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Elayan H, Eckford AW, Adve R. Selectivity of Protein Interactions Stimulated by Terahertz Signals. IEEE Trans Nanobioscience 2023; 22:318-328. [PMID: 35797314 DOI: 10.1109/tnb.2022.3189549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside protein molecules using THz signals can control changes in their structure and activate associated biochemical and biomechanical events. To establish that, we formulate a selectivity metric that quantifies the system performance and captures the capability of the nanoantenna to induce a conformational change in the desired protein molecule/population. The metric provides a score between -1 and 1 that indicates the degree of control we have over the system to achieve targeted protein interactions. To develop the selectivity measure, we first use the Langevin stochastic equation driven by an external force to model the protein behavior. We then determine the probability of protein folding by computing the steady-state energy of the driven protein and then generalize our model to account for protein populations. Our numerical analysis results indicate that a maximum selectivity score is attained when only the targeted population experiences a folding behavior due to the impinging THz signal. From the achieved selectivity values, we conclude that the system response not only depends on the resonant frequency but also on the system controlling parameters namely, the nanoantenna force, the damping constant, and the abundance of each protein population. Based on the selectivity metric, the nanoantenna must be tuned to a frequency that is not necessarily the resonant frequency of the protein. The presented work sheds light on the potential associated with the electromagnetic-based control of protein networks, which could lead to a plethora of applications in the medical field ranging from bio-sensing to targeted therapy.
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2
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Mernea M, Ulăreanu RȘ, Cucu D, Al-Saedi JH, Pop CE, Fendrihan S, Anghelescu GDC, Mihăilescu DF. Epithelial Sodium Channel Inhibition by Amiloride Addressed with THz Spectroscopy and Molecular Modeling. Molecules 2022; 27:3271. [PMID: 35630748 PMCID: PMC9144217 DOI: 10.3390/molecules27103271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/08/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
THz spectroscopy is important for the study of ion channels because it directly addresses the low frequency collective motions relevant for their function. Here we used THz spectroscopy to investigate the inhibition of the epithelial sodium channel (ENaC) by its specific blocker, amiloride. Experiments were performed on A6 cells' suspensions, which are cells overexpressing ENaC derived from Xenopus laevis kidney. THz spectra were investigated with or without amiloride. When ENaC was inhibited by amiloride, a substantial increase in THz absorption was noticed. Molecular modeling methods were used to explain the observed spectroscopic differences. THz spectra were simulated using the structural models of ENaC and ENaC-amiloride complexes built here. The agreement between the experiment and the simulations allowed us to validate the structural models and to describe the amiloride dynamics inside the channel pore. The amiloride binding site validated using THz spectroscopy agrees with previous mutagenesis studies. Altogether, our results show that THz spectroscopy can be successfully used to discriminate between native and inhibited ENaC channels and to characterize the dynamics of channels in the presence of their specific antagonist.
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Affiliation(s)
- Maria Mernea
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania; (M.M.); (R.Ș.U.); (J.H.A.-S.); (G.D.C.A.); (D.F.M.)
| | - Roxana Ștefania Ulăreanu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania; (M.M.); (R.Ș.U.); (J.H.A.-S.); (G.D.C.A.); (D.F.M.)
| | - Dana Cucu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania; (M.M.); (R.Ș.U.); (J.H.A.-S.); (G.D.C.A.); (D.F.M.)
| | - Jasim Hafedh Al-Saedi
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania; (M.M.); (R.Ș.U.); (J.H.A.-S.); (G.D.C.A.); (D.F.M.)
| | - Cristian-Emilian Pop
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania;
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania;
| | - Sergiu Fendrihan
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania;
- Faculty of Medicine, University “Vasile Goldis”, Bulevardul Revoluției 94, 310025 Arad, Romania
| | - Giorgiana Diana Carmen Anghelescu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania; (M.M.); (R.Ș.U.); (J.H.A.-S.); (G.D.C.A.); (D.F.M.)
| | - Dan Florin Mihăilescu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței Str., 050095 Bucharest, Romania; (M.M.); (R.Ș.U.); (J.H.A.-S.); (G.D.C.A.); (D.F.M.)
