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Ahmad M, Bushra R, Ritzoulis C. Pectin-mucin interactions: Insights from fluorimetry, thermodynamics and dual (static and dynamic) quenching mechanisms. Int J Biol Macromol 2024; 277:134564. [PMID: 39116979 DOI: 10.1016/j.ijbiomac.2024.134564] [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: 03/26/2024] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Binary systems of citrus peel pectin (a major food carbohydrate) and mucin (a principal oral-gastrointestinal glycoprotein) are studied, as to understand the interactions and thermodynamics between food and biofluids during oral processing and digestion. The fluorimetry emission spectra of mucin were quenched by pectin addition at 293, 301, 310 and 318 K, indicating direct contact between the two macromolecular populations. A red shift, suggesting pectin-induced alterations on mucin conformation, has been observed at 318 K. Intensity-based Stern - Volmer plots fitted second-order polynomial equations, suggesting the coexistence of both static and dynamic quenching, while the increase of the slopes with temperature points to the predominance of dynamic phenomena. Time-resolved fluorescence measurements also point to dynamic quenching related to transient interactions, rather than to specific bonding. Thermodynamic analysis yields negative free energy changes in all cases, with positive changes for enthalpy and large positive values for TΔS. These are in agreement with the Stern - Volmer analysis, suggesting the predominance of transient, dynamic (here entropic) interactions. These provide an image of mucin interacting with pectin macromolecules during the oral processing and digestion of foods, and can relate to the texture, flavor (e.g. astringency) and bioavailability of polysaccharide-based foods.
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Affiliation(s)
- Mehraj Ahmad
- Joint International Research Lab of Lignocellulosic Functional Materials and Provincial Key Lab of Pulp and Paper Sci. & Tech., Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Department of Food Science and Engineering, College of Light Industry and Food, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Rani Bushra
- Joint International Research Lab of Lignocellulosic Functional Materials and Provincial Key Lab of Pulp and Paper Sci. & Tech., Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Department of Food Science and Engineering, College of Light Industry and Food, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Christos Ritzoulis
- Department of Food Science and Technology, International Hellenic University, Alexander Campus, 57400 Thessaloniki, Greece.
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Khristin MS, Smolova TN, Khorobrykh AA. Dimerization of the Free and Photosystem II-Associated PsbO Protein upon Irradiation with UV Light. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922060100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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3
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Wujak M, Kozakiewicz A, Ciarkowska A, Loch JI, Barwiolek M, Sokolowska Z, Budny M, Wojtczak A. Assessing the Interactions of Statins with Human Adenylate Kinase Isoenzyme 1: Fluorescence and Enzyme Kinetic Studies. Int J Mol Sci 2021; 22:ijms22115541. [PMID: 34073952 PMCID: PMC8197361 DOI: 10.3390/ijms22115541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Statins are the most effective cholesterol-lowering drugs. They also exert many pleiotropic effects, including anti-cancer and cardio- and neuro-protective. Numerous nano-sized drug delivery systems were developed to enhance the therapeutic potential of statins. Studies on possible interactions between statins and human proteins could provide a deeper insight into the pleiotropic and adverse effects of these drugs. Adenylate kinase (AK) was found to regulate HDL endocytosis, cellular metabolism, cardiovascular function and neurodegeneration. In this work, we investigated interactions between human adenylate kinase isoenzyme 1 (hAK1) and atorvastatin (AVS), fluvastatin (FVS), pravastatin (PVS), rosuvastatin (RVS) and simvastatin (SVS) with fluorescence spectroscopy. The tested statins quenched the intrinsic fluorescence of hAK1 by creating stable hAK1-statin complexes with the binding constants of the order of 104 M−1. The enzyme kinetic studies revealed that statins inhibited hAK1 with significantly different efficiencies, in a noncompetitive manner. Simvastatin inhibited hAK1 with the highest yield comparable to that reported for diadenosine pentaphosphate, the only known hAK1 inhibitor. The determined AK sensitivity to statins differed markedly between short and long type AKs, suggesting an essential role of the LID domain in the AK inhibition. Our studies might open new horizons for the development of new modulators of short type AKs.
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Affiliation(s)
- Magdalena Wujak
- Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Jurasza 2, 85-089 Bydgoszcz, Poland;
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland;
| | - Anna Kozakiewicz
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (M.B.); (Z.S.); (A.W.)
- Correspondence: ; Tel.: +48-56-611-4511
| | - Anna Ciarkowska
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland;
| | - Joanna I. Loch
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland;
| | - Magdalena Barwiolek
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (M.B.); (Z.S.); (A.W.)
| | - Zuzanna Sokolowska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (M.B.); (Z.S.); (A.W.)
| | - Marcin Budny
- Synthex Technologies Sp. z o.o., Gagarina 7/134B, 87-100 Toruń, Poland;
| | - Andrzej Wojtczak
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (M.B.); (Z.S.); (A.W.)
