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Wani MJ, Salman KA, Hashmi MA, Siddiqui S, Moin S. Rutin impedes human low-density lipoprotein from non-enzymatic glycation: A mechanistic insight against diabetes-related disorders. Int J Biol Macromol 2023; 238:124151. [PMID: 36963546 DOI: 10.1016/j.ijbiomac.2023.124151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
Glycation of human low-density protein (LDL) has an essential contribution to cardiovascular diseases. Natural compounds like rutin have been extensively studied in preventing glycation-induced oxidative stress. This study examined rutin's anti-glycation potential with glycated LDL utilizing spectroscopic and in silico methods. Glycated LDL treated with rutin, showed around 80 % inhibition in advanced glycation end-product production. Carbonyl content and lipid peroxidation like assays were used to establish the development of oxidative stress. Rutin was seen to lower the generation of oxidative stress in a dose-dependent manner. Using thioflavin t-test and electron microscopy, rutin was suggested to restore the structural disturbances in glycated LDL. Moreover, CD spectroscopy suggested reinstation of secondary structure of glycated LDL treated with rutin. Mechanistic insights between rutin and LDL were observed through spectroscopic measures. Molecular docking study confirmed the LDL-rutin binding with a binding energy of -10.0 kcal/mol. The rutin-LDL complex was revealed to be highly stable by molecular dynamics simulation, with RMSD, RMSF, Rg, SASA, and the secondary structure of LDL remaining essentially unchanged during the simulation period. Our study suggests that rutin possesses strong anti-glycating properties, which can be useful in therapeutics, as glycated LDL has an important role in atherosclerotic cardiovascular diseases.
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Affiliation(s)
- Mohd Junaid Wani
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India.
| | - Khushtar Anwar Salman
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Sana Siddiqui
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Shagufta Moin
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
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2
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Ahanger IA, Parray ZA, Raina N, Bashir S, Ahmad F, Hassan MI, Shahid M, Sharma A, Islam A. Counteraction of the cetyltrimethylammonium bromide-induced protein aggregation by Heparin: Potential impact on protein aggregation and neurodegenerative diseases using biophysical approaches. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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3
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Lincon A, Das S, DasGupta S. Capturing protein denaturation using electrical impedance technique. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Mondal S, Bobbili KB, Paul S, Swamy MJ. DSC and FCS Studies Reveal the Mechanism of Thermal and Chemical Unfolding of CIA17, a Polydisperse Oligomeric Protein from Coccinia Indica. J Phys Chem B 2021; 125:7117-7127. [PMID: 34167304 DOI: 10.1021/acs.jpcb.1c02120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of thermal and chemical unfolding of Coccinia indica agglutinin (CIA17), a chitooligosacharide-specific phloem exudate lectin, was investigated by biophysical approaches. DSC studies revealed that the unfolding thermogram of CIA17 consists of three components (Tm ∼ 98, 106, and 109 °C), which could be attributed to the dissociation of protein oligomers into constituent dimers, dissociation of the dimers into monomers, and unfolding of the monomers. Intrinsic fluorescence studies on the chemical denaturation by guanidinium thiocyanate and guanidinium chloride indicated the presence of two distinct steps in the unfolding pathway, which could be assigned to dissociation of the dimeric protein into monomers and unfolding of the monomers. Results of fluorescence correlation spectroscopic studies could be interpreted in terms of the following model: CIA17 forms oligomeric structures in a concentration dependent manner, with the protein existing as a monomer below 1 nM concentration but associating to form dimers at higher concentrations (KD ≈ 2.9 nM). The dimers associate to yield tetramers with a KD of ∼50 μM, which further associate to form higher oligomers with further increase in concentration. These results are consistent with the proposed role of CIA17 as a key player in the defense response of the plant against microbes and insects.
