1
|
Basu A, Mahammad A, Das A. Inhibition of the formation of lysozyme fibrillar assemblies by the isoquinoline alkaloid coralyne. NEW J CHEM 2022. [DOI: 10.1039/d1nj06007d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The isoquinoline alkaloid coralyne can efficiently attenuate fibrillogenesis in lysozyme.
Collapse
Affiliation(s)
- Anirban Basu
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| | - Adil Mahammad
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| | - Arindam Das
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| |
Collapse
|
2
|
Chernysheva MG, Shnitko AV, Skrabkova HS, Badun GA. Peculiarities of alkylamidopropyldimethylbenzylammonium (Miramistin) in the relationship to lysozyme in comparison with quaternary ammonium surfactants: Coadsorption at the interfaces, enzymatic activity and molecular docking. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.127503] [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]
|
3
|
Zhang C, Liu Y, Sun Y, Dong X. Complicated effects of a zwitterionic polymer containing dimethyl chains on the structures, activities and stabilities of different enzymes. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
4
|
Cation Specific Effects on the Domain-Domain Interaction of Heterogeneous Dimeric Protein Revealed by FRET Analysis. J Fluoresc 2020; 30:1121-1129. [PMID: 32648172 DOI: 10.1007/s10895-020-02558-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/11/2020] [Indexed: 10/23/2022]
Abstract
Specific monovalent cation effects on the domain-domain interaction of heterogeneous dimeric protein were investigated using green fluorescent protein (GFP)-glutathione-s-transferase (GST) fusion protein as a model protein. Conjugating N-terminal of GST domain with a fluorescence probe Cyanine3, complementary increase and decrease of fluorescence intensities of Cyanine3 and GFP were recognized on the exclusive excitation of GFP and further the fluorescence decay of GFP was remarkably accelerated to show that an excellent Förster type of resonance excitation energy transfer (FRET) pair was constructed between GFP- and GST-domain. The spectral overlap integral and critical distance of the FRET pair were estimated to be 5.96×1013 M-1cm3 and 62.5 Å, respectively. The FRET rate and efficiency evaluated by fluorescence lifetime of the energy donor, GFP, were influenced by the monovalent cations included in the buffer solution to suggest that the domain-domain interactions of GFP-GST fusion protein would be susceptible to cation species and their concentrations. The order affecting the domain-domain interaction was estimated to be Li+>NH4+ >Na+>K+>Cs+, almost corresponding to the reverse Hofmeister series.
Collapse
|
5
|
Impact of polyelectrolytes on lysozyme properties in colloidal dispersions. Colloids Surf B Biointerfaces 2019; 183:110419. [DOI: 10.1016/j.colsurfb.2019.110419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 11/20/2022]
|
6
|
Investigating the effects of different natural molecules on the structure and oligomerization propensity of hen egg-white lysozyme. Int J Biol Macromol 2019; 134:189-201. [DOI: 10.1016/j.ijbiomac.2019.05.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/25/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022]
|
7
|
Zuo Y, Rui Y, Xu J, Yang L, Yi Z. Multi-spectroscopic and molecular dynamics simulations investigation of the binding mechanism of polybrominated diphenyl ethers to hen egg white lysozyme. LUMINESCENCE 2019; 34:749-758. [PMID: 31264372 DOI: 10.1002/bio.3669] [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: 11/28/2018] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022]
Abstract
Three PBDEs (BDE25, BDE47, and BDE154) were selected to investigate the interactions between PBDEs and hen egg white lysozyme (HEWL) by molecular modeling, fluorescence spectroscopy, and FT-IR spectra. The docking results showed that hydrogen bonds were formed between BDE25 and residue TRP63 and between BDE47 and TRP63 with bond lengths of 2.178 Å and 2.146 Å, respectively. The molecular dynamics simulations indicated that van der Waals forces played a predominant role in the binding of three PBDEs to HEWL. The observed fluorescence quenching can be attributed to the formation of complexes between HEWL and PBDEs, and the quenching mechanism is a static quenching. According to Förster's non-radiative energy transfer theory, the binding distances r were < 7 nm, indicating a high probability of energy transfer from HEWL to the three PBDEs. The synchronous fluorescence showed that the emission maximum wavelength of tryptophan (TRP) residues emerged a red-shift. FT-IR spectra indicated that BDE25, BDE47 and BDE154 induced the α-helix percentage of HEWL decreased from 32.70% ± 1.64% to 28.27% ± 1.41%, 27.50% ± 1.38% and 29.78% ± 1.49%, respectively, whereas the percentage of random coil increased from 26.67% ± 1.33% to 27.60% ± 1.38%, 29.18% ± 1.46% and 30.59% ± 1.53%, respectively.