- Biometric Psychiatric Genetics Research Unit, Alexandru Obregia Psychiatric Hospital, 10 Șoseaua Berceni Str., 041914 Bucharest, Romania
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3
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Pal S, Chattopadhyay A. Hydration Dynamics in Biological Membranes: Emerging Applications of Terahertz Spectroscopy. J Phys Chem Lett 2021; 12:9697-9709. [PMID: 34590862 DOI: 10.1021/acs.jpclett.1c02576] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Water drives the spontaneous self-assembly of lipids and proteins into quasi two-dimensional biological membranes that act as catalytic scaffolds for numerous processes central to life. However, the functional relevance of hydration in membrane biology is only beginning to be addressed, predominantly because of challenges associated with direct measurements of hydration microstructure and dynamics in a biological milieu. Our recent work on the novel interplay of membrane electrostatics and crowding in shaping membrane hydration dynamics utilizing terahertz (THz) spectroscopy represents an important step in this context. In this Perspective, we provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules. We further highlight the immense (and largely untapped) potential of the THz toolbox in addressing contemporary problems in membrane biology, while emphasizing the adaptability of the analytical framework reported recently by us to such studies.
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Affiliation(s)
- Sreetama Pal
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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4
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Zhu Z, Zhang J, Song Y, Chang C, Ren G, Shen J, Zhang Z, Ji T, Chen M, Zhao H. Broadband terahertz signatures and vibrations of dopamine. Analyst 2021; 145:6006-6013. [PMID: 32756617 DOI: 10.1039/d0an00771d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.
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Affiliation(s)
- Zhongjie Zhu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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5
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Sun Y, Huang J, Shan L, Fan S, Zhu Z, Liu X. Quantitative analysis of bisphenol analogue mixtures by terahertz spectroscopy using machine learning method. Food Chem 2021; 352:129313. [PMID: 33657480 DOI: 10.1016/j.foodchem.2021.129313] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022]
Abstract
Quantitative analysis of complex mixtures is a great challenge for spectral analysis. Bisphenol A (BpA) is a chemical predominantly used in manufacturing and is being replaced by other analogs due to its potential toxicity. Reliability methods is hence crucial for identification and quantification of bisphenol mixtures. In this study we present an attractive strategy for composition determination of BpA incorporated in its analogue mixtures. Terahertz spectra of four bisphenol components are analyzed using machine learning method (SVR) to learn the underlying model of the frequency against the target concentration of BpA in mixtures. The learned mode predicts the concentrations of the unknown samples with decision coefficient R2 = 0.98. Absorption spectra for bisphenols mixtures were successfully reconstructed by a hold-out validation scheme. The results indicate the terahertz spectroscopy in combination with SVR is robust and accurate in mixture quantitative analysis and should play a significant role for industrial applications in the future.
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Affiliation(s)
- Yiwen Sun
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Jialiang Huang
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Lianxin Shan
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Shuting Fan
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zexuan Zhu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xudong Liu
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong, Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China.
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6
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Elayan H, Eckford AW, Adve RS. Information Rates of Controlled Protein Interactions Using Terahertz Communication. IEEE Trans Nanobioscience 2020; 20:9-19. [PMID: 32886612 DOI: 10.1109/tnb.2020.3021825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior, can be selectively stimulated using Terahertz (THz) band frequencies. By triggering protein vibrational modes using THz waves, we induce changes in protein conformation, resulting in the activation of a controlled cascade of biochemical and biomechanical events. To analyze such an interaction, we formulate a communication system composed of a nanoantenna transmitter and a protein receiver. We adopt a Markov chain model to account for protein stochasticity with transition rates governed by the nanoantenna force. Both two-state and multi-state protein models are presented to depict different biological configurations. Closed form expressions for the mutual information of each scenario is derived and maximized to find the capacity between the input nanoantenna force and the protein state. The results we obtain indicate that controlled protein signaling provides a communication platform for information transmission between the nanoantenna and the protein with a clear physical significance. The analysis reported in this work should further research into the EM-based control of protein networks.
