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Zang Z, Li Z, Wang J, Lu X, Lyu Q, Tang M, Cui HL, Yan S. Terahertz spectroscopic monitoring and analysis of citrus leaf water status under low temperature stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:52-59. [PMID: 36375327 DOI: 10.1016/j.plaphy.2022.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Low temperature stress, in the form of chilling and freezing, is one of the major environmental factors impacting on citrus yield, which changes plant's water state and results in the crops' sub-health or injury. The innovative terahertz (THz) spectroscopy and imaging based sensing technology has been shown to be a suitable tool for plant leaf water status determination, due to THz radiation's innate sensitivity to hydrogen bond vibration in aqueous solutions, which is usually related to plant phenotype change. We demonstrate experimentally that the THz absorption coefficient of leaf could be used for distinguishing plant's physiological stress status, exhibiting clear decreasing or increasing trend under chilling or freezing stress respectively. The underlying rationale might be that membrane damage shows a diverse pattern, changing the intra- or extra-cellular liquid environments, likely being linked to the various THz spectral characteristics. There were different adaptations in leaf morphology, leading to different leaf density, which in turn affects the water volume fraction. Moreover, different patterns of the dynamic equilibrium state of free water and bound water under chilling and freezing treatment were revealed by THz spectroscopy. Here, THz spectroscopic monitoring has shown unique potential for judging citrus's low temperature stress state through bio-water detection and discrimination.
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Affiliation(s)
- Ziyi Zang
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Zaoxia Li
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Jie Wang
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Xingxing Lu
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Qiang Lyu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Mingjie Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Hong-Liang Cui
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China.
| | - Shihan Yan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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2
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Hu M, Tang M, Wang H, Zhang M, Zhu S, Yang Z, Zhou S, Zhang H, Hu J, Guo Y, Wei X, Liao Y. Terahertz, infrared and Raman absorption spectra of tyrosine enantiomers and racemic compound. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119611. [PMID: 33689998 DOI: 10.1016/j.saa.2021.119611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 05/26/2023]
Abstract
The application of terahertz (THz)-based techniques in biomolecule study is very promising but still in its infancy. In the present work, we employed THz time-domain spectroscopy (THz-TDS) and THz time-domain attenuated total reflection (THz-TD-ATR) spectroscopy to investigate the properties of tyrosine (Tyr) enantiomers (L- and D-Tyr) and racemate (DL-Tyr) in solid state and aqueous solutions, respectively. THz absorption spectra of solid L- and D-Tyr show similar absorption spectra with peaks at 0.95, 1.92, 2.06 and 2.60 THz, which are obviously different from the spectrum of DL-Tyr with peaks at 1.5, 2.15 and 2.40 THz. In contrast, although THz absorption spectra of L-Tyr solution and D-Tyr solution are similar and different from the spectrum of DL-Tyr solution, both of them have no observable peaks. Interestingly, it was found that the solution containing equal amounts of L- and D-Tyr has a similar spectrum as that of DL-Tyr solution, as far as the mass concentrations of the two types of solutions are kept the same. On other hand, solid L-, D- and DL-Tyr were also investigated with infrared spectroscopy and Raman spectroscopy, respectively. The results show that the spectra of L- and D-Tyr can be regarded the same but they are slightly different from the spectrum of DL-Tyr. With the aid of principal component analysis (PCA), the difference between L-/D-Tyr and DL-Tyr can be confirmed without any ambiguity. Overall, this work systematically interrogated and evaluated the performance of THz-based techniques in the detection of the chirality of tyrosine.
