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From genes to proteins
Published in Raimund J. Ober, E. Sally Ward, Jerry Chao, Quantitative Bioimaging, 2020
Raimund J. Ober, E. Sally Ward, Jerry Chao
α-helices are the most common form of secondary structure in proteins, and have 3.6 amino acid residues per turn (Fig. 5.14). This means that amino acids with bulky side chains that are 3 or 4 residues apart in the primary sequence disfavor α-helix formation. The α-helix is stabilized by hydrogen bonds between the C=O group and the N-H group of amino acids that are four residues apart. Other helical structures (3 and 4.4 residues per turn) can also form in proteins, but these are not present for more than a few residues. α-helices can also be right-handed or left-handed (analogous to screws that turn in the clockwise and anticlockwise directions as they move away from the observer, respectively).
Biomolecules
Published in Volodymyr Ivanov, Environmental Microbiology for Engineers, 2020
There are four levels of protein structure (Figure 2.8): The primary structure is the sequence of amino acids connected by peptide bonds.The secondary structure is the bonding pattern of the amino acids (e.g. helix or sheet) created by the hydrogen bonds.The tertiary 3D structure consists of the domain, where the sheets or helixes fold on each other and become stable due to hydrogen, hydrophobic, disulfide bonds, and salt bridges.The quaternary structure consists of several protein molecules connected together as one unit.
Helical Symmetry
Published in Mihai V. Putz, New Frontiers in Nanochemistry, 2020
The biochemical process through a protein structure attains its functional shape or conformation is called protein folding (Dill et al., 2012). The most plausible explanation is the distance-dependence behavior of the conduction, where in the case of shorter homogeneous base sequences the charge transport would be a coherent process, while at longer distances over the aperiodic base sequences the thermally induced hopping is more likely (Giese et al., 2001; Genereux et al., 2011). On the other hand, this special electron structure of the DNA chain could play an important role in detecting DNA damages (Sontz et al., 2012) or could be used as a very efficient spin filter at room temperature for spintronic applications (Göhler et al., 2011). This process is mainly guided by hydrophobic interactions, the formation of intramolecular hydrogen bonds, and van der Waals forces, and it is opposed by conformational entropy (Miller et al., 2014). As a result of this protein folding the most abundant class of secondary structures is the helical configuration, especially the so-called α-helix. The helical structure of the polypeptide chains was for the first time experimentally observed by Pauling et al. (1951), and different forms of the helical configuration can be seen in Figure 21.4.
Structural basis of different surface-modified fullerene derivatives as novel thrombin inhibitors: insight into the inhibitory mechanism through molecular modelling studies
Published in Molecular Physics, 2021
Zhijie Yang, Yongfeng Wan, Jingwen E, Zhijian Luo, Shanshan Guan, Song Wang, Hao Zhang
The secondary structure of the protein included an α-helix, β-sheet, β-bridge, bend, turn, and coil. The changes in the secondary structure observed using conformational analysis were found to mainly occur in the Thr40-Thr55 and Glu146-Gly155 regions. The distribution of the secondary structures of these two regions in different systems with the simulation time are shown in enlarged form in Figure 10a, b. As shown in Figure 11a, the short helix part of His43-Leu45 was loosened, while the α-helix state and Turn state shifted to each other, which was especially visible in complex 1 and 3, and to a certain extent in complex 4 and 5; only complex 2 maintained its initial α-helix state after reaching equilibrium.
Degradation of 2,4-dichlorophenol contaminated soil by ultrasound-enhanced laccase
Published in Environmental Technology, 2021
Mengjuan Zhuang, Dajun Ren, Huiwen Guo, Zhaobo Wang, Shuqin Zhang, Xiaoqing Zhang, Xiangyi Gong
Circular dichroism is a common method to study the secondary structure of proteins. The measurement results of circular dichroism are shown in Figure 4(b). From Figure 4(b), the contents of α-helix and β-sheet were increased, while the contents of β-turn and random crimp were decreased. The increase of α-helix and β-sheet may cause the active sites to be exposed and the activity of laccase to be increased. The decrease of random curl content indicated that the spatial structure of laccase molecule was more orderly, which promoted the stability of laccase [42].
Investigation of mutations (L41F, F17M, N57E, Y99F_Y134W) effects on the TolAIII-UnaG fluorescence protein's unconjugated bilirubin (UC-BR) binding ability and thermal stability properties
Published in Preparative Biochemistry & Biotechnology, 2022
Numan Eczacioglu, Yakup Ulusu, İsa Gokce, Jeremy H. Lakey
There is an indirect correlation between stability and the secondary structure of proteins. All folding and stability of the proteins are dependent on the temperature, buffer in which it resides, electric charge, pH and secondary structure, etc. The increase or decrease in π–π interactions, hydrogen bonds, and other molecular interactions as a result of the mutations caused changes in the secondary structures of the protein.