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Kadantsev VN, Goltsov A. Collective excitations in α-helical protein structures interacting with the water environment. Electromagn Biol Med 2020; 39:419-432. [PMID: 33023315 DOI: 10.1080/15368378.2020.1826961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Low-frequency vibrational excitations of protein macromolecules in the terahertz frequency region are suggested to contribute to many biological processes such as enzymatic catalysis, intra-protein energy/charge transport, recognition, and allostery. To explain high effectiveness of these processes, two possible mechanisms of the long-lived excitation were proposed by H. Fröhlich and A.S. Davydov, which relate to either vibrational modes or solitary waves, respectively. In this paper, we developed a quantum dynamic model of vibrational excitation in α-helical proteins interacting with the aqueous environment. In the model, we distinguished three coupled subsystems, i.e., (i) a chain of hydrogen-bonded peptide groups (PGs), interacting with (ii) the subsystem of the side-chain residuals which in turn interact with (iii) the environment, surrounding water responsible for dissipation and fluctuation in the system. It was shown that the equation of motion for phonon variables of the PG chain can be transformed to nonlinear Schrodinger equation which admits bifurcation into the solution corresponding to the weak-damped vibrational modes (Fröhlich-type regime) and Davydov solitons. A bifurcation parameter is derived through the strength of phonon-phonon interaction between the side-chains and hydration-shell water molecules. As shown, the energy of these excited states is pumped through the interaction of the side-chains with fluctuating water environment of the proteins. The suggested mechanism of the collective vibrational mode excitation is discussed in connection with the recent experiments on the long-lived collective protein excitations in the terahertz frequency region and vibrational energy transport pathways in proteins.
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Affiliation(s)
| | - Alexey Goltsov
- Russian Technological University (MIREA) , Moscow, Russia
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8
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Effect of aggregation on hydration of HSA protein: Steady-state Terahertz absorption spectroscopic study. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1696-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Danciu M, Alexa-Stratulat T, Stefanescu C, Dodi G, Tamba BI, Mihai CT, Stanciu GD, Luca A, Spiridon IA, Ungureanu LB, Ianole V, Ciortescu I, Mihai C, Stefanescu G, Chirilă I, Ciobanu R, Drug VL. Terahertz Spectroscopy and Imaging: A Cutting-Edge Method for Diagnosing Digestive Cancers. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E1519. [PMID: 31075912 PMCID: PMC6539301 DOI: 10.3390/ma12091519] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023]
Abstract
The Terahertz's wavelength is located between the microwave and the infrared region of the electromagnetic spectrum. Because it is non-ionizing and non-invasive, Terahertz (THz)-based detection represents a very attractive tool for repeated assessments, patient monitoring, and follow-up. Cancer acts as the second leading cause of death in many regions, and current predictions estimate a continuous increasing trend. Of all types of tumors, digestive cancers represent an important percentage and their incidence is expected to increase more rapidly than other tumor types due to unhealthy lifestyle habits. Because it can precisely differentiate between different types of molecules, depending on water content, the information obtained through THz-based scanning could have several uses in the management of cancer patients and, more importantly, in the early detection of different solid tumors. The purpose of this manuscript is to offer a comprehensive overview of current data available on THz-based detection for digestive cancers. It summarizes the characteristics of THz waves and their interaction with tissues and subsequently presents available THz-based technologies (THz spectroscopy, THz-tomography, and THZ-endoscope) and their potential for future clinical use. The third part of the review is focused on highlighting current in vitro and in vivo research progress in the field, for identifying specific digestive cancers known as oral, esophageal, gastric, colonic, hepatic, and pancreatic tumors.
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Affiliation(s)
- Mihai Danciu
- Pathology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Teodora Alexa-Stratulat
- Medical Oncology-Radiotherapy, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Gianina Dodi
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Bogdan Ionel Tamba
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Cosmin Teodor Mihai
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Gabriela Dumitrita Stanciu
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Andrei Luca
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Irene Alexandra Spiridon
- Pathology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | | | - Victor Ianole
- Pathology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Irina Ciortescu
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Catalina Mihai
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Gabriela Stefanescu
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Ioan Chirilă
- Environmental Health, National Institute of Public Health, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Romeo Ciobanu
- Electrical Engineering Faculty, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania.