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Affiliation(s)
- Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
| | | | - Sumanta Paul
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
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5
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Yang L, Jang SJ. Theoretical investigation of non-Förster exciton transfer mechanisms in perylene diimide donor, phenylene bridge, and terrylene diimide acceptor systems. J Chem Phys 2020; 153:144305. [PMID: 33086841 DOI: 10.1063/5.0023709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rates of exciton transfer within dyads of perylene diimide and terrylene diimide connected by oligophenylene bridge units have been shown to deviate significantly from those of Förster's resonance energy transfer theory, according to single molecule spectroscopy experiments. The present work provides a detailed computational and theoretical study investigating the source of such a discrepancy. Electronic spectroscopy data are calculated by time-dependent density functional theory and then compared with experimental results. Electronic couplings between the exciton donor and the acceptor are estimated based on both the transition density cube method and transition dipole approximation. These results confirm that the delocalization of the exciton to the bridge parts contributes to significant enhancement of donor-acceptor electronic coupling. Mechanistic details of exciton transfer are examined by estimating the contributions of the bridge electronic states, vibrational modes of the dyads commonly coupled to both donor and acceptor, inelastic resonance energy transfer mechanism, and dark exciton states. These analyses suggest that the contribution of common vibrational modes serves as the main source of deviation from Förster's spectral overlap expression.
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Affiliation(s)
- Lei Yang
- Center for Molecular Systems and Organic Devices, Key Laboratory for Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, USA and PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, USA
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6
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Ghosh S, Sakshi, Swain BC, Chakraborty R, Tripathy U, Chattopadhyay K. A Novel Tool to Investigate the Early and Late Stages of α-Synuclein Aggregation. ACS Chem Neurosci 2020; 11:1610-1619. [PMID: 32407096 DOI: 10.1021/acschemneuro.0c00068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The accumulation of an inherently disordered protein α-synuclein (α-syn) aggregates in brain tissue play a pivotal role in the pathology and etiology of Parkinson's disease. Aggregation of α-syn has been found to be complex and heterogeneous, occurring through multitudes of early- and late-stage intermediates. Because of the inherent complexity and large dynamic range (between a few microseconds to several days under in vitro measurement conditions), it is difficult for the conventional biophysical and biochemical techniques to sample the entire time window of α-syn aggregation. Here, for the first time, we introduced the Z-scan technique as a novel tool to investigate different conformations formed in the early and late stage of temperature and mechanical stress-induced α-syn aggregation, in which different species showed its characteristic nonlinear characteristics. A power-dependent study was also performed to observe the changes in the protein nonlinearity. The perceived nonlinearity was accredited to the thermal-lensing effect. A switch in the sign of the refractive nonlinearity was observed for the first time as a signature of the late oligomeric conformation, a prime suspect that triggers cell death associated with neurodegeneration. We validate Z-scan results using a combination of different techniques, like thioflavin-T fluorescence assay, fluorescence correlation spectroscopy, Fourier-transform infrared spectroscopy, and atomic force microscopy. We believe that this simple, inexpensive, and sensitive method can have potential future applications in detecting/monitoring conformations in other essential peptides/proteins related to different neurodegenerative and other human diseases.
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Affiliation(s)
- Sumanta Ghosh
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sakshi
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, Jharkhand, India
| | - Bikash Chandra Swain
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, Jharkhand, India
| | - Ritobrita Chakraborty
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Umakanta Tripathy
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, Jharkhand, India
| | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
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7
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Basak S, Sengupta S, Chattopadhyay K. Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells. Biophys Rev 2019; 11:851-872. [PMID: 31444739 PMCID: PMC6957588 DOI: 10.1007/s12551-019-00580-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 01/24/2023] Open
Abstract
In order to maintain cellular function, biomolecules like protein, DNA, and RNAs have to diffuse to the target spaces within the cell. Changes in the cytosolic microenvironment or in the nucleus during the fulfillment of these cellular processes affect their mobility, folding, and stability thereby impacting the transient or stable interactions with their adjacent neighbors in the organized and dynamic cellular interior. Using classical Brownian motion to elucidate the diffusion behavior of these biomolecules is hard considering their complex nature. The understanding of biomolecular diffusion inside cells still remains elusive due to the lack of a proper model that can be extrapolated to these cases. In this review, we have comprehensively addressed the progresses in this field, laying emphasis on the different aspects of anomalous diffusion in the different biochemical reactions in cell interior. These experiment-based models help to explain the diffusion behavior of biomolecules in the cytosolic and nuclear microenvironment. Moreover, since understanding of biochemical reactions within living cellular system is our main focus, we coupled the experimental observations with the concept of sub-diffusion from in vitro to in vivo condition. We believe that the pairing between the understanding of complex behavior and structure-function paradigm of biological molecules would take us forward by one step in order to solve the puzzle around diseases caused by cellular dysfunction.