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Huang X, Slavkovic S, Song E, Botta A, Mehrazma B, Lento C, Johnson PE, Sweeney G, Wilson DJ. A Unique Conformational Distortion Mechanism Drives Lipocalin 2 Binding to Bacterial Siderophores. ACS Chem Biol 2020; 15:234-242. [PMID: 31613081 DOI: 10.1021/acschembio.9b00820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Lcn2 is a host defense protein induced via the innate immune response to sequester iron-loaded bacterial siderophores. However, excess or prolonged elevation of Lcn2 levels can induce adverse cellular effects, including oxidative stress and inflammation. In this work, we use Hydrogen-Deuterium eXchange (HDX) and Isothermal Titration Calorimetry (ITC) to characterize the binding interaction between Lcn2 and siderophores enterobactin and 2,3-DHBA, in the presence and absence of iron. Our results indicate a rare "Type II" interaction in which binding of siderophores drives the protein conformational equilibrium toward an unfolded state. Linking our molecular model to cellular assays, we demonstrate that this "distorted binding mode" facilitates a deleterious cellular accumulation of reactive oxygen species that could represent the molecular origin of Lcn2 pathology. These results add important insights into mechanisms of Lcn2 action and have implications in Lcn2-mediated effects including inflammation.
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Unsupervised classification of PSII with and without water-oxidizing complex samples by PARAFAC resolution of excitation-emission fluorescence images. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 195:58-66. [PMID: 31100638 DOI: 10.1016/j.jphotobiol.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 11/19/2022]
Abstract
The potential of excitation-emission fluorescence spectroscopy combined with three-way analysis was investigated for discriminating the photosystem II (PSII) (with the water-oxidizing complex) and without the water-oxidizing complex (wPSII) using unsupervised classification methods. The water-oxidizing complex within PSII carry out the reaction of water splitting which is as a vital process on the earth. Therefore, discriminating the presence of the water-oxidizing complex in protein samples is crucial. Low cost and accurate spectroscopic determination of the amount of clusters inside PSII or any other protein containing species are important when investigating the inclusion and exclusion of such clusters into and from species. Fluorescence data of samples were similar, and we showed the potential usefulness of multivariate methods, such as parallel factor analysis (PARAFAC) and principal component analysis (PCA) for recognition of the two types of samples. Both techniques were applied to the excitation-emission fluorescence matrices (EEM) of solutions at two of different pH values (2.0 and 12.0). Three fluorescent components were found for all samples that are related to tyrosine (Tyr), tryptophan (Trp) and phenylalanine (Phe) amino acids. These three amino acids are representative of all datasets and indicate their similarities and differences. We then found the effectual wavelengths for separation of samples in a specific acidity, including the excitation wavelengths of 220 and 230 nm and the emission wavelengths of 300 and 305 nm. The acidity of the solutions has various influences on the conformation of proteins. In PSII and PSII the without water-oxidizing complex samples conformational changes can change their spectra which was applied for discrimination purpose. This separation was better in pH = 12.0. We also showed the effect of time on small conformational changes within datasets were higher in pH = 2.0. In the end, for indicating the high distribution of spectral data from proteins which is the result of conformational changes, we compared the distribution of measured spectral data with that from a simple organic molecule, fluorescein. Altogether, we could distinguish between the two groups of protein samples properly at pH = 12.0 using low-cost EEM spectral images and PARAFAC.
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Roy S, Bhat R. Suppression, disaggregation, and modulation of γ-Synuclein fibrillation pathway by green tea polyphenol EGCG. Protein Sci 2018; 28:382-402. [PMID: 30394624 DOI: 10.1002/pro.3549] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/31/2018] [Indexed: 12/24/2022]
Abstract
Oligomerization of γ-Synuclein is known to have implications for both neurodegeneration and cancer. Although it is known to co-exist with the fibrillar deposits of α-Synuclein (Lewy bodies), a hallmark in Parkinson's disease (PD), the effect of potential therapeutic modulators on the fibrillation pathway of γ-Syn remains unexplored. By a combined use of various biophysical tools and cytotoxicity assays we demonstrate that the flavonoid epigallocatechin-3-gallate (EGCG) significantly suppresses γ-Syn fibrillation by affecting its nucleation and binds with the unstructured, nucleus forming oligomers of γ-Syn to modulate the pathway to form α-helical containing higher-order oligomers (~158 kDa and ~ 670 kDa) that are SDS-resistant and conformationally restrained in nature. Seeding studies reveal that these oligomers although "on-pathway" in nature, are kinetically retarded and rate-limiting species that slows down fibril elongation. We observe that EGCG also disaggregates the protofibrils and mature γ-Syn fibrils into similar SDS-resistant oligomers. Steady-state and time-resolved fluorescence spectroscopy and isothermal titration calorimetry (ITC) reveal a weak non-covalent interaction between EGCG and γ-Syn with the dissociation constant in the mM range (Kd ~ 2-10 mM). Interestingly, while EGCG-generated oligomers completely rescue the breast cancer (MCF-7) cells from γ-Syn toxicity, it reduces the viability of neuroblastoma (SH-SY5Y) cells. However, the disaggregated oligomers of γ-Syn are more toxic than the disaggregated fibrils for MCF-7cells. These findings throw light on EGCG-mediated modulation of γ-Syn fibrillation and suggest that investigation on the effects of such modulators on γ-Syn fibrillation is critical in identifying effective therapeutic strategies using small molecule modulators of synucleopathies.
