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Quantitative Measurements of DP in Cellulose Paper Based on Terahertz Spectroscopy. Polymers (Basel) 2023; 15:polym15010247. [PMID: 36616596 PMCID: PMC9823725 DOI: 10.3390/polym15010247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
The power transformer is vital to the reliability of the power grid which is most commonly insulated with Kraft paper and immersed in mineral oil, among which the aged state of the paper is mainly correlated to the operating life of the transformer. Degree of polymerization (DP) is a direct parameter to assess the aged condition of insulating paper, but existing DP measurement by viscosity methods are destructive and complicated. In this paper, terahertz time-domain spectroscopy (THz-TDS) was introduced to reach rapid, non-destructive detection of the DP of insulating paper. The absorption spectra of insulating paper show that characteristic peak regions at 1.8 and 2.23 THz both exhibit a log-linear quantitative relationship with DP, and their universalities are confirmed by conducting the above relationship on different types of insulating paper. Fourier transform infrared spectroscopy (FTIR) analysis and molecular dynamics modeling further revealed that 1.8 and 2.23 THz were favorably associated with the growth of water-cellulose hydrogen bond strength and amorphous cellulose, respectively. This paper demonstrates the viability of applying THz-TDS to the non-destructive detection of DP in insulating paper and assigned the vibration modes of the characteristic absorption peaks.
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2
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Kyaw KS, Adegoke SC, Ajani CK, Nwabor OF, Onyeaka H. Toward in-process technology-aided automation for enhanced microbial food safety and quality assurance in milk and beverages processing. Crit Rev Food Sci Nutr 2022; 64:1715-1735. [PMID: 36066463 DOI: 10.1080/10408398.2022.2118660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ensuring the safety of food products is critical to food production and processing. In food processing and production, several standard guidelines are implemented to achieve acceptable food quality and safety. This notwithstanding, due to human limitations, processed foods are often contaminated either with microorganisms, microbial byproducts, or chemical agents, resulting in the compromise of product quality with far-reaching consequences including foodborne diseases, food intoxication, and food recall. Transitioning from manual food processing to automation-aided food processing (smart food processing) which is guided by artificial intelligence will guarantee the safety and quality of food. However, this will require huge investments in terms of resources, technologies, and expertise. This study reviews the potential of artificial intelligence in food processing. In addition, it presents the technologies and methods with potential applications in implementing automated technology-aided processing. A conceptual design for an automated food processing line comprised of various operational layers and processes targeted at enhancing the microbial safety and quality assurance of liquid foods such as milk and beverages is elaborated.
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Affiliation(s)
- Khin Sandar Kyaw
- Department of International Business Management, Didyasarin International College, Hatyai University, Songkhla, Thailand
| | - Samuel Chetachukwu Adegoke
- Joint School of Nanoscience and Nanoengineering, Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Clement Kehinde Ajani
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Ozioma Forstinus Nwabor
- Infectious Disease Unit, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia and Natural Product Research Center of Excellence, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, United Kingdom
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3
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Pyne P, Das Mahanta D, Gohil H, Prabhu SS, Mitra RK. Correlating solvation with conformational pathways of proteins in alcohol-water mixtures: a THz spectroscopic insight. Phys Chem Chem Phys 2021; 23:17536-17544. [PMID: 34369530 DOI: 10.1039/d1cp01841h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water, being an active participant in most of the biophysical processes, is important to trace how protein solvation changes as its conformation evolves in the presence of solutes or co-solvents. In this study, we investigate how the secondary structures of two diverse proteins - lysozyme and β-lactoglobulin - change in the aqueous mixtures of two alcohols - ethanol and 2,2,2-trifluoroethanol (TFE) using circular dichroism measurements. We observe that these alcohols change the secondary structures of these proteins and the changes are protein-specific. Subsequently, we measure the collective solvation dynamics of these two proteins both in the absence and in the presence of alcohols by measuring the frequency-dependent absorption coefficient (α(ν)) in the THz (0.1-1.2 THz) frequency domain. The alcohol-water mixtures exhibit a non-ideal behaviour with the highest absorption difference (Δα) obtained at Xalcohol = 0.2. The protein solvation in the presence of the alcohols shows an oscillating behaviour in which Δαprotein changes with Xalcohol. Such an oscillatory behaviour of protein solvation results from a delicate interplay between the protein-water, protein-alcohol and water-alcohol associations. We attempt to correlate the various structural conformations of the proteins with the associated solvation.