| | - Vasile Liviu Drug
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
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10
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Cheng C, Zhu Z, Li S, Ren G, Zhang J, Cong H, Peng Y, Han J, Chang C, Zhao H. Broadband terahertz recognizing conformational characteristics of a significant neurotransmitter γ-aminobutyric acid. RSC Adv 2019; 9:20240-20247. [PMID: 35514707 PMCID: PMC9065752 DOI: 10.1039/c9ra02971k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 06/19/2019] [Indexed: 11/28/2022] Open
Abstract
γ-Aminobutyric acid (GABA) is the chief inhibitory neurotransmitter in the central nervous system, its conformational behavior is critical for selective biological functions and the process of signal transmission. Although this neuroactive molecule has been extensively studied, its vibrational properties related to the conformation and intermolecular interactions in the terahertz (THz) band have not been identified experimentally yet. In this study, we applied a broadband THz time-domain spectroscopy (THz-TDS) system from 0.5 to 18 THz to characterize a unique THz fingerprint of GABA. The density functional theory calculation results agree well with the THz experimental spectrum. The study shows that the vibrational modes of GABA at 1.15 and 1.39 THz originate from distinct collective vibrations. The absorptions at the higher THz frequencies also carry part of collective vibrations, but more reflect the specific and local vibrational information, including the skeleton deformation and the rocking of the functional groups, which are closely associated with the conformation and flexibility of GABA. This study may help to understand the conformational transitions of neurotransmitter molecules and the resonant response to THz waves. γ-Aminobutyric acid (GABA) is the chief inhibitory neurotransmitter in the central nervous system, its conformational behavior is critical for selective biological functions and the process of signal transmission.![]()
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11
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The effect of conformational freedom of side chain on low-frequency motions of amino acids in solid-state. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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12
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Gagkaeva ZV, Zhukova ES, Grinenko V, Grebenko AK, Sidoruk KV, Voeikova TA, Dressel M, Gorshunov BP. Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix. J Biol Phys 2018; 44:401-417. [PMID: 29732506 PMCID: PMC6082806 DOI: 10.1007/s10867-018-9497-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/13/2018] [Indexed: 01/30/2023] Open
Abstract
Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈ 200 and ≈ 600 cm-1, respectively. The sharp excitations seen above 1000 cm-1 are assigned to intramolecular vibrations.
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Affiliation(s)
- Z V Gagkaeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - E S Zhukova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - V Grinenko
- Institute for Metallic Materials, IFW Dresden, Dresden, Germany
| | - A K Grebenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - K V Sidoruk
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - T A Voeikova
- Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - M Dressel
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Physikalisches Institut, Universität Stuttgart, Stuttgart, Germany
| | - B P Gorshunov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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13
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Yamamoto N, Ito S, Nakanishi M, Chatani E, Inoue K, Kandori H, Tominaga K. Effect of Temperature and Hydration Level on Purple Membrane Dynamics Studied Using Broadband Dielectric Spectroscopy from Sub-GHz to THz Regions. J Phys Chem B 2018; 122:1367-1377. [PMID: 29304273 DOI: 10.1021/acs.jpcb.7b10077] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate the effects of temperature and hydration on the dynamics of purple membrane (PM), we measured the broadband complex dielectric spectra from 0.5 GHz to 2.3 THz using a vector network analyzer and terahertz time-domain spectroscopy from 233 to 293 K. In the lower temperature region down to 83 K, the complex dielectric spectra in the THz region were also obtained. The complex dielectric spectra were analyzed through curve fitting using several model functions. We found that the hydrated states of one relaxational mode, which was assigned as the coupled motion of water molecules with the PM surface, began to overlap with the THz region at approximately 230 K. On the other hand, the relaxational mode was not observed for the dehydrated state. On the basis of this result, we conclude that the protein-dynamical-transition-like behavior in the THz region is due to the onset of the overlap of the relaxational mode with the THz region. Temperature hysteresis was observed in the dielectric spectrum at 263 K when the hydration level was high. It is suggested that the hydration water behaves similarly to supercooled liquid at that temperature. The third hydration layer may be partly formed to observe such a phenomenon. We also found that the relaxation time is slower than that of a globular protein, lysozyme, and the microscopic environment in the vicinity of the PM surface is suggested to be more heterogeneous than lysozyme. It is proposed that the spectral overlap of the relaxational mode and the low-frequency vibrational mode is necessary for the large conformational change of protein.
