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Structures
Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
The interactions addressed above also apply to other protein secondary structures. We have seen α helices in protein structures viewed in the PDB. We have also encountered another structure cartooned as a flattened arrow, such as that visible in Figure 5.25. Such arrows indicate a structure called the β sheet. The Ramachandran diagram (Figure 5.16, arrow symbols in upper left) suggests that the structure is not far from that of an α helix, but the details differ considerably. Beta sheet structures have sections of the polypeptide chain aligned parallel or anti-parallel to each other. There must, of course, be breaks in the β structure to allow the chain to curl back on itself. The hydrogen bonds that stabilize the β sheet are between amino acids on these (anti) aligned strands of polypeptide, shown in Figure 5.26. In typical globular proteins a sheet may be made up of 2–15 strands, each strand of length about 2 nm. Beta sheets in larger globular proteins are often twisted in a right-handed manner, especially when they occur in the center of the protein. See Figure 5.27.
Naturally Occurring Polymers—Animals
Published in Charles E. Carraher, Carraher's Polymer Chemistry, 2017
The other major structural feature is pleated sheets. Two kinds of pleated sheets are found. When the chains have their N → C directions running parallel, they are called parallel beta-sheets. The N → C directions can run opposite to one another, giving what is called an antiparallel beta-sheet. The beta-keratin (Figure 10.5) that occurs in silk produced by insects and spiders is of the antiparallel variety. While alpha-keratin is especially rich in glycine and leucine, beta-keratin is mostly composed of glycine and alanine with smaller amounts of other amino acids, including serine and tyrosine. Sizewise, leucine offers a much larger grouping attached to the alpha-carbon than does alanine. The larger size of the leucine causes the alpha-keratin to form a helical structure to minimize steric factors. By comparison, the smaller size of the alanine allows the beta-keratin to form sheets. This sheet structure is partially responsible for the “softness” felt when we touch silk. While silk is not easily elongated because the protein chains are almost fully extended, beta-keratin is flexible because of the low-secondary bonding between sheets, allowing the sheets to flow past one another.
Protein-based Wood Adhesives Current Trends of Preparation and Application
Published in Zhongqi He, Bio-based Wood Adhesives, 2017
Birendra B. Adhikari, Pooran Appadu, Michael Chae, David C. Bressler
In a beta sheet conformation, a localized region of the polypeptide chain is folded in a zigzag orientation. The basic unit of this conformation is a beta strand of 5- to 10-amino acid residues. The sheet occurs due to hydrogen bonding interactions between adjacent beta strands. Beta sheets are stabilized by hydrogen bonds formed between the C=O groups of one polypeptide chain and the NH groups of another chain (Fig. 2).
Hydrophobin-enhanced stability, dispersions and release of curcumin nanoparticles in water
Published in Journal of Biomaterials Science, Polymer Edition, 2020
Baolong Niu, Meilin Li, Jianhong Jia, Ce Zhang, Yan-Ying Fan, Wenfeng Li
According to previous studies [33–35], FTIR enables measure the secondary structure of protein samples in different states, such as solids, thin films and solution, by determining with characteristic bands including amide I and amide II. So the FTIR spectra of pristine Cur, rHGFI and rHGFI-Cur were used extensively to study the conformational changes of Aβ during assembly [36]. In the inset of Figure 3(b), the presence of characteristic peaks at 1643.45 and 1652.43 cm−1 in rHGFI and rHGFI-Cur, respectively, could be attributed to the vibration bands of amide I, which was caused by C = O stretching vibrations of the peptide linkages, indicating rHGFI before and after modifying Cur contained mainly beta-sheet structure. According to the FTIR spectra of rHGFI and rHGFI-Cur, the appearance of both characteristic peaks of rHGFI and rHGFI-Cur without new bonds stated rHGFI absorbed onto the surface of Cur by physical hydrophobic force without protein structure change [37], which is consistent with the result of XPS.
Free energy reaction root mapping of alanine tripeptide in water
Published in Molecular Physics, 2019
Yuki Mitsuta, Johannes Kästner, Shusuke Yamanaka, Takashi Kawakami, Mitsutaka Okumura
The solvation effect of explicit water can be explained by the comparing this study and previous study that calculates alanine tripeptide in vacuum by using the FERRMap method [30]. This result provides an insight into the solvation effect for peptide chains; in vacuum, the beta-sheet structure is more stable than the beta-turn structure and the solvation of water makes the beta-turn structure more stable than the beta-sheet structure (see supporting information). We believe the FERRMap method helps the elucidation of the reaction mechanisms that depend on free energy.