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Affiliation(s)
- Sneha Roy
- Biophysical Chemistry Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Rajiv Bhat
- Biophysical Chemistry Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
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Stubenrauch JA, Mevissen C, Schulte MF, Bochenek S, Albrecht M, Subramanian PS. Highly specific “sensing” of tryptophan by a luminescent europium(III) complex. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2016. [DOI: 10.1515/znb-2016-0096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The europium(III) complex 1-Cl3 (S,S-2,2′-(((1,10-phenanthroline-2,9-diyl)bis(methanylylidene))bis(azanylylidene))bis(3-methylbutanamide)europiumtrichloride) undergoes, only in the presence of the amino acid tryptophan, a change of emission at 615 nm. In the presence of few equivalents of tryptophan, emission of the europium complex is enhanced while it disappears upon addition of large amounts. This behavior can be assigned to displacement of the sensitizing phenanthroline ligand of 1-Cl2•Trp in the latter case.
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Affiliation(s)
- Jan A. Stubenrauch
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Christian Mevissen
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Marie F. Schulte
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Steffen Bochenek
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Markus Albrecht
- Institut für Organische Chemie, RWTH Aachen, Landoltweg 1, 52074 Aachen, Germany
| | - Palani S. Subramanian
- Central Salt and Marine Chemicals, Research Institute (CSRI), Bhavnagar, 364 002, Gujarat, India
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Sanfeld A, Royer C, Steinchen A. Thermodynamic, kinetic and conformational analysis of proteins diffusion-sorption on a solid surface. Adv Colloid Interface Sci 2015; 222:639-60. [PMID: 25433959 DOI: 10.1016/j.cis.2014.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022]
Abstract
In this paper we examine particularly some of the more fundamental properties of protein conformational changes at a solid surface coupled with diffusion from the bulk of an aqueous solution and with the adsorption-desorption processes. We focus our attention on adsorbed protein monolayers upon a solid surface using a thermodynamic and kinetic analytical development. Account is also taken of the effects on the overall rate of the conformational change on a solid surface of deviation from ideality, of protein flexibility, of surface free energy and of interaction with reactive solid sites. Our theory applied to steady states is illustrated by examples such as folding-misfolding-unfolding of RNase and SNase on a solid surface after diffusion and adsorption from an aqueous solution. For this purpose, we put forward the determining steps which shall lead to the steady state. The existence of three situations is highlighted according to the values of the typical constants relevant for the protein considered: reaction rate determining step, diffusion and sorption determining steps, mixed adsorption diffusion and reaction rate. Finally, we have tried to link the developments of our theories to a large literature based on experimental results encountered during proteins diffusion-sorption-reaction processes, fundamental topics that has been since long investigated by Miller's team in MPKG.
