1
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Penkov NV. Peculiarities of the Dynamical Hydration Shell of Native Conformation Protein Using a Bovine Serum Albumin Example. APPLIED SPECTROSCOPY 2024:37028241261097. [PMID: 38881287 DOI: 10.1177/00037028241261097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
This paper describes an approach based on the method of terahertz time-domain spectroscopy, which allows the analysis of dynamical hydration shells of proteins with a thickness of 1-2 nm. Using the example of bovine serum albumin in three conformations, it is shown that the hydration shells of the protein are characterized by increased binding of water molecules in the primary hydration layers, and in more distant areas of hydration, on the contrary, the water structure is somewhat destroyed. The fraction of free or weakly bound molecules, usually observed in the structure of liquid water in hydration shells, become more numerous but its average binding is greater than in undisturbed water. The energy distribution of hydrogen bonds in hydration shells is narrowed compared to undisturbed water. All these manifestations of hydration are most pronounced for the native conformation of the protein. Also, the hydration shells of the native protein are characterized by a smaller number of hydrogen bonds and a tendency to decrease their average energy compared to non-native conformations. The fact of a pronounced peculiarity of the hydration shells of the protein in the native conformation has been noted for different proteins before. However, the methodological approach used in this work for the first time allowed this peculiarity to be described by specific parameters of the intermolecular structure and dynamics of water.
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Affiliation(s)
- Nikita V Penkov
- Institute of Cell Biophysics, Federal Research Center, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
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2
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Chakraborty S, Bhattacharya I, Mitra RK. Solvation Plays a Key Role in Antioxidant-Mediated Attenuation of Elevated Creatinine Level: An In Vitro Spectroscopic Investigation. J Phys Chem B 2023; 127:8576-8585. [PMID: 37769128 DOI: 10.1021/acs.jpcb.3c05334] [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: 09/30/2023]
Abstract
An elevated level of creatinine (CRN) is a mark of kidney ailment, and prolonged retention of such condition could lead to renal failure, associated with severe ischemia. Antioxidants are clinically known to excrete CRN from the body through urine, thereby reducing its level in blood. The molecular mechanism of such an exclusion process is still illusive. As the excretion channel is urine, solvation of the solute is expected to play a pivotal role. Here, we report a detailed time-domain and frequency-domain terahertz (THz) spectroscopic investigation to understand the solvation of CRN in the presence of two model antioxidants, mostly used to treat elevated CRN level: N-Acetyl-l-cysteine (NAC) and ascorbic acid (ASC). FTIR spectroscopy in the mid-infrared region and UV absorption spectroscopy measurements coupled with quantum chemical calculations [at the B3LYP/6-311G++(d,p) level] reveal that both NAC and ASC form HBonded complexes with CRN and rapidly undergo a barrier-less proton transfer process to form creatinium ions. THz measurements provide explicit evidence of the formation of highly solvated complexes compared with bare CRN, which eventually enables its excretion through urine. These observations could provide a foundation for designing more beneficial drugs to resolve kidney diseases..
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Affiliation(s)
- Subhadip Chakraborty
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences; Block-JD; Sector-III; Salt Lake, Kolkata 700106, India
| | - Indrani Bhattacharya
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences; Block-JD; Sector-III; Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences; Block-JD; Sector-III; Salt Lake, Kolkata 700106, India
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3
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Penkov NV. Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules. Biophys Rev 2023; 15:833-849. [PMID: 37974994 PMCID: PMC10643733 DOI: 10.1007/s12551-023-01131-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.
