Terahertz spectroscopy and machine learning algorithm for non-destructive evaluation of protein conformation

Cao, Can; Zhang, Zhaohui; Zhao, Xingke; Wang, Ziyang

doi:10.1007/s11082-020-02345-1

Cited by 30 publications

(19 citation statements)

References 34 publications

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“…Because the fingerprints of many organic molecules fall in the terahertz band, terahertz technology can be used to identify them, such as proteins and amino acids. e combination of the THz time domain system, the T-SNE dimension reduction system, and the XGBoost algorithm has been confirmed to be an effective nondestructive and nonlabelled method for evaluating the conformation and activity of proteins [3]. Water is the source of life, and the formation of the protein liquid state is typically accompanied by the solvation effect of its various structures, in which the polypeptides in the chain of aqueous solution have higher flexibility, which makes the conformational transformation of proteins more agile, and the hydrophobicity of amino acids is conducive to the formation of the stable folding structure of protein [4].…”

Section: Introductionmentioning

confidence: 97%

Terahertz Absorption Properties of Two Solid Amino Acids and Their Aqueous Solutions

Wang

Yang

et al. 2021

International Journal of Optics

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A new type of embedded cyclic olefin copolymer microfluidic chip was designed and combined with terahertz (THz) technology to study the effects of glycine and arginine on the THz wave absorption characteristics. This study aims to understand the interactions between solid amino acid molecules and between amino acid and water molecules and to determine the changes in their microstructure. By observing the intensity of the time domain spectra in the range of 0.2–2.6 THz, we found that, as the concentration of glycine and arginine increased, the THz transmission gradually decreased. It can be inferred that the molecular structure and quantity of different amino acids have different influence on the hydrogen bond, which affects the absorption coefficient in solution. It was also found that the terahertz technique is able to identify the solid amino acid species better, and it can also perform some species identification for liquid amino acids. These results provide a reference for future studies on the terahertz absorption properties of amino acid samples. Moreover, Gaussian16 software was used to calculate the terahertz spectra using the density functional theory, B3LYP functional, and 6-31G basis set. Additionally, Gaussian View6 video software provided the frequency values, molecular vibration modes of the theoretical absorption peaks of glycine, arginine, and its aqueous solutions in the frequency range of 0.2–2.6 THz, which offers theoretical support for future studies.

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Section: Introductionmentioning

confidence: 97%

Terahertz Absorption Properties of Two Solid Amino Acids and Their Aqueous Solutions

Wang

Yang

et al. 2021

International Journal of Optics

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“…The transformed variables are called principal components (PCs). PCA is a linear algorithm and cannot explain the complex polynomial relationships between features [ 17 , 18 ]. Under normal circumstances, when the cumulative variance contribution rate of the current n PCs is large enough (generally 85%), the original data can be replaced with the first n PCs.…”

Section: Methodsmentioning

confidence: 99%

Research on anthracnose grade of Camellia oleifera based on the combined LIBS and THz technology

Li¹,

Qiu²,

Zhan³

et al. 2022

Plant Methods

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Background Anthracnose of Camellia oleifera is a very destructive disease that commonly occurs in the Camellia oleifera industry, which severely restricts the development of the Camellia oleifera industry. In the early stage of the Camellia oleifera suffering from anthracnose, only the diseased parts of the tree need to be repaired in time. With the aggravation of the disease, the diseased branches need to be eradicated, and severely diseased plants should be cut down in time. At present, aiming at the problems of complex experiments and low accuracy in detecting the degree of anthracnose of Camellia oleifera, a method is proposed to detect the degree of anthracnose of Camellia oleifera leaves by using terahertz spectroscopy (THz) combined with laser-induced breakdown spectroscopy (LIBS), so as to realize the rapid, efficient, non-destructive and high-precision determination of the degree of anthracnose of Camellia oleifera. Results Mn, Ca, Ca II, Fe and other elements in the LIBS spectrum of healthy and infected Camellia oleifera leaves with different degrees of anthracnose are significantly different, and the Terahertz absorption spectra of healthy Camellia oleifera leaves, and Camellia oleifera leaves with different degrees of anthracnose there are also significant differences. Partial least squares discriminant analysis (PLS-DA), support vector machine (SVM), and linear discriminant analysis (LDA) are used to establish the fusion spectrum anthracnose classification model of Camellia oleifera. Among them, the Root mean square error of prediction (RMSEP) and the prediction determination coefficient R2p of THz-LIBS-CARS-PLS-DA of prediction set are 0.110 and 0.995 respectively, and the misjudgment rate is 1.03%; The accuracy of the modeling set of THz (CARS)-LIBS (CARS)-SVM is 100%, and the accuracy of prediction set is 100%, after preprocessing of the multivariate scattering correction (MSC), the accuracy of the THz-LIBS-MSC-CARS modeling set is 100%, and the accuracy of prediction set is 100%; The accuracy rate of THz-LIBS-MSC-CARS-LDA of modeling set is 98.98%, and the accuracy rate of the prediction set is 96.87%. Conclusion The experimental results show that: the SVM model has higher qualitative analysis accuracy and is more stable than the PLS-DA and LDA models. The results showed that: the THz spectrum combined with the LIBS spectrum could be used to separate healthy Camellia oleifera leaves from various grades of anthracnose Camellia oleifera leaves non-destructively, quickly and accurately.

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“…As mentioned above, it is clear that molecular conformation affects the biological activity and functionality of proteins [162], so it is strategic to characterize the native protein conformation. With the advance in THz technologies, research on proteins and their conformation in the THz spectral region has been extensively carried out [163][164][165][166]. All findings demonstrated that the collective vibration mode related to the protein molecular conformation is optically active in the THz range [167,168].…”

Section: Current Status Of Thz Spectroscopy For Protein Researchmentioning

confidence: 99%

Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status

et al. 2022

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Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.

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Terahertz spectroscopy and machine learning algorithm for non-destructive evaluation of protein conformation

Cited by 30 publications

References 34 publications

Terahertz Absorption Properties of Two Solid Amino Acids and Their Aqueous Solutions

Terahertz Absorption Properties of Two Solid Amino Acids and Their Aqueous Solutions

Research on anthracnose grade of Camellia oleifera based on the combined LIBS and THz technology

Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status

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