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Affiliation(s)
- Albert Sanfeld
- MADIREL UMR 7246 Aix-Marseille University, Bd Escadrille Normandie Niemen, 13397, Marseille Cedex 20, France
| | - Catherine Royer
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR 5048, 29, rue de Navacelles, 34090 Montpellier, France
| | - Annie Steinchen
- MADIREL UMR 7246 Aix-Marseille University, Bd Escadrille Normandie Niemen, 13397, Marseille Cedex 20, France
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Hasan T, Ali M, Saluja D, Singh LR. pH Might play a role in regulating the function of paired amphipathic helices domains of human Sin3B by altering structure and thermodynamic stability. BIOCHEMISTRY (MOSCOW) 2015; 80:424-32. [PMID: 25869359 DOI: 10.1134/s0006297915040057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tauheed Hasan
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
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Spectroscopic and thermodynamic properties of recombinant heat shock protein A6 from Camelus dromedarius. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 44:17-26. [DOI: 10.1007/s00249-014-0997-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 12/30/2022]
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11
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Chemical- and thermal-induced unfolding of Leishmania donovani ribose-5-phosphate isomerase B: a single-tryptophan protein. Appl Biochem Biotechnol 2014; 173:1870-84. [PMID: 24907042 DOI: 10.1007/s12010-014-0973-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/16/2014] [Indexed: 10/25/2022]
Abstract
Ribose-5-phosphate isomerase B (RpiB), a crucial enzyme of pentose phosphate pathway, was proposed to be a potential drug target for visceral leishmaniasis. In this study, we have analyzed the biophysical properties of Leishmania donovani RpiB (LdRpiB) enzyme to gain insight into its unfolding pathway under various chemical and thermal denaturation conditions by using fluorescence and CD spectroscopy. LdRpiB inactivation precedes the structural transition at lower concentrations of both urea and guanidine hydrochloride (GdHCl). 8-Anilinonapthalene 1-sulfonic (ANS) binding experiments revealed the presence of molten globule intermediate at 1.5 M GdHCl and a nonnative intermediate state at 6-M urea concentration. Acrylamide quenching experiments further validated the above findings, as solvent accessibility of tryptophan residues increased with increase in GdHCl and urea concentration. The recombinant LdRpiB was completely unfolded at 6 M GdHCl, whereas the enzyme molecule was resistant to complete unfolding even at 8-M urea concentration. The GdHCl- and urea-mediated unfolding involves a three-state transition process. Thermal-induced denaturation revealed complete loss of enzyme activity at 65 °C with only 20 % secondary structure loss. The formation of the well-ordered β-sheet structures of amyloid fibrils was observed after 55 °C which increased linearly till 85 °C as detected by thioflavin T dye. This study depicts the stability of the enzyme in the presence of chemical and thermal denaturants and stability-activity relationship of the enzyme. The presence of the intermediate states may have major implications in the way the enzyme binds to its natural ligand under various conditions. Also, the present study provides insights into the properties of intermediate entities of this important enzyme.
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Chattopadhyay A, Haldar S. Dynamic insight into protein structure utilizing red edge excitation shift. Acc Chem Res 2014; 47:12-9. [PMID: 23981188 DOI: 10.1021/ar400006z] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proteins are considered the workhorses in the cellular machinery. They are often organized in a highly ordered conformation in the crowded cellular environment. These conformations display characteristic dynamics over a range of time scales. An emerging consensus is that protein function is critically dependent on its dynamics. The subtle interplay between structure and dynamics is a hallmark of protein organization and is essential for its function. Depending on the environmental context, proteins can adopt a range of conformations such as native, molten globule, unfolded (denatured), and misfolded states. Although protein crystallography is a well established technique, it is not always possible to characterize various protein conformations by X-ray crystallography due to transient nature of these states. Even in cases where structural characterization is possible, the information obtained lacks dynamic component, which is needed to understand protein function. In this overall scenario, approaches that reveal information on protein dynamics are much appreciated. Dynamics of confined water has interesting implications in protein folding. Interfacial hydration combines the motion of water molecules with the slow moving protein molecules. The red edge excitation shift (REES) approach becomes relevant in this context. REES is defined as the shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of absorption spectrum. REES arises due to slow rates (relative to fluorescence lifetime) of solvent relaxation (reorientation) around an excited state fluorophore in organized assemblies such as proteins. Consequently, REES depends on the environment-induced motional restriction imposed on the solvent molecules in the immediate vicinity of the fluorophore. In the case of a protein, the confined water in the protein creates a dipolar field that acts as the solvent for a fluorophore in the protein. In this Account, we focus on REES to monitor organization and dynamics of soluble and membrane proteins utilizing intrinsic protein fluorescence. We discuss here the application of REES in various conformations of proteins. While application of REES to proteins in native conformation has been in use for a long time, our work highlights the potential of this approach in case of molten globule and denatured conformations. For example, we have demonstrated the presence of residual structure, that could not be detected using other methods, by REES of denatured spectrin. Given the functional relevance of such residual structures, these results are very far reaching. We discuss here the application of REES to molten globule conformation and to the green fluorescent protein (GFP). The case of GFP is particularly interesting since the dipolar field in this case is provided by the protein matrix itself and not confined water. We envision that future applications of REES in proteins will involve generating a dynamic hydration map of the protein, which would allow us to explore protein function in terms of local dynamics and hydration.