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Affiliation(s)
- Nikita V. Penkov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics RAS, 142290 Pushchino, Russia
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4
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Negi I, Jangra R, Gharu A, Trant JF, Sharma P. Guanidinium–amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation. Phys Chem Chem Phys 2023; 25:857-869. [DOI: 10.1039/d2cp04943k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structural analysis of guanidinium–amino acid interaction pairs in protein crystal structures is coupled with an effective scheme for classifying the optimized pairs, to gain understanding of the guanidinium:protein hydrogen bonding modes.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Raman Jangra
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Amit Gharu
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - John F. Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave. Windsor ON, N9B 3P4, Canada
- Binary Star Research Services, LaSalle, ON, N9J 3 X 8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave. Windsor ON, N9B 3P4, Canada
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5
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Pyne S, Pyne P, Kumar Mitra R. The inner hydration in surfactant/cholesterol vesicles differs from the outer one: a spectroscopic investigation. Chemphyschem 2022; 23:e202200337. [PMID: 35775165 DOI: 10.1002/cphc.202200337] [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] [Received: 05/20/2022] [Revised: 06/21/2022] [Indexed: 11/07/2022]
Abstract
Vesicles contain two aqueous regions: inner core and outer-to-bulk . It has remained an open question whether hydration behaviour in the inner core differs from the outer-to-bulk region, mostly owning to the inability of the conventional spectroscopic techniques to deconvolute the contribution from these two regions. We, using THz-FTIR spectroscopy (1.5-13.5 THz) experimentally probe the inner hydration of three differently charged surfactant/cholesterol vesicles composed of SDS, CTAB and Brij 30. Both dynamic light scattering (DLS) and atomic force microscopy (AFM) measurements affirm the transition from micelles to vesicles as cholesterol is added into surfactant solutions. FTIR measurements show that hydration behaviour changes significantly as micelles are converted into vesicles, the change been exclusively caused due to the formation of an inner core . Our measurements on the hydrogen bond stretch and librational motion of the inner hydration show distinct features compared to the overall hydration, which in turn is found to be surfactant type and cholesterol concentration dependent.
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Affiliation(s)
- Sumana Pyne
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Partha Pyne
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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Das N, Yadav S, Negi KS, Tariff E, Sen P. Microsecond Active-Site Dynamics Primarily control Proteolytic Activity of Bromelain: A Single Molecular Level Study with a Denaturant, a Stabilizer and a Macromolecular Crowder. BBA ADVANCES 2022; 2:100041. [PMID: 37082607 PMCID: PMC10074955 DOI: 10.1016/j.bbadva.2022.100041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022] Open
Abstract
Proteins are dynamic entity with various molecular motions at different timescale and length scale. Molecular motions are crucial for the optimal function of an enzyme. It seems intuitive that these motions are crucial for optimal enzyme activity. However, it is not easy to directly correlate an enzyme's dynamics and activity due to biosystems' enormous complexity. amongst many factors, structure and dynamics are two prime aspects that combinedly control the activity. Therefore, having a direct correlation between protein dynamics and activity is not straightforward. Herein, we observed and correlated the structural, functional, and dynamical responses of an industrially crucial proteolytic enzyme, bromelain with three versatile classes of chemicals: GnHCl (protein denaturant), sucrose (protein stabilizer), and Ficoll-70 (macromolecular crowder). The only free cysteine (Cys-25 at the active-site) of bromelain has been tagged with a cysteine-specific dye to unveil the structural and dynamical changes through various spectroscopic studies both at bulk and at the single molecular level. Proteolytic activity is carried out using casein as the substrate. GnHCl and sucrose shows remarkable structure-dynamics-activity relationships. Interestingly, with Ficoll-70, structure and activity are not correlated. However, microsecond dynamics and activity are beautifully correlated in this case also. Overall, our result demonstrates that bromelain dynamics in the microsecond timescale around the active-site is probably a key factor in controlling its proteolytic activity.
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Lai Z, Bai S, Li A, Feng X, He Q. Trimacrocyclic hexasubstituted benzenes for recognition of guanidinium and their anti-cancer and antimicrobial activities. Org Chem Front 2022. [DOI: 10.1039/d2qo00619g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report the facile synthesis of two trimacrocyclic hexasubstituted benzenes for selective guanidinium recognition and extraction, along with their anti-cancer and antimicrobial activities.
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Affiliation(s)
- Zhenzhen Lai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Silei Bai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Aimin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xinxin Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qing He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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8
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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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9
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Chen J, Dai Y, Gong X, Zhang G. Cation-amino acid interactions: Implications for protein destabilization. Biochem Biophys Res Commun 2021; 548:47-52. [PMID: 33631673 DOI: 10.1016/j.bbrc.2021.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/04/2021] [Indexed: 11/28/2022]
Abstract
The mechanism for protein stabilization or destabilization has long been an open quest. In the present study, we have studied the interactions between amino acids and guanidinium (Gdm+)/ammonium (NH4+) ions by using low field nuclear magnetic resonance (LF-NMR), where Gdm+ and NH4+ are denaturant and stabilizer for proteins, respectively. It shows that Gdm+ favors to bind to the thiol group or the hydroxyl group on the side chain but weakly interacts with the α-carboxyl group. In contrast, NH4+ prefers to bind to the α-carboxyl group but slightly interacts with the thiol group or the hydroxyl group on the side chain of amino acids. 1HNMR reveals the hydrogen bonding between NH4+ and the α-carboxyl group, which is not involved in the interactions between Gdm+ and cysteine. Our study demonstrates that the strong interactions between the denaturant and the sulfur atom or the disulfide bond promote the direct binding of the denaturant toward proteins, leading to the destabilization.