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Affiliation(s)
- Partha Pyne
- Department of Chemical, Biological & Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD; Sector-III; Salt Lake, Kolkata-700106, India.
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4
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Tenenbaum A. Kinetic coherence underlies the dynamics of disordered proteins. RSC Adv 2021; 11:36242-36249. [PMID: 35492753 PMCID: PMC9043365 DOI: 10.1039/d1ra06823g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/29/2021] [Indexed: 11/21/2022] Open
Abstract
The dynamics of two proteins of similar size, the globular lysozyme and the intrinsically disordered Huntingtin interacting protein, has been simulated in three states resembling a globule, a pre-molten globule, and a molten globule. A coherence time τ has been defined, measuring the delay in the display of a stochastic behaviour after a perturbation of the system. This time has been computed for two sets of collective variables: the projection of the phase point onto the positions and momenta subspaces (τr and τp), and the principal components (PCs) of positions q and momenta π produced by a covariance analysis in these subspaces (τq and τπ). In all states τp ≈ 3.5τr, and τπ ≈ 3.5τq. The coherence times of individual PCs, τ(l)q and τ(l)π, have also been computed, and τ(l)π > τ(l)q in all states. The prevalence of τp over τr, or of τπ over τq, drives the dynamics of the protein over a time range of ≈1–2 ps; moreover, a hidden synchronism appears to raise the momenta subspace's coherence above that of its individual PCs. In the transition of lysozyme to the molten globule the τ(l)q decrease but, unexpectedly, the τ(l)π increase; after this transition τp ≈ 5τr and τπ ≈ 5τq. A gain of kinetic coherence accompanies thus the loss of structural coherence caused by the denaturation of the protein in the transition from globule to molten globule. The increase of the τ(l)π does not take place in the analogous transition of the Huntingtin protein. These results are compared with those of a similar analysis performed on three pseudo-proteins designed by scrambling the primary sequence of the Huntingtin interacting protein, and on two oligopeptides. The hidden synchronism appears to be a generic property of these polypeptides. The τ(l)π spectrum is similar in denaturated and in intrinsically disordered biomolecules; but the gain of kinetic coherence as a result of denaturation seems to be a specific property of the biologically functional lysozyme. In the phase space of a globular or intrinsically disordered protein, the momenta's dynamics is less chaotic than the coordinates' dynamics. When a protein is denaturated, a gain in kinetic coherence accompanies the loss of structural coherence.![]()
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Affiliation(s)
- Alexander Tenenbaum
- Physics Department, Sapienza University, Piazzale Aldo Moro 5, 00185 Roma, Italy
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5
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Adams EM, Lampret O, König B, Happe T, Havenith M. Solvent dynamics play a decisive role in the complex formation of biologically relevant redox proteins. Phys Chem Chem Phys 2020; 22:7451-7459. [PMID: 32215444 DOI: 10.1039/d0cp00267d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer processes between proteins are vital in many biological systems. Yet, the role of the solvent in influencing these redox reactions remains largely unknown. In this study, terahertz-time domain spectroscopy (THz-TDS) is used to probe the collective hydration dynamics of flavoenzyme ferredoxin-NADP+-reductase (FNR), electron transfer protein ferredoxin-1 (PetF), and the transient complex that results from their interaction. Results reveal changes in the sub-picosecond hydration dynamics that are dependent upon the surface electrostatic properties of the individual proteins and the transient complex. Retarded solvent dynamics of 8-9 ps are observed for FNR, PetF, and the FNR:PetF transient complex. Binding of the FNR:PetF complex to the substrate NADP+ results in bulk-like solvent dynamics of 7 ps, showing that formation of the ternary complex is entropically favored. Our THz measurements reveal that the electrostatic interaction of the protein surface with water results in charge sensitive changes in the solvent dynamics. Complex formation between the positively charged FNR:NADP+ pre-complex and the negatively charged PetF is not only entropically favored, but in addition the solvent reorganization into more bulk-like water assists the molecular recognition process. The change in hydration dynamics observed here suggests that the interaction with the solvent plays a significant role in mediating electron transfer processes between proteins.
