Sabbir Shuvo

Multidrug-resistant P. aeruginosa has potential to cause nosocomial infections. In this study, whole-genome sequencing was performed of two extremely drug-resistant novel strains SRS1 and SRS4 isolated from Bangladesh. The size of draft genome of SRS1 is 6.8 Mbp, and 7.0 Mbp for SRS4. In silico analysis predicted that the genome of SRS1 has 82 and SRS4 has 75 antibiotic-resistant genes (ARGs). Antibiogram results revealed that both SRS1 and SRS4 were resistant to multiple members of the antibiotic groups of β−lactam, quinolones, and aminoglycosides families. In addition, the genomes of both SRS1 and SRS4 were predicted to have multiple mobile elements like prophages and plasmids. Comparative genome analysis with wildtype PAO1 and another drug-resistant P. aeruginosa strain JNQH-PA57 revealed that SRS1 and SRS4 contain more antibiotic resistance genes like AAC (6´)-II, ANT (2´´)-Ia, ANT (3´´)-IIa, OXA-395, PME-1, qacEΔ1, tet(A), tet(D), VEB-9 than PAO1 and JNQH-PA57. This study shows...

Voltage-dependent anion-selective channels (VDAC) maintain the bidirectional flow of small metabolites across the mitochondrial outer membrane and participate in the regulation of multiple cellular processes. To understand the roles of VDAC in cellular homeostasis, preliminary proteomic analyses of S100 cytosolic and mitochondria-enriched fractions from a VDAC-less Neurospora crassa strain (ΔPor-1) were performed. In the variant cells, less abundant proteins include subunits of translation initiation factor eIF-2, enzymes in the shikimate pathway leading to precursors of aromatic amino acids, and enzymes involved in sulfate assimilation and in the synthesis of methionine, cysteine, alanine, serine, and threonine. In contrast, some of the more abundant proteins are involved in electron flow, such as the α subunit of the electron transfer flavoprotein and lactate dehydrogenase, which is involved in one pathway leading to pyruvate synthesis. Increased levels of catalase and catalase ac...

Mitochondrial porin, which forms voltage-dependent anion-selective channels (VDAC) in the outer membrane, can be folded into a 19 β-stranded barrel. The N-terminus of the protein is external to the barrel, and contains α-helical structure. Targeted modifications of the N‑terminal region have been assessed in artificial membranes, leading to different models for gating <i>in vitro</i>. However, the i<i>n vivo</i> requirements for gating and the N-terminal segment of porin are less well-understood. Using <i>Neurospora crassa</i> porin as a model, the effects of a partial deletion of the N-terminal segment were investigated. The protein, ΔN2‑12porin, is assembled into the outer membrane, albeit at lower levels than the wild-type protein. The resulting strain displays electron transport chain deficiencies, concomitant expression of alternative oxidase, and decreased growth rates. Nonetheless, its mitochondrial genome does not contain any significant m...

A novel feature of the voltage-dependent anion channel (VDAC, mitochondrial porin), is the barrel, comprising an odd number of β-strands and closed by parallel strands. Recent research has focused on the N-terminal segment, which in the available structures, resides in the lumen and is not part of the barrel. In this review, the structural data obtained from vertebrate VDAC are integrated with those from VDAC in artificial bilayers, emphasizing the array of native and tagged versions of VDAC used. The data are discussed with respect to a recent gating model (Zachariae et al. (2012) Structure 20:1-10), in which the N-terminus acts not as a gate on a stable barrel, but rather stabilizes the barrel, preventing its shift into a partially collapsed, low-conductance, closed state. Additionally, the role of the N-terminus in VDAC oligomerization, apoptosis through interactions with hexokinase and its interaction with ATP are discussed briefly.

On average, the oxidation of a single Met residue to Mso (methionine S-oxide, methionine sulfoxide) and Msn (methionine S,S-dioxide, methionine sulfone) decreases peptide retention in RP HPLC by 2.37 and 1.95 Hydrophobicity Index units (% acetonitrile), respectively. At the same time, the magnitude of the retention shift varies greatly (-9.1 to +0.4% acetonitrile for Mso) depending on peptide sequence. The latter effects are mostly associated with the stabilization of secondary structures upon peptide interaction with the hydrophobic stationary phase: when an oxidized residue is located in the hydrophobic face of an amphipathic helix, the decrease in retention is profound. The same amino acid positioning leads to complete or partial resolution of pairs of peptides containing diastereomeric Mso residues. Contrary to all previously reported observations, and the nature of this modification, we also demonstrate for the first time that methionine oxidation may increase peptide hydrophob...

In eukaryotic cells communication and dynamic interactions among different organelles are important for maintaining cellular homeostasis. The Endoplasmic-Reticulum (ER) Mitochondria Encounter Structure (ERMES) complex establishes membrane contact sites between ER and mitochondria and is essential for phospholipid transport, protein import and mitochondrial dynamics and inheritance. In this work, in-silico analyses were used to probe the intramolecular interactions in ERMES proteins and the interactions that support the ERMES complex. Based on Mutual Information (MI), sites of intramolecular co-evolution are predicted in the core proteins Mmm1, Mdm10, Mdm12, Mdm34, the peroxisomal protein Pex11, and cytoplasmic Lam6; these sites are linked to structural features of the proteins. Intermolecular co-evolution is predicted among the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domains of Mmm1, Mdm12 and Mdm34. Segments of Pex11 and Lam6 also share MI with the SMP domains ...