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Affiliation(s)
- Naoki Yamamoto
- Graduate School of Science, Kobe University , 1-1 Rokkodai-cho, Nada, Kobe, 657-8501, Japan
| | - Shota Ito
- Graduate School of Engineering, Nagoya Institute of Technology , Gokisho-cho, Shouwa-ku, Nagoya, 466-8555, Japan
| | - Masahiro Nakanishi
- Department of Electrical Engineering, Fukuoka Institute of Technology , 3-30-1 Wajiro-higashi, Higashi-ku, Fukuoka, 811-0295, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University , 1-1 Rokkodai-cho, Nada, Kobe, 657-8501, Japan
| | - Keiichi Inoue
- Graduate School of Engineering, Nagoya Institute of Technology , Gokisho-cho, Shouwa-ku, Nagoya, 466-8555, Japan
| | - Hideki Kandori
- Graduate School of Engineering, Nagoya Institute of Technology , Gokisho-cho, Shouwa-ku, Nagoya, 466-8555, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University , 1-1 Rokkodai-cho, Nada, Kobe, 657-8501, Japan.,Molecular Photoscience Research Center, Kobe University , 1-1 Rokkodai-cho, Nada, Kobe, 657-8501, Japan
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14
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Wu X, Wu X, Shao M, Yang B. Structural changes of Bombyx mori fibroin from silk gland to fiber as evidenced by Terahertz spectroscopy and other methods. Int J Biol Macromol 2017; 102:1202-1210. [PMID: 28487194 DOI: 10.1016/j.ijbiomac.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/17/2017] [Accepted: 05/02/2017] [Indexed: 11/25/2022]
Abstract
Here we investigated the structural changes of silk fibroin during Bombyx mori silkworm spinning and reconstitution process. X-ray diffraction, Fourier transform infrared spectroscopy, polarized optical microscopy, and terahertz (THz) spectroscopy were applied to monitor the structural features of silk fibroin from posterior, middle silk glands, to cocoons, and then to reconstituted silk. Results show that from silk gland to cocoon, fibroin experiences a significant transformation in crystal structure from a typical silk I, to a silk I-rich mixed structure, and finally to a typical silk II state, accompanied with a change in secondary structure from α-helix and random coil structures to preferential orientation β-sheets. Compared with natural silk fibroins, the reconstituted silk fibroin lacks β-sheet conformation and orientation crystallization. Terahertz spectroscopy readily follows these silk fibroin structural changes. Two characteristic peaks for silk fibroin is observed in 2-10 THz. Their strength ratio is strongly correlated with the β-sheet conformation. The absorbance properties in 0.2-2.0THz also significantly change as a function of changing their crystal structures caused by diverse sources. All of these observations will help in the study of overall structure in silk fibroin to understand more completely the fibroin assembly process in natural spinning and reconstitution process.
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Affiliation(s)
- Xu Wu
- College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiaodong Wu
- College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Min Shao
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Bin Yang
- College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou 310018, China; Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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15
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Thirumuruganandham SP, Gómez EA, Lakshmanan S, Hamblin MR. Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study. IEEE TRANSACTIONS ON TERAHERTZ SCIENCE AND TECHNOLOGY 2017; 7:131-143. [PMID: 30881732 PMCID: PMC6419770 DOI: 10.1109/tthz.2016.2637380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Infrared (IR) and Terahertz (THz) spectroscopy simulations were carried out using CHARMM35b2 to determine protein stability. The stabilities of three bacterial cold shock proteins (Csps) originating from mesophiles, thermophiles and hyper- thermophiles respectively were investigated in this study. The three different Csps were investigated by Normal-Mode analysis and Molecular Dynamics simulation of THz spectra using the Hessian matrix for solvated systems, interpreted in the harmonic approximation at optimum near-melting temperatures of each homologue, by incorporating differences in the hydrous and anhydrous states of the Csps. The results show slight variations in the large scale protein motion. However, the IR spectra of Csps observed at the low frequency saddle surface region, clearly distinguishes the thermophilic and mesophilic proteins based on their stability. Further studies on protein stability employing low-frequency collective modes have the potential to reveal functionally important conformational changes that are biologically significant.