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Affiliation(s)
- Ellen M Adams
- Lehrstuhl für Physkalische Chemie II, Ruhr Universität Bochum, 44801 Bochum, Germany.
| | - Oliver Lampret
- AG Photobiotechnologie, Ruhr Universität Bochum, 44801 Bochum, Germany
| | - Benedikt König
- Lehrstuhl für Physkalische Chemie II, Ruhr Universität Bochum, 44801 Bochum, Germany.
| | - Thomas Happe
- AG Photobiotechnologie, Ruhr Universität Bochum, 44801 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physkalische Chemie II, Ruhr Universität Bochum, 44801 Bochum, Germany.
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6
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A Nondestructive Eggshell Thickness Measurement Technique Using Terahertz Waves. Sci Rep 2020; 10:1052. [PMID: 31974471 PMCID: PMC6978418 DOI: 10.1038/s41598-020-57774-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/02/2020] [Indexed: 12/03/2022] Open
Abstract
Eggshells play a number of important roles in the avian and reptile kingdom: protection of internal contents and as a major source of minerals for developing embryos. However, when researching these respective roles, eggshell thickness measurement remains a bottleneck due to the lack of a non-destructive measurement techniques. As a result, many avian and reptile research protocols omit consideration of eggshell thickness bias on egg or embryo growth and development. Here, we validate a non-destructive method to estimate eggshell thickness based on terahertz (THz) reflectance spectroscopy using chicken white coloured eggs. Since terahertz waves are reflected from outer air-eggshell interface, as well as the inner eggshell-membrane boundary, the resulting interference signals depend on eggshell thickness. Thus, it is possible to estimate shell thickness from the oscillation distance in frequency-domain. A linear regression-based prediction model for non-destructive eggshell thickness measurement was developed, which had a coefficient of determination (R2) of 0.93, RMSEP of 0.009, RPD of 3.45 and RER 13.67. This model can estimate eggshell thickness to a resolution of less than 10 μm. This method has the potential to expand the protocols in the field of avian and reptile research, as well as be applied to industrial grading of eggs.
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7
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Xu L, Li Y, Zhou Q, Deng X. A comparative study of the low-frequency vibrations of l-histidine molecule in different solid states. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117468. [PMID: 31425861 DOI: 10.1016/j.saa.2019.117468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/04/2019] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
Low-frequency vibrations of l-histidine in a neat solid state and its monohydrochloride monohydrate are both investigated using THz spectroscopy and DFT calculations. The molecular motions in those modes are further quantitatively decomposed into a number of submotions and discussed in terms of their contributions to a mode. The results show significant differences in the averaged contribution percentage of intermolecular motions and the dihedral angle distortions of the imidazole ring between these two crystals. Those phenomena are interpreted from the viewpoint of their hydrogen-bond configurations.
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Affiliation(s)
- Li Xu
- Department of Chemical Engineering and Technology, School of Chemistry, Biology and Materials of Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Yin Li
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
| | - Qi Zhou
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Xiaohua Deng
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China; Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
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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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Afsah-Hejri L, Hajeb P, Ara P, Ehsani RJ. A Comprehensive Review on Food Applications of Terahertz Spectroscopy and Imaging. Compr Rev Food Sci Food Saf 2019; 18:1563-1621. [PMID: 33336912 DOI: 10.1111/1541-4337.12490] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/11/2022]
Abstract
Food product safety is a public health concern. Most of the food safety analytical and detection methods are expensive, labor intensive, and time consuming. A safe, rapid, reliable, and nondestructive detection method is needed to assure consumers that food products are safe to consume. Terahertz (THz) radiation, which has properties of both microwave and infrared, can penetrate and interact with many commonly used materials. Owing to the technological developments in sources and detectors, THz spectroscopic imaging has transitioned from a laboratory-scale technique into a versatile imaging tool with many practical applications. In recent years, THz imaging has been shown to have great potential as an emerging nondestructive tool for food inspection. THz spectroscopy provides qualitative and quantitative information about food samples. The main applications of THz in food industries include detection of moisture, foreign bodies, inspection, and quality control. Other applications of THz technology in the food industry include detection of harmful compounds, antibiotics, and microorganisms. THz spectroscopy is a great tool for characterization of carbohydrates, amino acids, fatty acids, and vitamins. Despite its potential applications, THz technology has some limitations, such as limited penetration, scattering effect, limited sensitivity, and low limit of detection. THz technology is still expensive, and there is no available THz database library for food compounds. The scanning speed needs to be improved in the future generations of THz systems. Although many technological aspects need to be improved, THz technology has already been established in the food industry as a powerful tool with great detection and quantification ability. This paper reviews various applications of THz spectroscopy and imaging in the food industry.