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Affiliation(s)
- Jiantao Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Yingkang Dai
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Xiangjun Gong
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China; Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, PR China.
| | - Guangzhao Zhang
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
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10
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Moritsugu N, Nara T, Koda SI, Tominaga K, Saito S. Molecular Mechanism of Acceleration and Retardation of Collective Orientation Relaxation of Water Molecules in Aqueous Solutions. J Phys Chem B 2020; 124:11730-11737. [PMID: 33320675 DOI: 10.1021/acs.jpcb.0c10036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The collective orientation relaxation (COR) of water molecules in aqueous solutions is faster or slower with an increase in the concentration of the solutions than that in pure water; for example, acceleration (deceleration) of the COR is observed in a solution of sodium chloride (tetramethylammonium chloride) with increasing concentration. However, the molecular mechanism of the solution and concentration dependence of the relaxation time of the COR has not yet been clarified. We theoretically investigate the concentration dependence of the COR of water molecules in solutions of tetramethylammonium chloride (TMACl), guanidinium chloride (GdmCl), and sodium chloride (NaCl). Based on the Mori-Zwanzig equation, we identify two opposing factors that determine the COR of water molecules in any aqueous solution: the correlation of dipole moments and the single-molecule orientation relaxation. We reveal the molecular mechanism of the concentration dependence of the relaxation time of the COR in the TMACl, GdmCl, and NaCl solutions in terms of these two factors.
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Affiliation(s)
- Norifumi Moritsugu
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takafumi Nara
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Shin-Ichi Koda
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan.,Molecular Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Shinji Saito
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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11
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Cao C, Serita K, Kitagishi K, Murakami H, Zhang ZH, Tonouchi M. Terahertz Spectroscopy Tracks Proteolysis by a Joint Analysis of Absorptance and Debye Model. Biophys J 2020; 119:2469-2482. [PMID: 33189688 DOI: 10.1016/j.bpj.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/26/2020] [Accepted: 11/05/2020] [Indexed: 01/06/2023] Open
Abstract
Terahertz waves have attracted great attention in biomolecule research because of the fact that they cover the range of energy levels of weak interactions, skeleton vibrations, and dipole rotations during inter- and intramolecular interactions in biomacromolecules. In this study, we validated the feasibility of employing terahertz time-domain spectroscopy (THz-TDS) for the nondestructive and label-free monitoring of protein digestion. The acid protease, pepsin, was used at its optimal pH to hydrolyze bovine serum albumin. Correspondingly, the control group experiment was also conducted by adjusting the pH value to inactivate pepsin. The progress of these two experiments was tracked by a compact commercial THz-TDS for 1 h. On one hand, the reaction-time-dependent absorption coefficient was calculated, and a direct absorption coefficient analysis was completed. The results indicate that protein hydrolysis can be easily monitored over time by focusing on the variation tendency of the absorption coefficient from a macroscopic perspective. On the other hand, we explored the use of the Debye model to analyze the dielectric properties of the solution during protein hydrolysis. The results of the Debye analysis prove that it is possible to investigate in detail the microscopic dynamics of biomacromolecule solutions at the molecular level by THz-TDS. Our research examined the process of protein hydrolysis by a combination of absorption spectra and Debye analysis and demonstrated that terahertz spectroscopy is a powerful technology for the investigation of biomolecular reactions, with potential applications in variety of fields.
