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Anoxybacteroides (previously Anoxybacillus) is a relatively new genus, proposed in the year 2000, and comprised of many species which are reported to play a vital role in bioprocessing and bioremediation.Very few reports described the whole genome sequence (WGS) of this genus.Therefore, in this study, WGS of a new strain, UE27, was analyzed.This thermophilic strain was previously isolated from the crocodile pond of Manghopir, Karachi.The genome of A. rupiense (previously Anoxybacillus rupiensis) UE27 was submitted to NCBI GenBank with the accession number JBHLFH010000000.1.Genome size was found to be 3,771,980 bp with 76 contigs and 42.33 % GC content.Among 3789 genes, 3708 were found as protein coding genes.Interestingly, intake prophage genome was found which has not been previously reported in A. rupiense.The prophage region contained 68 coding sequence among which 48 were identified as phage-related genes with 40.09 % GC content.The xylan degradation genes were also annotated in the genome.Moreover, many genes responsible for azo dye degradation, heavy metal detoxification and hydrocarbon removal were found in the genome.Conclusively, this study provided insight into gene repertoire of A. rupiense and a basis for the potential application of this thermophilic bacterium in bioremediation and bioprospecting.

24 Mar 2025·Molecular Simulation

Structural and dynamical insights revealed the disaccharide glycosylation in vitamin D-binding protein (VDBP) enhances the vitamin D-binding stability

Author: Bux, Khair ; Ali, Kashif ; Hasan, Khwaja Ali ; Herwig, Ralf ; Naz, Shahida

The difference in the levels of glycosylation in Vitamin D--Binding Protein (VDBP) has a significant effect on its biol. function and role in immune modulation and cancer treatments.This study reports the impact of differential glycosylation on the structural dynamics and binding efficiency of Vitamin D-Binding Protein (VDBP) with Vitamin D3 (VitD3).The focus is to understand how glycosylation affects protein conformation and then associated immune modulation based therapeutic applications specially in cancer treatment.Mol. Modeling and Mol. Dynamics Simulations were used to investigate the conformational dynamics of the dimer in both forms, un-glycosylated (VitD3-VDBP) with no sugar moiety attached (VitD3-VDBP) and with disaccharide linkage (VitD3-dgVDBP).Vitamin D-binding protein dimer, (VitD3-dgVDBP) was identified in the samples through SDS-PAGE followed by UV/VIS and CD/ORD anal. to confirm protein and vitamin D3 dimer.The mol. Structure of the protein with disaccharide sugars (VitD3-dgVDBP) was modelled and aligned with the reported sequence and structure of the protein.RMSD and RMSF anal. helped to estimate the effect of differential glycosidic linkage on the conformational integrity of protein.Dynamical Cross-Correlation Movement (DCCM) further revealed that (VitD3-dgVDBP) got opposite movements upon disaccharide linkage.Principal Component Anal. (PCA) Investigations showed that both forms of the protein, (VitD3-VDBP) and (VitD3-dgVDBP) have different dominant movements across the protein surface and solvent-accessible surface SASA anal. in addition showed the disaccharide linkage to have a larger accessible surface area comparatively.Binding energy estimation of vitamin D and protein dimer using MMPBSA method along with hydrogen bond anal. revealed higher binding energy in the case of (VitD3-dgVDBP), - 116.09 ± 16.04, thus suggesting the disaccharide linkage enhances the binding of protein with VitD3 and its availability in the blood cells.

100 Deals associated with Shaheed Zulfikar Ali Bhutto Institute of Science & Technolog

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100 Translational Medicine associated with Shaheed Zulfikar Ali Bhutto Institute of Science & Technolog

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Pipeline

Pipeline Snapshot as of 03 Aug 2025

The statistics for drugs in the Pipeline is the current organization and its subsidiaries are counted as organizations,Early Phase 1 is incorporated into Phase 1, Phase 1/2 is incorporated into phase 2, and phase 2/3 is incorporated into phase 3

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