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Affiliation(s)
- Leili Afsah-Hejri
- Mechanical Engineering Dept., School of Engineering, Univ. of California, Merced, 5200 N. Lake Rd., Merced, CA, 95343
| | - Parvaneh Hajeb
- Dept. of Environmental Science, Aarhus Univ., Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Parsa Ara
- College of Letters and Sciences, Univ. of California, Santa Barbara, Santa Barbara, CA, 93106
| | - Reza J Ehsani
- Mechanical Engineering Dept., School of Engineering, Univ. of California, Merced, 5200 N. Lake Rd., Merced, CA, 95343
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10
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State-of-the-art in terahertz sensing for food and water security – A comprehensive review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.01.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Mohanta D, Jana M. Effects of ethanol on the secondary structure specific hydration properties of Chymotrypsin Inhibitor 2 in its folded and unfolded forms. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1496246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dayanidhi Mohanta
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
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12
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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13
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Relative Contributions of Core Protein and Solvation Shell in the Terahertz Dielectric Properties of Protein Solutions. J Phys Chem B 2017; 121:9508-9512. [DOI: 10.1021/acs.jpcb.7b06442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Carpinteri A, Lacidogna G, Piana G, Bassani A. Terahertz mechanical vibrations in lysozyme: Raman spectroscopy vs modal analysis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Novelli F, Ostovar Pour S, Tollerud J, Roozbeh A, Appadoo DRT, Blanch EW, Davis JA. Time-Domain THz Spectroscopy Reveals Coupled Protein-Hydration Dielectric Response in Solutions of Native and Fibrils of Human Lysozyme. J Phys Chem B 2017; 121:4810-4816. [PMID: 28430436 DOI: 10.1021/acs.jpcb.7b02724] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the amplitude and phase of the oscillating dipole induced by the THz field in the volume containing the protein and its hydration water. At low concentrations, the amplitude of this induced dipolar response decreases with increasing concentration. Beyond a certain threshold, marking the onset of the interactions between the extended hydration shells, the amplitude remains fixed but the phase of the induced dipolar response, which is initially in phase with the applied THz field, begins to change. The changes observed in the THz response reveal protein-protein interactions mediated by extended hydration layers, which may control fibril formation and may have an important role in chemical recognition phenomena.
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Affiliation(s)
- Fabio Novelli
- Centre for Quantum and Optical Science, Swinburne University of Technology , Hawthorn, Victoria 3122, Australia
| | - Saeideh Ostovar Pour
- School of Science, RMIT University , GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Jonathan Tollerud
- Centre for Quantum and Optical Science, Swinburne University of Technology , Hawthorn, Victoria 3122, Australia
| | - Ashkan Roozbeh
- Centre for Quantum and Optical Science, Swinburne University of Technology , Hawthorn, Victoria 3122, Australia
| | | | - Ewan W Blanch
- School of Science, RMIT University , GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Jeffrey A Davis
- Centre for Quantum and Optical Science, Swinburne University of Technology , Hawthorn, Victoria 3122, Australia.,ARC Centre of Excellence for Future Low-Energy Electronics Technologies, Swinburne University of Technology , Hawthorn, Victoria 3122, Australia
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16
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Nonmonotonic Hydration Behavior of Bovine Serum Albumin in Alcohol/Water Binary Mixtures: A Terahertz Spectroscopic Investigation. Chemphyschem 2017; 18:749-754. [DOI: 10.1002/cphc.201601217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Indexed: 11/07/2022]
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17
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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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18
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George DK, Charkhesht A, Hull OA, Mishra A, Capelluto DGS, Mitchell-Koch KR, Vinh NQ. New Insights into the Dynamics of Zwitterionic Micelles and Their Hydration Waters by Gigahertz-to-Terahertz Dielectric Spectroscopy. J Phys Chem B 2016; 120:10757-10767. [DOI: 10.1021/acs.jpcb.6b06423] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deepu K. George
- Department
of Physics and Center of Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ali Charkhesht
- Department
of Physics and Center of Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Olivia A. Hull
- Department
of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Archana Mishra
- Department
of Chemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Daniel G. S. Capelluto
- Protein
Signaling Domains Laboratory, Department of Biological Sciences, Biocomplexity
Institute, and Center of Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Nguyen Q. Vinh
- Department
of Physics and Center of Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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19
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Preferential solvation of lysozyme in dimethyl sulfoxide/water binary mixture probed by terahertz spectroscopy. Biophys Chem 2016; 216:31-36. [DOI: 10.1016/j.bpc.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 11/21/2022]
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20
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Woods KN, Pfeffer J. Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes. Mol Biol Evol 2016; 33:40-61. [PMID: 26337549 PMCID: PMC4693973 DOI: 10.1093/molbev/msv178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein's function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function.