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Affiliation(s)
- Can Cao
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China; Institute of Laser Engineering, Osaka University, Suita, Osaka, Japan
| | - Kazunori Serita
- Institute of Laser Engineering, Osaka University, Suita, Osaka, Japan
| | - Keiko Kitagishi
- Institute of Laser Engineering, Osaka University, Suita, Osaka, Japan
| | - Hironaru Murakami
- Institute of Laser Engineering, Osaka University, Suita, Osaka, Japan
| | - Zhao-Hui Zhang
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China
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12
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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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13
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Das Mahanta D, Islam SI, Choudhury S, Das DK, Mitra RK, Barman A. Contrasting hydration dynamics in DME and DMSO aqueous solutions: A combined optical pump-probe and GHz-THz dielectric relaxation investigation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Naz F, Anis H, Hasan Z, Islam A, Khan LA. Exploration of Fungal Lipase as Direct Target of Eugenol through Spectroscopic Techniques. Protein Pept Lett 2019; 26:919-929. [PMID: 31057096 DOI: 10.2174/0929866526666190506113455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/13/2019] [Accepted: 04/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Fungal lipase dependent processes are important for their pathogenicity. Lipases can therefore be explored as direct target of promising herbal antifungals. OBJECTIVE We explored Aspergillus niger lipase as a direct target of eugenol through spectroscopic techniques and compare results with Bovine Serum Albumin and lysozyme to comment on selectivity of eugenol towards lipase. METHODS In vitro activity assays of lipase are used to determine concentration ranges. UV-Visible, Fluorescence and Circular dichroism spectroscopy were employed to determine binding constant, stoichiometric binding sites and structural changes in Lipase, BSA and lysozyme following incubation with varying concentrations of eugenol. RESULTS In activity assays 50% inhibition of lipase was obtained at 0.913 mmoles/litre eugenol. UV-vis spectroscopy shows formation of lipase-eugenol, Bovine Serum Albumin-eugenol and lysozyme-eugenol complex well below this concentration of eugenol. Eugenol binding caused blue shift with Bovine Serum Albumin and lysozyme suggestive of compaction, and red shift with lipase. Negative ellipticity decreased with lipase but increased with Bovine Serum Albumineugenol and lysozyme-eugenol complexes suggesting loss of helical structure for lipase and compaction for Bovine Serum Albumin and lysozyme. Binding of eugenol to lipase was strong (Ka= 4.7 x 106 M-1) as compared to Bovine Serum Albumin and lysozyme. The number of stoichiometric eugenol binding sites on lipase was found to be 2 as compared to 1.37 (Bovine Serum Albumin) and 0.32 (lysozyme). Docking results also suggest strong binding of eugenol with lipase followed by Bovine Serum Albumin and lysozyme. CONCLUSION Eugenol is found to be effective inhibitor and disruptor of secondary and tertiary structure of lipase, whereas its binding to Bovine Serum Albumin and lysozyme is found to be weak and less disruptive of structures suggesting selectivity of eugenol towards lipase.
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Affiliation(s)
- Farheen Naz
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Haider Anis
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ziaul Hasan
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Luqman A Khan
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India
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15
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Wei L, Yu L, Jiaoqi H, Guorong H, Yang Z, Weiling F. Application of terahertz spectroscopy in biomolecule detection. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.flm.2019.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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16
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Pal S, Samanta N, Das Mahanta D, Mitra RK, Chattopadhyay A. Effect of Phospholipid Headgroup Charge on the Structure and Dynamics of Water at the Membrane Interface: A Terahertz Spectroscopic Study. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b01633] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sreetama Pal
- Academy of Scientific and Innovative Research, India
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
| | - Nirnay Samanta
- S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Debasish Das Mahanta
- S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Rajib Kumar Mitra
- S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research, India
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17
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Das Mahanta D, Samanta N, Mitra RK. Decisive Role of Hydrophobicity on the Effect of Alkylammonium Chlorides on Protein Stability: A Terahertz Spectroscopic Finding. J Phys Chem B 2017; 121:7777-7785. [DOI: 10.1021/acs.jpcb.7b04088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debasish Das Mahanta
- Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block-JD, Sector-III, Salt Lake, Kolkata, 700106, India
| | - Nirnay Samanta
- Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block-JD, Sector-III, Salt Lake, Kolkata, 700106, India
| | - Rajib Kumar Mitra
- Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block-JD, Sector-III, Salt Lake, Kolkata, 700106, India
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18
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Neeraj K, Choudhury S, Polley D, Acharya R, Sinha J, Barman A, Mitra RK. Efficient terahertz anti-reflection properties of metallic anti-dot structures. OPTICS LETTERS 2017; 42:1764-1767. [PMID: 28454155 DOI: 10.1364/ol.42.001764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report the use of micrometer-sized copper (Cu) anti-dot structures as a novel terahertz (THz) anti-reflection coating (ARC) material and their superior performance over conventionally used metallic (Cu) thin films. Cu anti-dot structures of two different thicknesses (7 and 10 nm) with varying anti-dot diameters (100, 200, and 300 μm, inter-anti-dot separation fixed at 100 μm) are deposited on silicon substrates by RF magnetron sputtering and e-beam evaporation. The anti-reflection performance of these samples is studied in the frequency range of 0.3-2.2 THz. While continuous metallic (Cu) thin film minimizes the Fabry-Perot (FP) peak, it also suppresses the primary transmission peak, reducing the advantage due to the former effect. On the contrary, the anti-dot arrays reduce both the absolute amplitude of the FP peak and the amplitude ratio (AR) of the FP peak to the primary peak, making them a superior material for ARC applications. The AR can be further manipulated by varying the anti-dot size. A universal conductivity phase-matching condition, which is a prerequisite for the disappearance of the FP peak, is observed in these samples. The enhanced anti-reflection performance promotes these anti-dot structures as an efficient terahertz ARC material.
