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Bacterial Small RNA and Nanotechnology
Published in Sunil K. Deshmukh, Mandira Kochar, Pawan Kaur, Pushplata Prasad Singh, Nanotechnology in Agriculture and Environmental Science, 2023
Hfq belongs to the Sm(L) protein superfamily which is known to be involved in RNA metabolism. It has been established that the structural core of Hfq protein possesses α-β1-5 folds of which β1-3 forms the conserved Sml motif and β4-5 forms the variable Sm2 motif (Vogel and Luisi, 2011). They also described the two faces of the Hfq protein which interacts with the RNA molecules (sRNA or mRNA): “proximal face”, the surface on which the aminoterminal ahelix is exposed and the opposite side as “distal face”. Though, the proximal face has preferential binding towards the U-rich RNA strand and the distal face towards the RNA containing sequence motif ARN or ARNN, the two faces cannot be exclusively labelled as mRNA or sRNA binding faces (Vogel and Luisi, 2011; Sauer et al., 2012; De Lay et al., 2013).
Modeling of Micro- and Nanoscale Electromechanical Systems and Devices
Published in Sergey Edward Lyshevski, Nano- and Micro-Electromechanical Systems, 2018
Complex three-dimensional organic complexes and assemblies in E. coli and S. typhimurium bacteria have been covered in previous sections. For example, the 45-nm E. coli nanorotor is the so-called MS ring, which consists of FliF and FliG proteins. These proteins’ geometry and folding are unknown. We assume that short-circuited nanowindings can be formed by these proteins. It should be emphasized that complex three-dimensional organic circuits (windings) can be engineered. As another example, consider the AAA (ATPases Associated with various cellular Activities) interacting protein superfamily. The AAA protein superfamily is characterized by a highly conserved module of more than 230 amino acid residues including an ATP binding consensus, present in one or two copies in the AAA proteins. The AAA proteins are found in all organisms and are essential for their functionality. Specific attention should be focused on the geometry and folding of different protein complexes and assemblies. Thus, the E. coli nanobiomotor and synthesized micro- and nanomachines can operate as induction nanomachines, as will be discussed later. (See Figure 6.39.)
The Role of Nanoparticles in Cancer Therapy through Apoptosis Induction
Published in Hala Gali-Muhtasib, Racha Chouaib, Nanoparticle Drug Delivery Systems for Cancer Treatment, 2020
Marveh Rahmati, Saeid Amanpour, Hadiseh Mohammadpour
Apoptosis is an energy-dependent process. Two main apoptotic signaling pathways, including the extrinsic death receptor pathway and the intrinsic mitochondrial pathway, have been well-characterized. However, there are additional pathways that involve the T-cell-mediated cytotoxicity and the perforin-granzyme pathway. The perforin/granzyme pathway induces apoptosis through either granzyme B or granzyme A. Another recent pathway of apoptosis is mediated by the endoplasmic reticulum (ER) which plays important roles in cell fate and will be discussed in details later [17]. Apoptosis is mediated by chronological activation of protein superfamily of caspases [16]. Caspases are expressed in an inactive form of proenzymes in most cells. When activated, they activate other procaspases, leading to the initiation of the cascade of caspase-dependent apoptosis pathway. Caspases are highly conserved cysteine-dependent aspartate-specific proteases. There are different types of caspases: initiator caspases, including CASP-2, 8, 9, and 10; effector caspases, such as CASP-3, 6, and 7; and inflammatory caspases which are CASP-1, 4, and 5). The other caspases that have been recently studied are (i) caspase-11, which is involved in the regulation of apoptosis and cytokine maturation during septic shock, (ii) caspase-12, which mediates apoptosis through the endoplasmic reticulum, (iii) caspase-13, which is believed to be a bovine gene, and (iv) caspase-14, which is highly expressed just in embryonic tissues [23]. Initiator caspases are inactive until specific oligomeric activator protein binds to them. Subsequently, they bind to effector caspases. Effector caspases are then activated through proteolytic cleavage. The activated caspases then proteolytically degrade the intracellular proteins necessary for programmed cell death.
Cytoplasmic and periplasmic expression of recombinant shark VNAR antibody in Escherichia coli
Published in Preparative Biochemistry and Biotechnology, 2019
Herng C. Leow, Katja Fischer, Yee C. Leow, Katleen Braet, Qin Cheng, James McCarthy
The periplasmic disulfide oxidoreductase A protein (DsbA) belongs to the thioredoxin protein superfamily and is responsible for disulfide bond formation and rearrangement in E. coli.[34,35] DsbA, otherwise, in combination with other Dsb peptide family has been widely used to produce functional recombinant proteins in biomedical research. For instances, the performance and yield of functional scFv,[36] horseradish peroxidase,[37] human plasma retinol-binding protein,[38] nerve growth factor beta,[39] and brain-derived neurotrophic factor[40] have been improved using this fusion approach.
A critical review on the bioaccumulation, transportation, and elimination of per- and polyfluoroalkyl substances in human beings
Published in Critical Reviews in Environmental Science and Technology, 2023
Yao Lu, Ruining Guan, Nali Zhu, Jinghua Hao, Hanyong Peng, Anen He, Chunyan Zhao, Yawei Wang, Guibin Jiang
LFABP, which belongs to the intercellular lipid-binding protein superfamily that governs the metabolism of fatty acids, is a lipid-binding protein that is highly expressed in hepatocytes and other fatty acids binding protein-type in small intestines. LFABP can bind to saturated, unsaturated, and branched long-chain fatty acids as well as to some non-fatty acid ligands (Andersen et al., 2008; De Geronimo et al., 2010; Wu et al., 2012). Owing to the structural resemblance of PFAS to fatty acids, previous studies reported that the PFAS could bind to LFABP (Luebker et al., 2002; Zhang et al., 2013a), facilitating the transport of PFAS into hepatocytes. Therefore, the binding to LFABP plays an important role in the bioaccumulation and transportation of PFAS in human. Zhang et al. investigated the interactions of 17 structurally diverse PFAS (carbon chain length between 4 and 18 and functional groups including carboxylic acid, sulfonic acids, and alcohol) with human LFABP (Zhang et al., 2013a). Fluorescence displacement assay results indicated that the binding affinities of 12 PFCAs were associated with the chain length. Additionally, circular dichroism results demonstrated that the binding of PFAS to proteins could induce distinctive structural changes in the proteins. The binding of PFAS to LFABP was also revealed by molecular docking, indicating that the driving forces for binding were mainly hydrophobic and hydrogen-bonding interactions. Additionally, the binding geometry was dependent on the size and rigidity of the PFAS. Overall, Zhang et al. demonstrated that the possibility of displacement of fatty acids by PFAS to LFABP should not be ignored.