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Affiliation(s)
- Sujit Basak
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
| | - Sombuddha Sengupta
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
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8
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Dominguez-Medina S, Chen S, Blankenburg J, Swanglap P, Landes CF, Link S. Measuring the Hydrodynamic Size of Nanoparticles Using Fluctuation Correlation Spectroscopy. Annu Rev Phys Chem 2017; 67:489-514. [PMID: 27215820 DOI: 10.1146/annurev-physchem-040214-121510] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluctuation correlation spectroscopy (FCS) is a well-established analytical technique traditionally used to monitor molecular diffusion in dilute solutions, the dynamics of chemical reactions, and molecular processes inside living cells. In this review, we present the recent use of FCS for measuring the size of colloidal nanoparticles in solution. We review the theoretical basis and experimental implementation of this technique and its advantages and limitations. In particular, we show examples of the use of FCS to measure the size of gold nanoparticles, monitor the rotational dynamics of gold nanorods, and investigate the formation of protein coronas on nanoparticles.
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Affiliation(s)
| | - Sishan Chen
- Department of Chemistry, Rice University, Houston, Texas 77005;
| | - Jan Blankenburg
- Department of Chemistry, Rice University, Houston, Texas 77005;
| | | | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas 77005; .,Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005.,Laboratory for Nanophotonics, Rice University, Houston, Texas 77005.,Smalley-Curl Institute, Rice University, Houston, Texas 77005
| | - Stephan Link
- Department of Chemistry, Rice University, Houston, Texas 77005; .,Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005.,Laboratory for Nanophotonics, Rice University, Houston, Texas 77005.,Smalley-Curl Institute, Rice University, Houston, Texas 77005
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9
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Haque N, Baratam K, Prabhu NP. Analysing the microenvironment of 2-p-toluidinylnaphthalene-6-sulfonate (TNS) in solvents and in different conformational states of proteins in relation to its fluorescence properties: a computational study. Phys Chem Chem Phys 2017; 19:24656-24666. [PMID: 28857104 DOI: 10.1039/c7cp03951d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Characterization of different conformational states of proteins is essential to understand their stability and activity. Biophysical techniques aid in analysing these conformational states and molecular fluorescence is one of the most reliable and quickly accessible methods. Apart from the intrinsic fluorescence of proteins, external fluorescence dyes such as TNS, ANS, nile red and thioflavin are also used to characterize partially unfolded, aggregated and fibrillar states of proteins, though their exact molecular-level interactions with proteins are yet to be completely unravelled. The present study attempts to investigate the binding of TNS molecules on different conformational states of proteins. Unconstrained molecular dynamics simulation of 50 molecules of TNS with the native state of BSA, native and two partially unfolded states of RNase A and α-lactalbumin in water was carried out. Dynamics simulation of TNS alone in different solvents such as water, ethanol, DMF and DMSO was also performed. Binding environments in all the proteins and the solvents were analysed in terms of H-bonding interactions, order of contacts, amino acid specificity and conformational changes of TNS, and correlated with experimentally observed fluorescence changes of the dye. The results suggest that TNS forms aggregates in water whereas in non-aqueous solvents the order of aggregates is lower which might result in an enhancement of its fluorescence intensity. Further, TNS preferably interacts with basic and aromatic amino acid residues of the proteins. In RNase A and α-lactalbumin, most of the TNS molecules tend to form aggregates even with the unfolded conformations of the proteins. However in BSA, the number of aggregated TNS molecules is less and TNS molecules in monomeric form are found in the hydrophobic crevices of the protein. This might result in an enhancement of the fluorescence in BSA compared to the other proteins. The distributions of angles and dihedrals of TNS in different environments suggest that the bending movement between the naphthyl and tolyl rings is constrained whereas significant planar rotations could be observed both in solvents and in protein-bound states.
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Affiliation(s)
- Neshatul Haque
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad - 500046, India.