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Affiliation(s)
- Meidie Hu
- College of Engineering and Technology, Southwest University, Chongqing 400716, China; Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Mingjie Tang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China; Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing 400714, China
| | - Huabin Wang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China; Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing 400714, China.
| | - Mingkun Zhang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China; Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing 400714, China
| | - Shiping Zhu
- College of Engineering and Technology, Southwest University, Chongqing 400716, China.
| | - Zhongbo Yang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China; Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing 400714, China
| | - Shengling Zhou
- College of Engineering and Technology, Southwest University, Chongqing 400716, China
| | - Hua Zhang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China; Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing 400714, China
| | - Jiao Hu
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Yuansen Guo
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiao Wei
- College of Engineering and Technology, Southwest University, Chongqing 400716, China
| | - Yunsheng Liao
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
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3
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Liang QI, Maocheng ZHAO, Jie ZHAO, Yuweiyi TANG. Preliminary investigation of Terahertz spectroscopy to predict pork freshness non-destructively. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.25718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- QI Liang
- Nanjing Forestry University, China; Nanjing Normal University, China
| | - ZHAO Maocheng
- Nanjing Forestry University, China; Taizhou University, China
| | - ZHAO Jie
- Nanjing Forestry University, China; Nanjing Institute of Industrial Professional Technology, China
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Calculated Terahertz Spectra of Glycine Oligopeptide Solutions Confined in Carbon Nanotubes. Polymers (Basel) 2019; 11:polym11020385. [PMID: 30960369 PMCID: PMC6419217 DOI: 10.3390/polym11020385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022] Open
Abstract
To reduce the intense terahertz (THz) wave absorption of water and increase the signal-to-noise ratio, the THz spectroscopy detection of biomolecules usually operates using the nanofluidic channel technologies in practice. The effects of confinement due to the existence of nanofluidic channels on the conformation and dynamics of biomolecules are well known. However, studies of confinement effects on the THz spectra of biomolecules are still not clear. In this work, extensive all-atom molecular dynamics simulations are performed to investigate the THz spectra of the glycine oligopeptide solutions in free and confined environments. THz spectra of the oligopeptide solutions confined in carbon nanotubes (CNTs) with different radii are calculated and compared. Results indicate that with the increase of the degree of confinement (the reverse of the radius of CNT), the THz absorption coefficient decreases monotonically. By analyzing the diffusion coefficient and dielectric relaxation dynamics, the hydrogen bond life, and the vibration density of the state of the water molecules in free solution and in CNTs, we conclude that the confinement effects on the THz spectra of biomolecule solutions are mainly to slow down the dynamics of water molecules and hence to reduce the THz absorption of the whole solution in confined environments.
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Zhang M, Yang Z, Tang M, Wang D, Wang H, Yan S, Wei D, Cui HL. Terahertz Spectroscopic Signatures of Microcystin Aptamer Solution Probed with a Microfluidic Chip. SENSORS 2019; 19:s19030534. [PMID: 30696003 PMCID: PMC6387113 DOI: 10.3390/s19030534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/13/2023]
Abstract
Terahertz signature detection of biological samples in aqueous solution remains a great challenge due to the strong terahertz absorption of water. Here we propose a new preparation process for fabricating a microfluidic chip and use it as an effective sensor to probe the terahertz absorption signatures of microcystin aptamer (a linear single-stranded DNA with 60 nucleotides) dissolved in TE buffer with different concentrations. The microfluidic chip made of silicon includes thousands of 2.4 μm × 2.4 μm square-cross-section channels. One repeatable terahertz absorption signature is detected and recognized around 830 GHz, fitted to a Lorentz oscillator. This signature is theorized to originate from the bending of hydrogen bonds formed between adjacent hydrated DNA bases surrounded by water molecules. Furthermore, the low-lying vibrational modes are also investigated by molecular dynamics simulations which suggest that strong resonant oscillations are highly probable in the 815–830 GHz frequency band.
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Affiliation(s)
- Mingkun Zhang
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong 523808, China.
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Zhongbo Yang
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Mingjie Tang
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Deqiang Wang
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Huabin Wang
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Shihan Yan
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Dongshan Wei
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong 523808, China.
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Hong-Liang Cui
- Chongqing Engineering Research Center of High-Resolution and 3D Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- College of Instrumentation Science and Electrical Engineering, Jilin University, Changchun 130061, China.