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Affiliation(s)
- Amitabha Chattopadhyay
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007 India
| | - Sourav Haldar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007 India
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Retinol binding to β-lactoglobulin or phosphocasein micelles under high pressure: Effects of isostatic high-pressure on structural and functional integrity. Food Res Int 2014. [DOI: 10.1016/j.foodres.2013.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Somkuti J, Smeller L. High pressure effects on allergen food proteins. Biophys Chem 2013; 183:19-29. [DOI: 10.1016/j.bpc.2013.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
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15
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Vinayaka AC, Thakur MS. Photoabsorption and Resonance Energy Transfer Phenomenon in CdTe−Protein Bioconjugates: An Insight into QD−Biomolecular Interactions. Bioconjug Chem 2011; 22:968-75. [DOI: 10.1021/bc200034a] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aaydha C. Vinayaka
- Fermentation Technology & Bioengineering Department, Central Food Technological Research Institute (A constituent laboratory of Council of Scientific and Industrial Research, New Delhi), Mysore-570020, India
| | - Munna S. Thakur
- Fermentation Technology & Bioengineering Department, Central Food Technological Research Institute (A constituent laboratory of Council of Scientific and Industrial Research, New Delhi), Mysore-570020, India
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Voicescu M, Rother D, Bardischewsky F, Friedrich CG, Hellwig P. A Combined Fluorescence Spectroscopic and Electrochemical Approach for the Study of Thioredoxins. Biochemistry 2010; 50:17-24. [DOI: 10.1021/bi1013112] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariana Voicescu
- Laboratoire de Spectroscopie Vibrationnelle et Electrochimie des Biomolécules, UMR 7177, Institut de Chimie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Dagmar Rother
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Frank Bardischewsky
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Cornelius G. Friedrich
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Petra Hellwig
- Laboratoire de Spectroscopie Vibrationnelle et Electrochimie des Biomolécules, UMR 7177, Institut de Chimie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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Chowdhury SR, Savithri HS. Interaction of Sesbania mosaic virus movement protein with the coat protein--implications for viral spread. FEBS J 2010; 278:257-72. [PMID: 21122074 DOI: 10.1111/j.1742-4658.2010.07943.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sesbania mosaic virus (SeMV) is a single-stranded positive-sense RNA plant virus belonging to the genus Sobemovirus. The movement protein (MP) encoded by SeMV ORF1 showed no significant sequence similarity with MPs of other genera, but showed 32% identity with the MP of Southern bean mosaic virus within the Sobemovirus genus. With a view to understanding the mechanism of cell-to-cell movement in sobemoviruses, the SeMV MP gene was cloned, over-expressed in Escherichia coli and purified. Interaction of the recombinant MP with the native virus (NV) was investigated by ELISA and pull-down assays. It was observed that SeMV MP interacted with NV in a concentration- and pH-dependent manner. Analysis of N- and C-terminal deletion mutants of the MP showed that SeMV MP interacts with the NV through the N-terminal 49 amino acid segment. Yeast two-hybrid assays confirmed the in vitro observations, and suggested that SeMV might belong to the class of viruses that require MP and NV/coat protein for cell-to-cell movement.
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René-Trouillefou M, Benzaria A, Marchal S, Lange R, Caporiccio B, Dumay E. Staphylococcal enterotoxin A: Partial unfolding caused by high pressure or denaturing agents enhances superantigenicity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1322-33. [DOI: 10.1016/j.bbapap.2010.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
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Chepelev NL, Bennitz JD, Wright JS, Smith JC, Willmore WG. Oxidative modification of citrate synthase by peroxyl radicals and protection with novel antioxidants. J Enzyme Inhib Med Chem 2010; 24:1319-31. [PMID: 19795928 DOI: 10.3109/14756360902852586] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In mammals, aging is linked to a decline in the activity of citrate synthase (CS; E.C. 2.3.3.1), the first enzyme of the citric acid cycle. We used 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH), a water-soluble generator of peroxyl and alkoxyl radicals, to investigate the susceptibility of CS to oxidative damage. Treatment of isolated mitochondria with AAPH for 8-24 h led to CS inactivation; however, the activity of aconitase, a mitochondrial enzyme routinely used as an oxidative stress marker, was unaffected. In addition to enzyme inactivation, AAPH treatment of purified CS resulted in dityrosine formation, increased protein surface hydrophobicity, and loss of tryptophan fluorescence. Propyl gallate, 1,8-naphthalenediol, 2,3-naphthalenediol, ascorbic acid, glutathione, and oxaloacetate protected CS from AAPH-mediated inactivation, with IC(50) values of 9, 14, 34, 37, 150, and 160 muM, respectively. Surprisingly, the antioxidant epigallocatechin gallate offered no protection against AAPH, but instead caused CS inactivation. Our results suggest that the current practice of using the enzymatic activity of CS as an index of mitochondrial abundance and the use of aconitase activity as an oxidative stress marker may be inappropriate, especially in oxidative stress-related studies, during which alkyl peroxyl and alkoxyl radicals can be generated.
