. A tibial osteotomy model (5 mm gap) was used to simulate an unstable fracture, and allograft repair used to simulate a stiffer healed fracture. A cadaveric tibia and a mechanically equivalent composite tibia mimic were cyclically loaded five times (0 - 400 N axial force) while fluid displacement was measured from radiographs. The sensor displayed reversible and repeatable behavior with a slope of 0.096 mm/kg and fluid level noise of 50 to 80 micrometers (equivalent to 5-10 N). The allograft-repaired composite fracture was 13 times stiffer than the unstable fracture. An analysis of prior external fracture fixation studies and fatigue curves for internal plates indicates that the threshold for safe weight bearing should be 1/5th -1/10th of the initial bending for an unstable fracture. The precision of our device (<2% body weight) should thus be sufficient to track fracture healing from unstable through safe weight bearing.

bioengineering↗

bioRxiv2018

In Silico Analysis of Non Synonymous Single Nucleotide Polymorphisms (nsSNPs) of SMPX Gene in Hearing Impairment

BackgroundMutations in SMPX gene can disrupt the normal activity of the SMPX protein which is involved in hearing process.\n\nObjectiveIn this study, deleterious non-synonymous single nucleotide polymorphisms were isolated from the neutral variants by using several bioinformatics tools.\n\nMethodFirstly, dbSNP database hosted by NCBI was used to retrieve the SNPs of SMPX gene, secondly, SIFT was used primarily to screen the damaging SNPs. Further, for validation PROVEAN, PredictSNP and PolyPhen 2 were used. I-Mutant 3 was utilized to analyze the protein stability change and MutPred predicted the molecular mechanism of protein stability change. Finally evolutionary conservation was done to study their conservancy by using ConSurf server.\n\nResultsA total of 26 missense (0.6517%) and 3 nonsense variants (0.075%) were retrieved and among them 4 mutations were found deleterious by all the tools of this experiment and are also highly conserved according to ConSurf server. rs772775896, rs759552778, rs200892029 and rs1016314772 are the reference IDs of deleterious mutations where the substitutions are S71L, N19D, A29T and K54N. Loss of Ubiquitination, loss of methylation, loss of glycosylation, and loss of MoRF binding motifs are the root causes of protein stability change.\n\nConclusionThis is the first study regarding nsSNPs of SMPX gene where the most damaging SNPs were screened that are associated with the SMPX gene and can be used for further research to study their effect on protein structure and function, their dynamic behavior and how they actually affect proteins flexibility.

bioinformatics↗