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Preformulation of New Biological Entities
Published in Sandeep Nema, John D. Ludwig, Parenteral Medications, 2019
Riccardo Torosantucci, Vasco Filipe, Jonathan Kingsbury, Atul Saluja, Yatin Gokarn
In addition to the primary, secondary, and tertiary structure, some proteins incorporate a functional arrangement of multiple folded protein subunits in a multi-subunit complex. This is usually referred to as higher order or quaternary structure. This can range from two subunits (dimers) to large multi-subunit homo- or hetero-oligomers or complexes. Covalent linkage between subunits generally results in the complex being referred to as monomeric, while non-covalent assemblages usually maintain the nomenclature based on the number of subunits. IgG molecules, for example, consist of two identical sets of heavy and light chain sequences forming a hetero-tetrameric quaternary structure held together covalently with disulfide bonds and referred to as “monomeric.” Insulin consists of two distinct peptide chains held together by disulfide bonds. This heterodimeric assemblage is most often referred to as a “monomer.” Active in this monomeric state, during biosynthesis and storage, it can either aggregate (unfavorable) or assemble into a dimer or hexamer in the presence of Zn. The stable Zn/insulin complex is non-covalently associated and can dissociate in serum back into an active monomer. Thus, for non-covalently associated complexes, the effect of solvent condition on higher order structure and the possibility of mass action association (monomer/multimer equilibrium) must be considered.
The electromagnetic nature of protein–protein interactions
Published in Ze Zhang, Mahmoud Rouabhia, Simon E. Moulton, Conductive Polymers, 2018
Anna Katharina Hildebrandt, Thomas Kemmer, Andreas Hildebrandt
Since all amino acids share the same backbone, atomic arrangements that lead to low-energy conformations of these backbone atoms occur very frequently in many proteins. For instance, if the backbone atoms are arranged in a spiral of roughly 3.6 residues per turn and a translation along the spiral’s axis of 1.5 Å, the resulting geometry is just right for the formation of hydrogen bonds between the C=O group of one amino acid and the N–H group of one amino acid and the N–H group of the amino acid four positions later in the primary structure. This so-called α-helix is a common motif in proteins (other kinds of helices exist, but are much less frequent). Similarly, a characteristic zigzag pattern of the backbone atoms of consecutive amino acids—called a β-strand—allows the formation of hydrogen bonds between backbone atoms of two strands that are close in space, but might be remote in the primary structure. The α-helices and β-strands are often connected by short turns or longer loops that are rather flexible. In addition, random coil elements denote parts of the protein without such a regular structure. These different motifs are known as secondary structure elements, and the sequence of secondary structure elements of a protein is known as its secondary structure. Knowledge of the secondary structure is highly useful and might be sufficient to answer many questions of scientific interest. But a detailed understanding of protein function or protein–protein interactions typically requires knowledge of the complete three-dimensional configuration of the protein, that is, the coordinates of all of its atoms. This is known as the protein’s tertiary structure. Finally, biological function is often not carried by a single protein alone, but rather by a complex composed of multiple protein subunits. The arrangement of these subunits with respect to each other is known as the quaternary structure of the complex.
Proteins and proteomics
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2018
There are four distinct types of protein structures: Primary structure: It is the amino acid sequence of the peptide chains. The wide variety of 3D protein structures corresponds to the diversity of functions proteins fulfill. Proteins fold in three dimensions. Protein structure is organized hierarchically from a so-called primary structure to quaternary structure. Higher-level structures are motifs and domains. Above all, the wide variety of conformations is due to the huge amount of different sequences of amino acid residues. The primary structure is the sequence of residues in the polypeptide chain.Secondary structure: Highly regular sub-structures (α helix and strands of β-sheet) that are locally defined, which means that there can be many different secondary motifs present in one single protein molecule. The secondary structure is a local regularly occurring structure in proteins and is mainly formed through hydrogen bonds between backbone atoms. So-called random coils, loops, or turns do not have a stable secondary structure. There are two types of stable secondary structures, α-helices and β-sheets, which are usually located at the core of the protein. On the other hand, loops are usually located in the outer regions.Tertiary structure: Three-dimensional structure of a single protein molecule, a spatial arrangement of the secondary structures. It also describes the completely folded and compacted polypeptide chain. Tertiary structure describes the packing of a-helices, 13-sheets, and random coils with respect to each other on the level of one whole polypeptide chain.Quaternary structure: Complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex. The quaternary structure only exists if there is more than one polypeptide chain present in a complex protein. Only then will quaternary structure describe the spatial organization of the chains (Figure 3.6).