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10
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Pinheiro S, Curutchet C. Can Förster Theory Describe Stereoselective Energy Transfer Dynamics in a Protein-Ligand Complex? J Phys Chem B 2017; 121:2265-2278. [PMID: 28235382 DOI: 10.1021/acs.jpcb.7b00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R-6 distance-dependent Förster rate expression. However, such an interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects, and deviations from the ideal dipole approximation. Here, we investigate how Förster approximations impact the prediction of energy transfer dynamics in the complex between flurbiprofen (FBP) and human serum albumin (HSA), as well as a model FBP-Trp dyad, in which recent observation of enantioselective fluorescence quenching has been ascribed to energy transfer from FBP to Trp. To this end, we combine classical molecular dynamics simulations with polarizable quantum mechanics/molecular mechanics calculations that allow overcoming Förster approximations. On the basis of our results, we discuss the potential of structure-based simulations in the characterization of drug-binding events through fluorescence techniques. Overall, we find an excellent agreement between theory and experiment both in terms of enantioselectivity and FRET times, thus strongly supporting the reliability of the binding modes proposed for the (S) and (R) enantiomers of FBP. In particular, we show that the dynamic quenching arises from a small fraction of drug bound to the secondary site of HSA at the interface between subdomains IIA and IIB, whereas the enantioselectivity arises from the larger flexibility of the (S)-FBP enantiomer in the binding pocket.
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Affiliation(s)
- Silvana Pinheiro
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona , Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona , Av. Joan XXIII s/n, Barcelona 08028, Spain
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11
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Jozawa H, Kabir MG, Zako T, Maeda M, Chiba K, Kuroda Y. Amorphous protein aggregation monitored using fluorescence self-quenching. FEBS Lett 2016; 590:3501-3509. [DOI: 10.1002/1873-3468.12439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/31/2016] [Accepted: 09/18/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroki Jozawa
- Department of Biotechnology and Life Science; Graduate School of Engineering; Tokyo University of Agriculture and Technology; Koganei-shi Japan
| | - Md. Golam Kabir
- Department of Biotechnology and Life Science; Graduate School of Engineering; Tokyo University of Agriculture and Technology; Koganei-shi Japan
| | - Tamotsu Zako
- Bioengineering Laboratory; RIKEN Institute; Wako Japan
| | - Mizuo Maeda
- Bioengineering Laboratory; RIKEN Institute; Wako Japan
| | - Kazuhiro Chiba
- Laboratory of Bio-Organic Chemistry; Tokyo University of Agriculture and Technology; Fuchu Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science; Graduate School of Engineering; Tokyo University of Agriculture and Technology; Koganei-shi Japan
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12
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Sarkar-Banerjee S, Chowdhury S, Paul SS, Dutta D, Ghosh A, Chattopadhyay K. The Non-native Helical Intermediate State May Accumulate at Low pH in the Folding and Aggregation Landscape of the Intestinal Fatty Acid Binding Protein. Biochemistry 2016; 55:4457-68. [DOI: 10.1021/acs.biochem.6b00390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suparna Sarkar-Banerjee
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Sourav Chowdhury
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Simanta Sarani Paul
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Debashis Dutta
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Anisa Ghosh
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
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13
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García-Plazaola JI, Fernández-Marín B, Duke SO, Hernández A, López-Arbeloa F, Becerril JM. Autofluorescence: Biological functions and technical applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:136-45. [PMID: 26025527 DOI: 10.1016/j.plantsci.2015.03.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/13/2015] [Accepted: 03/14/2015] [Indexed: 05/08/2023]
Abstract
Chlorophylls are the most remarkable examples of fluorophores, and their fluorescence has been intensively studied as a non-invasive tool for assessment of photosynthesis. Many other fluorophores occur in plants, such as alkaloids, phenolic compounds and porphyrins. Fluorescence could be more than just a physicochemical curiosity in the plant kingdom, as several functional roles in biocommunication occur or have been proposed. Besides, fluorescence emitted by secondary metabolites can convert damaging blue and UV into wavelengths potentially useful for photosynthesis. Detection of the fluorescence of some secondary phytochemicals may be a cue for some pollinators and/or seed dispersal organisms. Independently of their functions, plant fluorophores provide researchers with a tool that allows the visualization of some metabolites in plants and cells, complementing and overcoming some of the limitations of the use of fluorescent proteins and dyes to probe plant physiology and biochemistry. Some fluorophores are influenced by environmental interactions, allowing fluorescence to be also used as a specific stress indicator.