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González Torres M, Villarreal-Ramírez E, Moyaho Bernal MDLA, Álvarez M, González-Valdez J, Gutiérrez Uribe JA, Leyva Gómez G, Cortez JRC. Insights into the application of polyhydroxyalkanoates derivatives from the combination of experimental and simulation approaches. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Tang M, Zhang M, Yan S, Xia L, Yang Z, Du C, Cui HL, Wei D. Detection of DNA oligonucleotides with base mutations by terahertz spectroscopy and microstructures. PLoS One 2018; 13:e0191515. [PMID: 29364930 PMCID: PMC5783420 DOI: 10.1371/journal.pone.0191515] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/05/2018] [Indexed: 11/21/2022] Open
Abstract
DNA oligonucleotides with a 5-base mutation at the 3'-terminus were investigated by terahertz (THz) spectroscopy in a marker-free manner. The four single-stranded oligonucleotides with 17nt have been detected with specificity on a microfluidic chip, and corroborated by spectral measurements with split-ring resonators. The number of hydrogen bonds formed between the oligonucleotide and its surrounding water molecules, deemed a key contribution to the THz absorption of biological solutions, was explored by molecular dynamics simulations to explain the experimental findings. Our work underlies the feasibility of THz spectroscopy combined with microstructures for marker-free detection of DNA, which may form the basis of a prospective diagnostic tool for studying genic mutation.
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Affiliation(s)
- Mingjie Tang
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Mingkun Zhang
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shihan Yan
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Liangping Xia
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Zhongbo Yang
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Chunlei Du
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Hong-Liang Cui
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- College of Instrumentation Science and Electrical Engineering, Jilin University, Changchun, Jilin, China
| | - Dongshan Wei
- Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- * E-mail:
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8
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Ronen M, Kalanoor BS, Oren Z, Ron I, Tischler YR, Gerber D. Characterization of peptides self-assembly by low frequency Raman spectroscopy. RSC Adv 2018; 8:16161-16170. [PMID: 35542205 PMCID: PMC9080252 DOI: 10.1039/c8ra01232f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
Low Frequency Vibrational (LFV) modes of peptides and proteins are attributed to the lattice vibrations and are dependent on their structural organization and self-assembly. Studies taken in order to assign specific absorption bands in the low frequency range to self-assembly behavior of peptides and proteins have been challenging. Here we used a single stage Low Frequency Raman (LF-Raman) spectrometer to study a series of diastereomeric analogue peptides to investigate the effect of peptides self-assembly on the LF-Raman modes. The structural variation of the diastereomeric analogues resulted in distinct self-assembly groups, as confirmed by transmission electron microscopy (TEM) and dynamic light scattering (DLS) data. Using LF-Raman spectroscopy, we consistently observed discrete peaks for each of the self-assembly groups. The correlation between the spectral features and structural morphologies was further supported by principal component analysis (PCA). The LFV modes provide further information on the degrees of freedom of the entire peptide within the higher order organization, reflecting the different arrangement of its hydrogen bonding and hydrophobic interactions. Thus, our approach provides a simple and robust complementary method to structural characterization of peptides assemblies. Characterization of structural changes in peptide assemblies by low frequency Raman spectroscopy.![]()
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Affiliation(s)
- Maria Ronen
- Mina and Everard Goodman Faculty of Life Sciences
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
| | - Basanth S. Kalanoor
- Department of Chemistry
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
| | - Ziv Oren
- Department of Biotechnology
- Israel Institute for Biological Research
- Nes-Ziona 7410001
- Israel
| | - Izhar Ron
- Department of Physical Chemistry
- Israel Institute of Biological Research
- Nes-Ziona 7410001
- Israel
| | - Yaakov R. Tischler
- Department of Chemistry
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
| | - Doron Gerber
- Mina and Everard Goodman Faculty of Life Sciences
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
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Zhao X, Zhang M, Wei D, Wang Y, Yan S, Liu M, Yang X, Yang K, Cui HL, Fu W. Label-free sensing of the binding state of MUC1 peptide and anti-MUC1 aptamer solution in fluidic chip by terahertz spectroscopy. BIOMEDICAL OPTICS EXPRESS 2017; 8:4427-4437. [PMID: 29082075 PMCID: PMC5654790 DOI: 10.1364/boe.8.004427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 05/22/2023]