Ozone: A Potential Oxidant for COVID-19 Virus (SARS-CoV-2)
Published in Ozone: Science & Engineering, 2020
According to Figure 3 and among the fatty acids, arachidonic acid presents the highest reactivity toward ozone followed by linoleic acid, oleic acid, and palmitic acid. This is consistent with the number of unsaturated bonds (UB) in each fatty acid: AA (four UB), LA (two UB), OA (one UB), and PA (zero UB). The three fatty acids AA, LA, and OA have lower reactivity than phenol and methylbenzene but higher reactivity than benzene, while PA has the lowest reactivity due to the absence of unsaturated bonds in its molecular structure. Cysteine is also prone to ozone attack at pH 7 with a reactivity higher than benzene but lower than phenol and methylbenzene. On the other hand, the spike protein subunit 2 (GS2) has similar reactivity to benzene while protein subunit 1 (GS1) has slightly lower reactivity, possibly due to the absence of double bonds in their molecular structures. Considering these results, ozone appears effective to attack the amino acids (particularly tryptophan, methionine, and cysteine (at pH8)) and fatty acids (particularly arachidonic acid), thus able to disrupt the protein and lipid structures of the virus, which could lead to its destruction. Since these molecules play key roles in the pathogenesis of coronaviruses (Broer et al. 2006; Yan et al. 2019), their disruption could also disrupt and inhibit key events in the viral infection mechanism such as virus binding and fusion with the host cell, thus ozone oxidation renders the virus not infective. Besides molecular ozone, radicals produced from its decomposition could cause further damage to the virus’s structure, thereby increasing the likelihood of ozone efficacy against this deadly virus.
Role of NF-κB activation in mouse bone marrow stromal cells exposed to 900-MHz radiofrequency fields (RF)
Published in Journal of Toxicology and Environmental Health, Part A, 2019
Lin Zong, Zhen Gao, Wen Xie, Jian Tong, Yi Cao
Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is an inducible, primary transcription factor which plays a key role in several important cellular processes including cell proliferation and apoptosis (Gilmore 2006). This primary transcription factor is present in the cytoplasm as an inactive complex in association with inhibitor protein subunit I-κB (Baeuerle and Baltimore 1991). Upon activation, the sub-unit becomes dissociated and allows the active form of NF-κB to translocate into the nucleus (Ghosh and Baltimore 1990). Once in the nucleus, NF-κB binds sequence specifically to the promoter/enhancer regions of the target gene(s) and transactivates target gene expression (Baeuerle and Baltimore 1991; Baldwin 1996).
Role of NF-κB activation in mouse bone marrow stromal cells exposed to 900 MHz radiofrequency fields (RF)
Published in Journal of Toxicology and Environmental Health, Part A, 2019
Lin Zong, Zhen Gao, Wen Xie, Jian Tong, Yi Cao
Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is an inducible, primary transcription factor which plays a key role in several important cellular processes including cell proliferation and apoptosis (Gilmore 2006). This primary transcription factor is present in the cytoplasm as an inactive complex in association with inhibitor protein subunit I-κB (Bacuerle and Baltimore 1988). Upon activation, the sub-unit becomes dissociated and allows the active form of NF-κB to translocate into the nucleus (Ghosh and Baltimore 1990). Once in the nucleus, NF-κB binds sequence-specific to the promotor/enhancer regions of the target gene(s) and transactivates target gene expression (Bacuerle and Baltimore 1991; Baldwin 1996).