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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.
Disease Prediction and Drug Development
Published in Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam, Introduction to Computational Health Informatics, 2019
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam
The computational tools for epitope analysis include: 1) hydrophobicity analysis of different protein domains; 2) flexibility within the protein structure; 3) protein secondary structure prediction and 4) loop and side structure analysis in proteins. The analysis of linear epitopes is easier and can be identified experimentally. To predict linear sequence, antigen sequences are fragmented into small subsequences, and their bindings to antibodies are analyzed. However, only 10% of the epitopes are linear, and linear epitopes give a weak immunogenic response.
Biomedical Applications of Raman Scattering
Published in R. Michael Gendreau, Spectroscopy in the Biomedical Sciences, 1986
While each of the above schemes has some merit, none has been sufficiently tested to warrant comments on its general validity. Nevertheless, the ability of the technique to give qualitative evaluations of protein secondary structure is clear.
Relationship of digit ratio with sexual steroid hormone receptor related genes - single nucleotide polymorphisms in a sample from Northern China
Published in Annals of Human Biology, 2023
Jie Dang, Chengfeng Ma, Fan Li, Jing Zhang, Yuan Wang, Liang Peng, Zhenghao Huo, Hong Lu, Zhanbing Ma
In this study, different genotypes of rs1042839 showed a significant difference in male left 2D:4D. The left-hand 2D:4D of men with GG genotype was significantly lower than that of individuals with AG genotype, suggesting that this locus may affect phalanx development and digit ratio sex dimorphism. Through bioinformatics analysis, it was found that when the rs1042839 allele changed from G to A, the codon encoding protein at position 770 would change from CAC to CAT. However, the coding amino acid remains unchanged, and this mutation is considered synonymous. Furthermore, this site is not located in key parts, such as α helix, β fold, and corners of protein secondary structure, which have less impact on protein function. Therefore, further investigation is needed to determine whether rs1042839 can affect progesterone metabolism through other ways and then participate in the formation of digit ratio.
Computational models for studying physical instabilities in high concentration biotherapeutic formulations
Published in mAbs, 2022
In high-resolution CG models, residues are generally represented by four to seven CG sites. Most of these CG sites are assigned to the peptide backbone to preserve the dynamics of protein secondary structure, while the remaining sites represent the residue’s side chain to incorporate the identity of the protein sequence through amino acid-specific interactions. Examples of these models include the MARTINI model,35 the OPEP model,39 and the PRIMO model.46 Because of the high level of structural details that these CG models provide, they have been successfully implemented for studying protein–protein interactions,74 the mechanisms for protein folding and aggregation in small to medium size proteins and in crowded environments,13,44 the self-assembly pathways of virus proteins,75 as well as to facilitate the refinement of NMR and crystallographic structures.76 High-resolution models represent a significant improvement over atomistic models in terms of computational cost, enabling the evaluation of protein process with characteristic timescales on the order of milliseconds.9,77
Different effects of magnetic field on drug activity in human uterine sarcoma cell lines MES-SA and MES-SA/Dx5
Published in Electromagnetic Biology and Medicine, 2022
Several studies have reported the influence of MF on membrane proteins in human cells. Using Fourier transform infrared spectroscopy (FTIR), Ikehara et al. (2003) observed that 50 Hz MF exposure shifted the amide I band peak to a smaller wave number, reduced the amide II band peak, and altered the secondary structures of membrane proteins in HeLa cells. In the FTIR study by Calabrò (2016), 50 Hz MF shifted the amide I band to a low energy and increased hydrogen bonds in the membranes of neuro-like cells. Indeed, hydrogen bonds slightly increased as MF intensity was increased (Chang and Weng 2006). In addition, MF exposure also enhanced hydrogen bond strength (Inaba et al. 2004), and the hydrogen bond lifetimes were prolonged due to the electron delocalization of water dimers under MF exposure (Hosoda et al. 2004). These findings indicated that MF affected the hydrogen bonds that the determine protein secondary structure. As protein conformation is closely related to its function, MF appears to influence protein function.