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21
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Aoki K, Shiraki K, Hattori T. Salt effects on the picosecond dynamics of lysozyme hydration water investigated by terahertz time-domain spectroscopy and an insight into the Hofmeister series for protein stability and solubility. Phys Chem Chem Phys 2016; 18:15060-9. [DOI: 10.1039/c5cp06324h] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of salts into protein aqueous solutions causes changes in protein solubility and stability, the ability of which is known to be ordered in the Hofmeister series.
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Affiliation(s)
- Katsuyoshi Aoki
- Institute of Applied Physics
- University of Tsukuba
- Tsukuba
- Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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22
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Acbas G, Niessen KA, Snell EH, Markelz AG. Optical measurements of long-range protein vibrations. Nat Commun 2015; 5:3076. [PMID: 24430203 DOI: 10.1038/ncomms4076] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 12/09/2013] [Indexed: 12/20/2022] Open
Abstract
Protein biological function depends on structural flexibility and change. From cellular communication through membrane ion channels to oxygen uptake and delivery by haemoglobin, structural changes are critical. It has been suggested that vibrations that extend through the protein play a crucial role in controlling these structural changes. While nature may utilize such long-range vibrations for optimization of biological processes, bench-top characterization of these extended structural motions for engineered biochemistry has been elusive. Here we show the first optical observation of long-range protein vibrational modes. This is achieved by orientation-sensitive terahertz near-field microscopy measurements of chicken egg white lysozyme single crystals. Underdamped modes are found to exist for frequencies >10 cm(-1). The existence of these persisting motions indicates that damping and intermode coupling are weaker than previously assumed. The methodology developed permits protein engineering based on dynamical network optimization.
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Affiliation(s)
- Gheorghe Acbas
- Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260, USA
| | - Katherine A Niessen
- Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260, USA
| | - Edward H Snell
- Department of Structural Biology, Hauptman-Woodward Medical Research Institute, University at Buffalo, SUNY, 700 Ellicott St., Buffalo, New York 14203, USA
| | - A G Markelz
- 1] Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260, USA [2] Department of Structural Biology, Hauptman-Woodward Medical Research Institute, University at Buffalo, SUNY, 700 Ellicott St., Buffalo, New York 14203, USA
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23
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Woods KN. Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity. SOFT MATTER 2014; 10:4387-4402. [PMID: 24801988 DOI: 10.1039/c3sm53229a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this investigation we use THz time-scale spectroscopy to conduct an initial set of studies on myoglobin with the aim of providing further insight into the global, collective thermal fluctuations in the protein that have been hypothesized to play a prominent role in the dynamic formation of transient ligand channels as well as in shaping the molecular level basis for ligand discrimination. Using the two ligands O2 and CO, we have determined that the perturbation from the heme-ligand complex has a strong influence on the characteristics of the myoglobin collective dynamics that are excited upon binding. Further, the differences detected in the collective protein motions in Mb-O2 compared with those in Mb-CO appear to be intimately tied with the pathways of long-range allosteric communication in the protein, which ultimately determine the trajectories selected by the respective ligands on the path to and from the heme-binding cavity.