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Affiliation(s)
| | - Edgar A Gómez
- Programa de Física, Universidad del Quindío, Armenia, Colombia
| | - Shanmugamurthy Lakshmanan
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael R Hamblin
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
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16
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Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors. Sci Rep 2016; 6:37290. [PMID: 27849063 PMCID: PMC5110974 DOI: 10.1038/srep37290] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 10/28/2016] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors are a large family of membrane proteins activated by a variety of structurally diverse ligands making them highly adaptable signaling molecules. Despite recent advances in the structural biology of this protein family, the mechanism by which ligands induce allosteric changes in protein structure and dynamics for its signaling function remains a mystery. Here, we propose the use of terahertz spectroscopy combined with molecular dynamics simulation and protein evolutionary network modeling to address the mechanism of activation by directly probing the concerted fluctuations of retinal ligand and transmembrane helices in rhodopsin. This approach allows us to examine the role of conformational heterogeneity in the selection and stabilization of specific signaling pathways in the photo-activation of the receptor. We demonstrate that ligand-induced shifts in the conformational equilibrium prompt vibrational resonances in the protein structure that link the dynamics of conserved interactions with fluctuations of the active-state ligand. The connection of vibrational modes creates an allosteric association of coupled fluctuations that forms a coherent signaling pathway from the receptor ligand-binding pocket to the G-protein activation region. Our evolutionary analysis of rhodopsin-like GPCRs suggest that specific allosteric sites play a pivotal role in activating structural fluctuations that allosterically modulate functional signals.
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17
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Ueno K, Nozawa S, Misawa H. Surface-enhanced terahertz spectroscopy using gold rod structures resonant with terahertz waves. OPTICS EXPRESS 2015; 23:28584-28592. [PMID: 26561128 DOI: 10.1364/oe.23.028584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Terahertz (THz) spectroscopy is a promising method to measure the spectrum of low-frequency modes of molecules or ensembles, such as crystals and polymers, including proteins. However, the main drawback of THz spectroscopy is its extremely low sensitivity. In the present study, we report on signal enhancement in THz spectroscopy achieved by depositing amino acid molecules or their derivatives on a gold rod structured silicon substrate whose localized surface plasmon resonance is exhibited in the THz frequency region. The distinct peaks derived from the enhancement of the inherent spectrum based on a molecular crystal were clearly observed when a longitudinal plasmon resonance mode of the gold rod structure was excited and the plasmon resonance band overlapped the molecular/intermolecular vibrational mode. We discuss the mechanism by which surface-enhanced THz spectroscopy was induced from the viewpoint of the enhancement of light-matter coupling due to plasmon excitation and the modulation of the plasmon band by dipole coupling between the plasmon dipole and molecular/intermolecular vibrational modes.
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18
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Choi JH, Cho M. Terahertz Chiroptical Spectroscopy of an α-Helical Polypeptide: A Molecular Dynamics Simulation Study. J Phys Chem B 2014; 118:12837-43. [DOI: 10.1021/jp508547y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-Ho Choi
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
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19
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Lundholm I, Wahlgren WY, Piccirilli F, Di Pietro P, Duelli A, Berntsson O, Lupi S, Perucchi A, Katona G. Terahertz absorption of illuminated photosynthetic reaction center solution: a signature of photoactivation? RSC Adv 2014. [DOI: 10.1039/c4ra03787a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Physical Factors of the Environment. Biophysics (Nagoya-shi) 2012. [DOI: 10.1007/978-3-662-45845-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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21
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McIntosh AI, Yang B, Goldup SM, Watkinson M, Donnan RS. Terahertz spectroscopy: a powerful new tool for the chemical sciences? Chem Soc Rev 2011; 41:2072-82. [PMID: 22143259 DOI: 10.1039/c1cs15277g] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Terahertz spectroscopy is only now beginning to make its transition from initial development by physicists and engineers to broader use by chemists, materials scientists and biologists, thanks to the increasing availability of commercial terahertz spectrometers. With the unique insights that terahertz spectroscopy can provide into intermolecular bonding and crystalline matter, it could prove to be an invaluable addition to the chemist's analytical toolset. This tutorial review aims to give an introduction to terahertz spectroscopy, its techniques, equipment, current applications and potential for the chemical sciences to a broad readership.