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Affiliation(s)
| | - Beatriz Fernández-Marín
- Dpto Biología Vegetal y Ecología, Universidad del País Vasco (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; Institute of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Stephen O Duke
- Natural Products Utilization Research Unit, USDA, ARS, University of Mississippi, University, MS 38677, USA
| | - Antonio Hernández
- Dpto Biología Vegetal y Ecología, Universidad del País Vasco (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain
| | - Fernando López-Arbeloa
- Dpto Química Física, Universidad del País Vasco (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain
| | - José María Becerril
- Dpto Biología Vegetal y Ecología, Universidad del País Vasco (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain
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14
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Lyubchenko YL. Amyloid misfolding, aggregation, and the early onset of protein deposition diseases: insights from AFM experiments and computational analyses. AIMS MOLECULAR SCIENCE 2015; 2:190-210. [PMID: 27830177 PMCID: PMC5098429 DOI: 10.3934/molsci.2015.3.190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of Alzheimer's disease is believed to be caused by the assembly of amyloid β proteins into aggregates and the formation of extracellular senile plaques. Similar models suggest that structural misfolding and aggregation of proteins are associated with the early onset of diseases such as Parkinson's, Huntington's, and other protein deposition diseases. Initially, the aggregates were structurally characterized by traditional techniques such as x-ray crystallography, NMR, electron microscopy, and AFM. However, data regarding the structures formed during the early stages of the aggregation process were unknown. Experimental models of protein deposition diseases have demonstrated that the small oligomeric species have significant neurotoxicity. This highlights the urgent need to discover the properties of these species, to enable the development of efficient diagnostic and therapeutic strategies. The oligomers exist transiently, making it impossible to use traditional structural techniques to study their characteristics. The recent implementation of single-molecule imaging and probing techniques that are capable of probing transient states have enabled the properties of these oligomers to be characterized. Additionally, powerful computational techniques capable of structurally analyzing oligomers at the atomic level advanced our understanding of the amyloid aggregation problem. This review outlines the progress in AFM experimental studies and computational analyses with a primary focus on understanding the very first stage of the aggregation process. Experimental approaches can aid in the development of novel sensitive diagnostic and preventive strategies for protein deposition diseases, and several examples of these approaches will be discussed.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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15
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Haldar S, Sil P, Thangamuniyandi M, Chattopadhyay K. Conversion of amyloid fibrils of cytochrome c to mature nanorods through a honeycomb morphology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4213-23. [PMID: 25338286 DOI: 10.1021/la5029993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Amyloid species with various morphologies have been found for different proteins and disease systems. In this article, we aim to ask if these morphologies are unique to a particular protein or if they convert from one to another. Using a heme protein containing iron as the transition-metal activator of aggregation and a negatively charged surfactant, partial unfolding of the protein and its aggregation have been induced. In the pathway of aggregation, we have observed the formation of several morphological structures of a single protein, which were visualized directly using atomic force microscopy (AFM). These structures have been found to appear and disappear with time, and their formation could be monitored under normal buffer conditions and at room temperature without requiring any sophisticated chemical or biological methodologies. In addition, we have observed the formation of honeycomb-shaped morphology, which may serve as an intermediate. These amyloid-based nanostructures may have the potential to be explored in therapeutics delivery and other biomedical applications.
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Affiliation(s)
- Shubhasis Haldar
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Muruganandan Thangamuniyandi
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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16
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Ghosh S, Ghosh C, Nandi S, Bhattacharyya K. Unfolding and refolding of a protein by cholesterol and cyclodextrin: a single molecule study. Phys Chem Chem Phys 2015; 17:8017-27. [DOI: 10.1039/c5cp00385g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cholesterol induced unfolding of a globular protein, human serum albumin (HSA), and β-cyclodextrin induced refolding of the unfolded protein is demonstrated in this study.
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Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Catherine Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Somen Nandi
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
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17
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Ghisaidoobe ABT, Chung SJ. Intrinsic tryptophan fluorescence in the detection and analysis of proteins: a focus on Förster resonance energy transfer techniques. Int J Mol Sci 2014; 15:22518-38. [PMID: 25490136 PMCID: PMC4284722 DOI: 10.3390/ijms151222518] [Citation(s) in RCA: 510] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/08/2014] [Accepted: 11/18/2014] [Indexed: 12/18/2022] Open
Abstract
Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λ EX ≈ 280 nm, λ EM ≈ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the proteinlocal environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.
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Affiliation(s)
| | - Sang J Chung
- Department of Chemistry, Dongguk University, Seoul 100-715, Korea.
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18
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Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
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