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Affiliation(s)
- K N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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24
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Zhou L, Liu Q. Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics. J Phys Chem B 2014; 118:4069-79. [PMID: 24673391 PMCID: PMC4397101 DOI: 10.1021/jp4124327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The strength of X-ray crystallography in providing the information for protein dynamics has been under appreciated. The anisotropic B-factors (ADPs) from high-resolution structures are invaluable in studying the relationship among structure, dynamics, and function. Here, starting from an in-depth evaluation of the metrics used for comparing the overlap between two ellipsoids, we applied normal-mode analysis (NMA) to predict the theoretical ADPs and then align them with experimental results. Adding an extra layer of explicitly treated water on protein surface significantly improved the energy minimization results and better reproduced the anisotropy of experimental ADPs. In comparing experimental and theoretical ADPs, we focused on the overlap in shape, the alignment of dominant directions, and the similarity in magnitude. The choices of water molecules, NMA methods, and the metrics for evaluating the overlap of ADPs determined final results. This study provides useful information for exploring the physical basis and the application potential of experimental ADPs.
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Affiliation(s)
- Lei Zhou
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University , Richmond, Virginia 23298, United States
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25
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THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions. J Biol Phys 2014; 40:121-37. [PMID: 24682643 DOI: 10.1007/s10867-014-9341-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG)3. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG)3. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.
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26
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Zhang F, Kambara O, Tominaga K, Nishizawa JI, Sasaki T, Wang HW, Hayashi M. Analysis of vibrational spectra of solid-state adenine and adenosine in the terahertz region. RSC Adv 2014. [DOI: 10.1039/c3ra44285c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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27
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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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28
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Murakami H. Protein and water confined in nanometer-scale reverse micelles studied by near infrared, terahertz, and ultrafast visible spectroscopies. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:183-211. [PMID: 24018326 DOI: 10.1016/b978-0-12-416596-0.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Protein-containing reverse (PCR) micelles are suitable systems to study the properties of proteins and waters in a cell-like environment. A model for determining the structural parameters of PCR micelles, such as the aqueous cavity size and molecule number of water within the reverse micelle, is presented. The model is based on an important hypothesis that the structural parameters of the protein-unfilled reverse micelle do not change after solubilization of protein. I describe a procedure using near infrared spectroscopy of OH stretching vibration band of water to verify the hypothesis. Further, the terahertz (THz) absorption spectrum of myoglobin is derived from THz time-domain spectroscopy of the PCR micellar solution, and the states of waters in reverse micelles with and without protein are discussed on the basis of the structural parameters. The last topic is on internal dynamics of PCR micelles on timescales from femtoseconds to nanoseconds studied by femtosecond time-resolved fluorescence spectroscopy.
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Affiliation(s)
- Hiroshi Murakami
- Kansai Photon Science Institute, Japan Atomic Energy Agency, Kyoto, Japan.
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29
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Pal S, Bandyopadhyay S. Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:1162-1173. [PMID: 23289748 DOI: 10.1021/la303959m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein-water (PW) electrostatic interactions is compensated by enhanced water-water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.