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20
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Vlasova TN, Ugarova NN. Quenching of the fluorescence of Tyr and Trp residues of firefly luciferase from Luciola mingrelica by the substrates. BIOCHEMISTRY (MOSCOW) 2007; 72:962-7. [PMID: 17922654 DOI: 10.1134/s0006297907090064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Luciferase of the firefly Luciola mingrelica is characterized by fluorescence of not only the unique Trp residue (lambda(em) = 340 nm), but also that of Tyr residues (lambda(em) = 308 nm). Quenching of the intrinsic fluorescence of the luciferase by its substrates luciferin and ATP (AMP) has been studied. Luciferin (LH2) quenches Trp fluorescence more efficiently than the fluorescence of Tyr residues. Two centers of quenching of Tyr fluorescence by ATP have been found corresponding apparently to the allosteric and active sites of the luciferase with K(s(ATP)) = 20 and 110 microM, respectively. The influence of one substrate on the affinity of luciferase to the second was investigated using fluorescence. ATP (AMP) binding to the allosteric sites of the luciferase significantly affects the affinity of luciferase to LH2. Formation of the complex between the luciferase and LH2 affects the affinity of both allosteric and active sites of the luciferase to ATP (AMP). The observed effects are probably connected with conformational changes in the luciferase molecule upon its interaction with the substrates.
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Affiliation(s)
- T N Vlasova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.
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21
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Kornblatt JA, Barretto TA, Chigogidze K, Chirwa B. Canine Plasminogen: Spectral Responses to Changes in 6-Aminohexanoate and Temperature. ANALYTICAL CHEMISTRY INSIGHTS 2007. [DOI: 10.4137/117739010700200009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We studied the near UV absorption spectrum of canine plasminogen. There are 19 tryptophans, 19 phenylalanines and 34 tyrosines in the protein. 4th derivative spectra optimized for either tryptophan or tyrosine give a measure of the polarity of the environments of these two aromatic amino acids. Plasminogen at temperatures between 0°C and 37°C exists as a mixture of four conformations: closed-relaxed, open-relaxed, closed-compact, and open-compact. The closed to open transition is driven by addition of ligand to a site on the protein. The relaxed to compact transition is driven by increasing temperature from 0°C to above 15-20°C. When the conformation of plasminogen is mainly closed-relaxed, the 4th derivative spectra suggest that the average tryptophan environment is similar to a solution of 20% methanol at the same temperature. Under the same conditions, 4th derivative spectra suggest that the average tyrosine environment is similar to water. These apparent polarities change as the plasminogen is forced to assume the other conformations. We try to rationalize the information based on the known portions of the plasminogen structure.
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Affiliation(s)
- Jack A. Kornblatt
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
| | - Tanya A. Barretto
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
| | - Ketevan Chigogidze
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
| | - Bahati Chirwa
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
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22
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Generation of a green fluorescent protein gene chromosomal insertion containing Escherichia coli strain for gene induction-based quantification of bioavailable lysine. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11694-007-9007-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Gao JP, Zhang F, Zhang L, Guo YL, Ruan KC, Jiang DA, Xu CH. Six specific lysine residues are crucial in maintaining the structure and function of soluble manganese stabilizing protein. Acta Biochim Biophys Sin (Shanghai) 2006; 38:611-9. [PMID: 16953299 DOI: 10.1111/j.1745-7270.2006.00206.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
When manganese stabilizing protein (MSP) was treated with 0.5 mM N-succinimidyl propionate (NSP), the rebinding ability and oxygen-releasing capabilities of the modified MSP were not altered, in spite of changes of MSP surface Lys residues. Furthermore, far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed that 0.5 mM NSP-modified MSP retained most of its native secondary and tertiary structure. Mapping of the sites of NSP modification by Staphylococcus V(8) protease digestion of the modified protein, as well as analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry, indicated that seven Lys residues were modified. The results suggested that these residues are not absolutely essential to the structure and function of MSP. However, when the NSP concentration was increased to 4 mM, the modified MSP was unable to bind photosystem II and completely lost its reactivating capability. Both far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed a clear conformational change in MSP after 4 mM NSP treatment, suggesting that some Lys residues are involved in maintaining the structure and function of MSP. Analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry indicated that another six Lys residues, namely Lys20, Lys101, Lys196, Lys207, Lys130 (or Lys137) and Lys66 (or Lys76), were modified by 4 mM NSP. Therefore, these six Lys residues are crucial in maintaining the structure and function of soluble MSP.