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Samanta N, Das Mahanta D, Choudhury S, Barman A, Kumar Mitra R. Collective hydration dynamics in some amino acid solutions: A combined GHz-THz spectroscopic study. J Chem Phys 2017; 146:125101. [DOI: 10.1063/1.4978900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nirnay Samanta
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Debasish Das Mahanta
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Samiran Choudhury
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Anjan Barman
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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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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Li M, Chang T, Wei D, Tang M, Yan S, Du C, Cui HL. Label-free detection of anti-estrogen receptor alpha and its binding with estrogen receptor peptide alpha by terahertz spectroscopy. RSC Adv 2017. [DOI: 10.1039/c6ra28754a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Terahertz (THz) spectroscopic techniques were employed to study the hydration shell formation around anti-estrogen receptor alpha (AER-α) and to detect the binding reaction between AER-α and estrogen receptor peptide alpha (ERP-α).
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Affiliation(s)
- Mingliang Li
- College of Instrumentation & Electrical Engineering
- Jilin University
- Changchun
- China
| | - Tianying Chang
- College of Instrumentation & Electrical Engineering
- Jilin University
- Changchun
- China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
| | - Dongshan Wei
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Mingjie Tang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Shihan Yan
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Chunlei Du
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Hong-Liang Cui
- College of Instrumentation & Electrical Engineering
- Jilin University
- Changchun
- China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
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Das Mahanta D, Patra A, Samanta N, Luong TQ, Mukherjee B, Mitra RK. Non-monotonic dynamics of water in its binary mixture with 1,2-dimethoxy ethane: A combined THz spectroscopic and MD simulation study. J Chem Phys 2016; 145:164501. [DOI: 10.1063/1.4964857] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Debasish Das Mahanta
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Animesh Patra
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Nirnay Samanta
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Trung Quan Luong
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Biswaroop Mukherjee
- Thematic Unit for Excellence–Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
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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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Samanta N, Luong TQ, Das Mahanta D, Mitra RK, Havenith M. Effect of Short Chain Poly(ethylene glycol)s on the Hydration Structure and Dynamics around Human Serum Albumin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:831-837. [PMID: 26720549 DOI: 10.1021/acs.langmuir.5b03884] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report the changes in the hydration dynamics around a globular protein, human serum albumin (HSA), in the presence of two short chain crowding agents, namely poly(ethylene glycol)s (PEG 200 and 400). The change in the network water structure is investigated using FTIR spectroscopy in the far-infrared (FIR) frequency range. Site specific changes are obtained by time-resolved fluorescence spectroscopic technique using the intrinsic fluorophore tryptophan (Trp214) of HSA. The collective hydration dynamics of HSA in the presence of PEG molecules are obtained using terahertz (THz) time domain spectroscopy (TTDS) and high intensity p-Ge THz measurements. Our study affirms a considerable perturbation of HSA hydration beyond a critical concentration of PEG.
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Affiliation(s)
- Nirnay Samanta
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Trung Quan Luong
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Debasish Das Mahanta
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700098, India
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
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