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Protein–Nanoparticle Interactions
Published in Lajos P. Balogh, Nano-Enabled Medical Applications, 2020
Iseult Lynch, Kenneth A. Dawson
Proteins are chains of amino acids, where the exact sequence of the amino acids determines the protein’s shape, structure, and function. The principle units of protein secondary structure are α-helices and β-sheets, and the three-dimensional arrangement of these is the tertiary structure (α-helix, shown in red, and β-strand, blue, structures are illustrated in Fig. 8.1). The native conformation of a protein is tightly controlled by the shape complementarity of the hydrophobic residues that allow close packing of the cores [28]. Proteins are nevertheless marginally stable because the beneficial interactions that govern the native structure are counterbalanced by a large entropy loss associated with going from a large ensemble of states to a more restricted set of conformations, as well as by the repulsive electrostatic interactions present in the native state [29]. Thus, interaction with a surface can easily disrupt the native conformation and, therefore, the protein function. This has implications for the biological impact of nanoparticles.
Nanoscience of Large Immune Proteins
Published in Klaus D. Sattler, st Century Nanoscience – A Handbook, 2020
Alexey Ferapontov, Kristian Juul-Madsen, Thomas Vorup-Jensen
Protein structure has typically been divided into primary structure, or sequence of amino acid residues in the protein, secondary structure, essentially reflecting the propensity of that sequence to take either an alpha helical, beta stranded, or unfolded structure of the polypeptide chain, tertiary structure, describing spatial organization of the polypeptide chain into, e.g., a globular domain structure, and finally, quaternary structure, reflecting the organization of more polypeptide chains into a single structure (Linderstrøm-Lang 1952). While the borders of the quaternary structure, in principle, can cover even very large protein complexes, the structure of both IgM and MBL highlights some limitations of the classic definition. As noted above, IgM is built from units of the fundamental immunoglobulin structure of two heavy and two light chains. The unit itself contains a protein architecture with all levels of protein structure, from the primary to the quaternary structure. MBL also contains structural units made from the folded MBL chain, which at the quaternary level a forms trimeric structure, referred to as MBL3 (Gjelstrup et al. 2012). The fully assembled, polydisperse molecules apparently contain at least 3–8 of these units, and maybe even large assemblies (Gjelstrup et al. 2012; Jensenius et al. 2009). These assemblies are referred to as 3 × MBL3–8 × MBL3, in this way clearly highlighting the nature of the oligomeric structure (Vorup-Jensen 2012). It would seem awkward to mix the quaternary level of the MBL3 structure with the oligomerization of these units. Hence, we prefer to refer to the oligomerization of the structural unit as forming the ultrastructure of the MBL and IgM.
Product Quality and Process
Published in Wei-Shou Hu, Cell Culture Bioprocess Engineering, 2020
Circular dichroism in the far-UV region is used to reveal changes in protein secondary structure. Due to the chiral nature of proteins, they have different absorption of left-handed and right-handed circularly polarized light. The absorption spectra of a protein in circular dichroism spectroscopy is affected not only by its α-helix and β-sheet content, but also its three-dimensional structure. This type of investigation is thus a powerful tool in revealing secondary structural changes of a protein upon exposure to an agent of change.
Insights into the catalytic mechanism of ligninolytic peroxidase and laccase in lignin degradation
Published in Bioremediation Journal, 2022
Pankaj Bhatt, Meena Tiwari, Prasoon Parmarick, Kalpana Bhatt, Saurabh Gangola, Muhammad Adnan, Yashpal Singh, Muhammad Bilal, Shakeel Ahmed, Shaohua Chen
The Ramachandran plot results of lignin peroxidase (1LGA) represent the number of amino acids favored region is 97.6%, 2.4% is allowed area and 0.0% residue is outline region. This result confirmed that the Φ and Ψ values for the selected enzyme are significant for the experiment. It was observed that allowed region proteins contain the glycine and proline. The study of the Ramachandran plot of manganese peroxidase (1MNP) showed that the number of amino acids favored region is 96.1%,3.7% is allowed region and 0.3% residue is outline region. Result of the present study confirmed that the Φ and Ψ values for the selected enzyme are significant for the experiment. It was observed that allowed region proteins contain Glycine, Proline amino acid. The study of the Ramachandran plot of versatile peroxidase (3FJW) showed that the number of amino acids favored region is 97.0%, 3.0% is allowed region and 0.0% residue is outline region. This result confirmed that the Φ and Ψ values for the selected enzyme are significant for the experiment. It was observed that allowed region proteins contain Glycine, Proline amino acid. The study of the Ramachandran plot of Laccase (5EHF) showed that the number of the amino acid favored region is 97.6%, 2.0% is allowed region and 0.4% residue is outline region. This result confirmed that the Φ and Ψ values for the selected enzyme are significant for the experiment. It was observed that allowed region proteins contain Glycine, Proline amino acid. Based on the Ramachandran plot results, we further used the enzymes for molecular docking experiment. Previous researchers confirmed that the Ramachandran plot analysis found useful for the protein secondary structure (Tam, Sinha, and Wang 2020). In Ramachandran plot glycine monomer exhibited higher as compared to backbone peptides (Momen et al. 2017).