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Affiliation(s)
- Jin-Peng Gao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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24
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Tan CY, Xu CH, Ruan KC. Folding studies of two hydrostatic pressure sensitive proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:481-8. [PMID: 16446131 DOI: 10.1016/j.bbapap.2005.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 12/14/2005] [Accepted: 12/22/2005] [Indexed: 10/25/2022]
Abstract
High hydrostatic pressure combined with various spectroscopies is a powerful technique to study protein folding. An ideal model system for protein folding studies should have the following characteristics. (1) The protein should be sensitive to pressure, so that the protein can be unfolded under mild pressure. (2) The folding process of the protein should be easily modulated by several chemical or physical factors. (3) The folding process should be easily monitored by some spectroscopic parameters. Here, we summarized the pressure induced folding studies of two proteins isolated from spinach photosystem II, namely the 23-kDa and the 33-kDa protein. They have all the characteristics mention above and might be an ideal model protein system for pressure studies.
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Affiliation(s)
- Cui-Yan Tan
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai 200031, China
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25
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Torrent J, Font J, Herberhold H, Marchal S, Ribó M, Ruan K, Winter R, Vilanova M, Lange R. The use of pressure-jump relaxation kinetics to study protein folding landscapes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:489-96. [PMID: 16481228 DOI: 10.1016/j.bbapap.2006.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 12/07/2005] [Accepted: 01/03/2006] [Indexed: 10/25/2022]
Abstract
Pressure-jump induced relaxation kinetics can be used to study both protein unfolding and refolding. These processes can be initiated by upward and downward pressure-jumps of amplitudes of a few 10 to 100 MPa, with a dead-time on the order of milliseconds. In many cases, the relaxation times can be easily determined when the pressure cell is connected to a spectroscopic detection device, such as a spectrofluorimeter. Adiabatic heating or cooling can be limited by small pressure-jump amplitudes and a special design of the sample cell. Here, we discuss the application of this method to four proteins: 33-kDa and 23-kDa proteins from photo-system II, a variant of the green fluorescent protein, and a fluorescent variant of ribonuclease A. The thermodynamically predicted equivalency of upward and downward pressure-jump induced protein relaxation kinetics for typical two-state folders was observed for the 33-kDa protein, only. In contrast, the three other proteins showed significantly different kinetics for pressure-jumps in opposite directions. These results cannot be explained by sequential reaction schemes. Instead, they are in line with a more complex free energy landscape involving multiple pathways.
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Affiliation(s)
- Joan Torrent
- INSERM U710, Université Montpellier 2, CC105, Place Eugène Bataillon, 34095 Montpellier Cédex 5, France
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26
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Qin S, Pande AH, Nemec KN, He X, Tatulian SA. Evidence for the Regulatory Role of the N-terminal Helix of Secretory Phospholipase A2 from Studies on Native and Chimeric Proteins. J Biol Chem 2005; 280:36773-83. [PMID: 16103116 DOI: 10.1074/jbc.m506789200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phospholipase A(2) (PLA(2)) enzymes are activated by binding to phospholipid membranes. Although the N-terminal alpha-helix of group I/II PLA(2)s plays an important role in the productive mode membrane binding of the enzymes, its role in the structural aspects of membrane-induced activation of PLA(2)s is not well understood. In order to elucidate membrane-induced conformational changes in the N-terminal helix and in the rest of the PLA(2), we have created semisynthetic human group IB PLA(2) in which the N-terminal decapeptide is joined with the (13)C-labeled fragment, as well as a chimeric protein containing the N-terminal decapeptide from human group IIA PLA(2) joined with a (13)C-labeled fragment of group IB PLA(2). Infrared spectral resolution of the unlabeled and (13)C-labeled segments suggests that the N-terminal helix of membrane-bound IB PLA(2) has a more rigid structure than the other helices. On the other hand, the overall structure of the chimeric PLA(2) is more rigid than that of the IB PLA(2), but the N-terminal helix is more flexible. A combination of homology modeling and polarized infrared spectroscopy provides the structure of membrane-bound chimeric PLA(2), which demonstrates remarkable similarity but also distinct differences compared with that of IB PLA(2). Correlation is delineated between structural and membrane binding properties of PLA(2)s and their N-terminal helices. Altogether, the data provide evidence that the N-terminal helix of group I/II PLA(2)s acts as a regulatory domain that mediates interfacial activation of these enzymes.