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Affiliation(s)
- Somedatta Pal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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30
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Sinha SK, Bandyopadhyay S. Polar solvation dynamics of lysozyme from molecular dynamics studies. J Chem Phys 2012; 136:185102. [DOI: 10.1063/1.4712036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Laurette S, Treizebre A, Elagli A, Hatirnaz B, Froidevaux R, Affouard F, Duponchel L, Bocquet B. Highly sensitive terahertz spectroscopy in microsystem. RSC Adv 2012. [DOI: 10.1039/c2ra21320f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Panuszko A, Wojciechowski M, Bruździak P, Rakowska PW, Stangret J. Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation. Phys Chem Chem Phys 2012; 14:15765-73. [DOI: 10.1039/c2cp42229h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Sinha SK, Bandyopadhyay S. Local heterogeneous dynamics of water around lysozyme: a computer simulation study. Phys Chem Chem Phys 2012; 14:899-913. [DOI: 10.1039/c1cp22575h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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35
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Mazur K, Heisler IA, Meech SR. Water Dynamics at Protein Interfaces: Ultrafast Optical Kerr Effect Study. J Phys Chem A 2011; 116:2678-85. [DOI: 10.1021/jp2074539] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kamila Mazur
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Ismael A. Heisler
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
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36
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Vinh NQ, Allen SJ, Plaxco KW. Dielectric Spectroscopy of Proteins as a Quantitative Experimental Test of Computational Models of Their Low-Frequency Harmonic Motions. J Am Chem Soc 2011; 133:8942-7. [DOI: 10.1021/ja200566u] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Q. Vinh
- Institute for Terahertz Science and Technology, ‡Department of Physics, and §Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - S. James Allen
- Institute for Terahertz Science and Technology, ‡Department of Physics, and §Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W. Plaxco
- Institute for Terahertz Science and Technology, ‡Department of Physics, and §Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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37
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38
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Liu R, He M, Su R, Yu Y, Qi W, He Z. Insulin amyloid fibrillation studied by terahertz spectroscopy and other biophysical methods. Biochem Biophys Res Commun 2010; 391:862-7. [DOI: 10.1016/j.bbrc.2009.11.153] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 11/09/2009] [Indexed: 11/27/2022]
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39
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Dutta P, Tominaga K. Dependence of low frequency spectra on solute and solvent in solutions studied by terahertz time-domain spectroscopy. Mol Phys 2009. [DOI: 10.1080/00268970902744334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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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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41
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Born B, Kim SJ, Ebbinghaus S, Gruebele M, Havenith M. The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin. Faraday Discuss 2009; 141:161-73; discussion 175-207. [DOI: 10.1039/b804734k] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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42
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Sinha SK, Chakraborty S, Bandyopadhyay S. Thickness of the hydration layer of a protein from molecular dynamics simulation. J Phys Chem B 2008; 112:8203-9. [PMID: 18547099 DOI: 10.1021/jp8000724] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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43
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Castro-Camus E, Johnston M. Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.02.084] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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44
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Abstract
Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics.
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45
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Plusquellic DF, Siegrist K, Heilweil EJ, Esenturk O. Applications of terahertz spectroscopy in biosystems. Chemphyschem 2008; 8:2412-31. [PMID: 17990257 DOI: 10.1002/cphc.200700332] [Citation(s) in RCA: 230] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the binding force constants and anharmonic character of the force fields, properties necessary to improve predictability but not readily obtainable using any other method. These studies have provided benchmark vibrational data on extended periodic structures for direct comparisons with classical (CHARMm) and quantum chemical (density functional theory) theories. For the larger amorphous and/or aqueous phase samples, the THz modes form a continuum-like absorption that arises because of the full accessibility to conformational space and/or the rapid time scale for inter-conversion in these environments. Despite severe absorption by liquid water, detailed investigations have uncovered the photo- and hydration-induced conformational flexibility of proteins, the solvent shell depth of the water/biomolecule boundary layers and the solvent reorientation dynamics occurring in these interfacial layers that occur on sub-picosecond time scales. As such, THz spectroscopy has enhanced and extended the accessibility to intermolecular forces, length- and timescales important in biological structure and activity.
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Affiliation(s)
- David F Plusquellic
- Optical Technology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8443, USA.
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46
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Chakraborty S, Sinha SK, Bandyopadhyay S. Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study. J Phys Chem B 2007; 111:13626-31. [DOI: 10.1021/jp0746401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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47
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Vainshtein S, Kostamovaara J, Yuferev V, Knap W, Fatimy A, Diakonova N. Terahertz emission from collapsing field domains during switching of a gallium arsenide bipolar transistor. PHYSICAL REVIEW LETTERS 2007; 99:176601. [PMID: 17995354 DOI: 10.1103/physrevlett.99.176601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Indexed: 05/25/2023]
Abstract
Broadband pulsed THz emission with peak power in the sub-mW range has been observed experimentally during avalanche switching in a gallium arsenide bipolar junction transistor at room temperature, while significantly higher total generated power is predicted in simulations. The emission is attributed to very fast oscillations in the conductivity current across the switching channels, which appear as a result of temporal evolution of the field domains generated in highly dense electron-hole plasma. This plasma is formed in turn by powerful impact ionization in multiple field domains of ultrahigh amplitude.
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Affiliation(s)
- Sergey Vainshtein
- University of Oulu, Department of Electricity and Information Engineering, Electricity Laboratory, Oulu, FIN-90014, Finland
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48
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