Abstract
The aptamer and target molecule binding reaction has been widely applied for construction of aptasensors, most of which are labeled methods. In contrast, terahertz technology proves to be a label-free sensing tool for biomedical applications. We utilize terahertz absorption spectroscopy and molecular dynamics simulation to investigate the variation of binding-induced collective vibration of hydrogen bond network in a mixed solution of MUC1 peptide and anti-MUC1 aptamer. The results show that binding-induced alterations of hydrogen bond numbers could be sensitively reflected by the variation of terahertz absorption coefficients of the mixed solution in a customized fluidic chip. The minimal detectable concentration is determined as 1 pmol/μL, which is approximately equal to the optimal immobilized concentration of aptasensors.
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Affiliation(s)
- Xiang Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
- Contributed equally
| | - Mingkun Zhang
- Chongqing Key laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Contributed equally
| | - Dongshan Wei
- Chongqing Key laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunxia Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Shihan Yan
- Chongqing Key laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Mengwan Liu
- Chongqing Key laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiang Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Ke Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Hong-Liang Cui
- Chongqing Key laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Weiling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
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Kalanoor B, Ronen M, Oren Z, Gerber D, Tischler YR. New Method to Study the Vibrational Modes of Biomolecules in the Terahertz Range Based on a Single-Stage Raman Spectrometer. ACS OMEGA 2017; 2:1232-1240. [PMID: 28393138 PMCID: PMC5377281 DOI: 10.1021/acsomega.6b00547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 03/14/2017] [Indexed: 05/04/2023]
Abstract
The low-frequency vibrational (LFV) modes of biomolecules reflect specific intramolecular and intermolecular thermally induced fluctuations that are driven by external perturbations, such as ligand binding, protein interaction, electron transfer, and enzymatic activity. Large efforts have been invested over the years to develop methods to access the LFV modes due to their importance in the studies of the mechanisms and biological functions of biomolecules. Here, we present a method to measure the LFV modes of biomolecules based on Raman spectroscopy that combines volume holographic filters with a single-stage spectrometer, to obtain high signal-to-noise-ratio spectra in short acquisition times. We show that this method enables LFV mode characterization of biomolecules even in a hydrated environment. The measured spectra exhibit distinct features originating from intra- and/or intermolecular collective motion and lattice modes. The observed modes are highly sensitive to the overall structure, size, long-range order, and configuration of the molecules, as well as to their environment. Thus, the LFV Raman spectrum acts as a fingerprint of the molecular structure and conformational state of a biomolecule. The comprehensive method we present here is widely applicable, thus enabling high-throughput study of LFV modes of biomolecules.
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Affiliation(s)
- Basanth
S. Kalanoor
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maria Ronen
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ziv Oren
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Department
of Biotechnology, Israel Institute of Biological
Research, Nes-Ziona 7410001, Israel
| | - Doron Gerber
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- E-mail: (D.G.)
| | - Yaakov R. Tischler
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- E-mail: (Y.R.T.)
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11
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Goyal B, Srivastava KR, Durani S. Examination of the Effect of N-terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine-based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University, Fatehgarh; Sahib-140406, Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Life Sciences Institute; University of Michigan; Ann Arbor, MI USA 48105
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
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12
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Goyal B, Kumar A, Srivastava KR, Durani S. Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides. J Biomol Struct Dyn 2016; 35:1923-1935. [DOI: 10.1080/07391102.2016.1199972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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