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Affiliation(s)
- Shan Qin
- Biomolecular Science Center, University of Central Florida, Orlando, Florida 32826, USA
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27
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Pouvreau L, Kroef T, Gruppen H, van Koningsveld G, van den Broek LAM, Voragen AGJ. Structure and stability of the potato cysteine protease inhibitor group (cv. Elkana). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:5739-46. [PMID: 15998142 DOI: 10.1021/jf050306v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The conformational stability of potato cysteine protease inhibitor (PCPI), the second most abundant protease inhibitor group in potato tuber, was investigated at ambient temperature and upon heating using far- and near-UV circular dichroism spectroscopy, fluorescence spectroscopy, and differential scanning calorimetry (DSC). The PCPI isoforms investigated have a highly similar structure at both the secondary and the tertiary level. PCPI isoforms show structural properties similar to those of the potato serine protease inhibitor group and the Kunitz type soybean trypsin inhibitor, a known beta-II protein. Therefore, PCPI isoforms are also classified as members of the beta-II protein subclass. Results show that the thermal unfolding of PCPI isoforms does not follow a two-state mechanism and that at least one intermediate is present. The occurrence of this intermediate is most apparent in the thermal unfolding of PCPI 8.3 as indicated by the presence of two peaks in the DSC thermogram. Additionally, the formation of aggregates (>100 kDa), especially at low scan rates, increases the apparent cooperativity of the unfolding.
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Affiliation(s)
- Laurice Pouvreau
- Department of Agrotechnology and Food Sciences, Laboratory of Food Chemistry, Wageningen University, 6700 EV Wageningen, The Netherlands
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28
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Zhang L, Zhang F, Zhang SY, Guo YL, Xu CH. Acetonitrile-induced unfolding of the photosystem II manganese-stabilizing protein studied by electrospray mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:2151-6. [PMID: 15988731 DOI: 10.1002/rcm.2043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this paper an acetonitrile-induced unfolding of the manganese-stabilizing protein (MSP) of photosystem II was discovered. More distinct unfolding states of MSP were identified than previously by using mainly electrospray ionization mass spectrometry (ESI-MS), together with fluorescence spectra and far-UV circular dichroism (CD) at pH 2.0, 6.2 or 11.6, and with acetonitrile concentrations from 0 to 50%. At pH 6.2 with acetonitrile concentration changing from 0 to 10%, relatively broad charge-state distributions and poor intensity were observed in ESI-MS, indicating the presence of coexisting conformers. It was concluded that the structure of the MSP protein is unlikely to be a tightly folded form. When the concentration of acetonitrile was 20-40%, simulating the state in the biological membrane, changes in the state of unfolding of MSP were observed to a certain extent using ESI-MS, fluorescence and CD spectroscopy. The charge-state distribution in ESI-MS was found to move toward high states (from 13+ to 27+ to 15+ to 31+) with increasing acetonitrile concentration. At pH 2.0, the MSP structure is rearranged into an unfolded state, and at pH 11.6 the MSP structure is induced to assume another unordered state by deprotonation of appropriate residues. An interesting observation was that a second peak envelope emerged with 20-50% acetonitrile in the medium at pH 11.6.
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Affiliation(s)
- Li Zhang
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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29
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Trovaslet M, Dallet-Choisy S, Meersman F, Heremans K, Balny C, Legoy MD. Fluorescence and FTIR study of pressure-induced structural modifications of horse liver alcohol dehydrogenase (HLADH). EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:119-28. [PMID: 12492482 DOI: 10.1046/j.1432-1033.2003.03370.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The process of pressure-induced modification of horse liver alcohol dehydrogenase (HLADH) was followed by measuring in situ catalytic activity (up to 250 MPa), intrinsic fluorescence (0.1-600 MPa) and modifications of FTIR spectra (up to 1000 MPa). The tryptophan fluorescence measurements and the kinetic data indicated that the pressure-induced denaturation of HLADH was a process involving several transitions and that the observed transient states have characteristic properties of molten globules. Low pressure (< 100 MPa) induced no important modification in the catalytic efficiency of the enzyme and slight conformational changes, characterized by a small decrease in the centre of spectral mass of the enzyme's intrinsic fluorescence: a native-like state was assumed. Higher pressures (100-400 MPa) induced a strong decrease of HLADH catalytic efficiency and further conformational changes. At 400 MPa, a dimeric molten globule-like state was proposed. Further increase of pressure (400-600 MPa) seemed to induce the dissociation of the dimer leading to a transition from the first dimeric molten globule state to a second monomeric molten globule. The existence of two independent structural domains in HLADH was assumed to explain this transition: these domains were supposed to have different stabilities against high pressure-induced denaturation. FTIR spectroscopy was used to follow the changes in HLADH secondary structures. This technique confirmed that the intermediate states have a low degree of unfolding and that no completely denatured form seemed to be reached, even up to 1000 MPa.
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Affiliation(s)
- Marie Trovaslet
- Laboratoire de Génie Protéique et Cellulaire, Université de La Rochelle, France
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