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Affiliation(s)
- Alexander I McIntosh
- Queen Mary University of London, School of Electrical Engineering & Computer Science, Mile End Road, London, E1 4NS, UK
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23
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24
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Dielectric relaxation dynamics of water in model membranes probed by terahertz spectroscopy. Biophys J 2010; 97:2484-92. [PMID: 19883591 DOI: 10.1016/j.bpj.2009.08.024] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 08/10/2009] [Accepted: 08/17/2009] [Indexed: 11/22/2022] Open
Abstract
We study hydrated model membranes, consisting of stacked bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids, using terahertz time-domain spectroscopy and infrared spectroscopy. Terahertz spectroscopy enables the investigation of water dynamics, owing to its sensitivity to dielectric relaxation processes associated with water reorientation. By controlling the number of water molecules per lipid molecule in the system, we elucidate how the interplay between the model membrane and water molecules results in different water dynamics. For decreasing hydration levels, we observe the appearance of new types of water dynamics: the collective bulklike dynamics become less pronounced, whereas an increased amount of both very slowly reorienting (i.e., irrotational) and very rapidly reorienting (i.e., fast) water molecules appear. Temperature-dependent measurements reveal the interconversion between the three distinct types of water present in the system.
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25
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Murray AR, Fliesler SJ, Al-Ubaidi MR. Rhodopsin: the functional significance of asn-linked glycosylation and other post-translational modifications. Ophthalmic Genet 2010; 30:109-20. [PMID: 19941415 DOI: 10.1080/13816810902962405] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Rhodopsin, the G-protein coupled receptor in retinal rod photoreceptors, is a highly conserved protein that undergoes several types of post-translational modifications. These modifications are essential to maintain the protein's structure as well as its proper function in the visual transduction cycle. Rhodopsin is N-glycosylated at Asn-2 and Asn-15 in its extracellular N-terminal domain. Mutations within the glycosylation consensus sequences of rhodopsin cause autosomal dominant retinitis pigmentosa, a disease that leads to blindness. Several groups have studied the role of rhodopsin's N-linked glycan chains in protein structure and function using a variety of approaches. These include the generation of a transgenic mouse model, study of a naturally occurring mutant animal model, in vivo pharmacological inhibition of glycosylation, and in vitro analyses using transfected COS-1 cells. These studies have provided insights into the possible role of rhodopsin glycosylation, but have yielded conflicting results.
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Affiliation(s)
- Anne R Murray
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
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27
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Thirumuruganandham SP, Urbassek HM. Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. J Mol Model 2009; 15:959-69. [DOI: 10.1007/s00894-008-0446-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 12/23/2008] [Indexed: 11/25/2022]
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28
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Zhang H, Zukowski E, Balu R, Gregurick SK. A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis. J Mol Graph Model 2008; 27:655-63. [PMID: 19095477 DOI: 10.1016/j.jmgm.2008.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 10/21/2008] [Accepted: 10/22/2008] [Indexed: 11/27/2022]
Abstract
We studied the terahertz (THz) spectroscopy and low frequency normal modes of both apo- and holo- (adenosine monophosphate (AMP)-bound) ricin-A-chain (RTA) as a means to understand the dynamical changes that RTA undergoes upon substrate binding. The calculated THz spectra of apo- and holo-RTAs demonstrated a general intensity suppression upon substrate binding, which is attributed to the reduced number of collective motion in THz region. In normal mode analysis of RTA we find a shearing motion that is shared by both the apo- and holo-RTAs, whereas a breathing motion, and an upward hinge rising and an alpha-G bending characteristic motion are dampened significantly upon AMP binding, suggesting these motions are involved in the necessary flexibility of the active site. In contrast, we find a normal mode motion that separates domains I and II of RTA at the interface that is more common in the holo-protein. We hypothesized that the flexibility of the entrance of RTA can facilitate the entry of rRNA and allow the substrate to adjust its conformation and orientation prior to depurination. This process suggests an rRNA binding pathway which is supplemental the current RTA depurination mechanism.
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Affiliation(s)
- Hailiang Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 100 Hilltop Circle, Baltimore, MD 21250, USA
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