Collapse
Affiliation(s)
- Yanqiu Zuo
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Yuefan Rui
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Jie Xu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Lulu Yang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Zhongsheng Yi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| |
Collapse
|
8
|
Matsunaga C, Okada Y, Nishimoto E. Ligand-Induced Conformational Changes near the Active Site Regulating Enzyme Activity of Momorcharins from Seeds of Bitter Gourd. J Fluoresc 2018; 29:231-240. [PMID: 30569384 DOI: 10.1007/s10895-018-2332-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/10/2018] [Indexed: 11/27/2022]
Abstract
It is reasonable to consider that Type I-ribosomal inactivation proteins (RIP) retain some specific affinity to harmful pathogens to complete the role as a bio-defense relating protein. In the present studies, it was shown that two Type I-RIPs, α- and β-momorcharins, maintained the abilities to bind with N-acetylglucosamine (NAG) to change the conformation around the active sites and to regulate their N-glycosidase activities. By the binding of NAG, the freedom of internal motion of Trp192 in α-momorcharin was increased 1.5 times near the active site and, on the other hand, the corresponding motion of Trp190 was limited 50% in β-momorcharin. The results in the fluorescence resonance excitation energy transfer experiments demonstrated that Trp-190 of β-momorcharin was kept away from Tyr-70 but Trp192 contrarily approached closer to the nearest neighboring Tyr residue consisting of the active center of α-momorcharin by the binding with NAG. These conformational changes near the active site close correlated with promotion and/or suppression of the N-glucosidase activities of β- and α-momorcharins.
Collapse
Affiliation(s)
- Chie Matsunaga
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuuki Okada
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Etsuko Nishimoto
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| |
Collapse
|
9
|
|
10
|
Basu A, Bhattacharya SC, Kumar GS. Influence of the ionic liquid 1-butyl-3-methylimidazolium bromide on amyloid fibrillogenesis in lysozyme: Evidence from photophysical and imaging studies. Int J Biol Macromol 2018; 107:2643-2649. [DOI: 10.1016/j.ijbiomac.2017.10.152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/24/2017] [Accepted: 10/24/2017] [Indexed: 01/23/2023]
|
11
|
|
12
|
Chernysheva MG, Badun GA, Shnitko AV, Petrova VI, Ksenofontov AL. Lysozyme-surfactant adsorption at the aqueous-air and aqueous-organic liquid interfaces as studied by tritium probe. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2017.10.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
13
|
Antonov YA, Zhuravleva I, Volodine A, Moldenaers P, Cardinaels R. Effect of the Helix-Coil Transition in Bovine Skin Gelatin on Its Associative Phase Separation with Lysozyme. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13530-13542. [PMID: 29131633 DOI: 10.1021/acs.langmuir.7b01477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
It is known that the formation of electrostatic polyelectrolyte complexes can induce conformational changes in the interacting macromolecules. However, the opposite effect, namely, that of the helix-coil transition of one of the interacting polyelectrolytes on its associative phase separation with another polyelectrolyte and the possible phase transitions in such systems, has not been determined. Atomic force and confocal laser scanning microscopy, phase analysis, dynamic and electrophoretic light scattering, turbidimetry, absorption, and fluorescence measurements as well as differential scanning calorimetry and rheology were used to study the effect of the helix-coil transition in bovine skin gelatin (Gel) on its associative phase separation with hen egg white lysozyme (Lys) at different temperatures (18-40 °C) and various Lys/Gel weight ratios (0.01-100) at low ionic strength (0.01) and pH 7.0. The effects of the main variables on the phase state, the phase diagram, and the main complexation and binding parameters as well as the temperature and enthalpy of the helix-coil transition of Gel within the complexes were investigated. Associative phase separation is observed only for the system with Gel in the helix state. Effective charge and structure and the solution and rheological behavior of the formed complexes proved to be dependent on the [An-]/[Cat+] charge ratio. The localization of Lys within the complex particles has irregular character without the formation of a single center of binding. The binding of Lys with Gel does not lead to the disruption of its tertiary structure or to an appreciable change in the thermodynamic parameters of the thermal transitions of Lys. Gel in the coil state interacts only weakly with Lys, forming water-soluble complex associates. It is suggested that the Voorn-Overbeek model could potentially describe the stronger binding and phase separation in the case of Gel in the helix state.
Collapse
Affiliation(s)
- Yurij A Antonov
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Kosygin Str. 4., 119334 Moscow, Russia
| | - Irina Zhuravleva
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Kosygin Str. 4., 119334 Moscow, Russia
| | - Alexander Volodine
- Department of Physics and Astronomy, Laboratory of Solid State Physics and Magnetism, KU Leuven , Celestijnenlaan 200D, Box 2414, B-3001 Leuven, Belgium
| | - Paula Moldenaers
- Soft Matter Rheology and Technology, Department of Chemical Engineering, KU Leuven , Celestijnenlaan 200f, Box 2424, B-3001 Leuven, Belgium
| | - Ruth Cardinaels
- Soft Matter Rheology and Technology, Department of Chemical Engineering, KU Leuven , Celestijnenlaan 200f, Box 2424, B-3001 Leuven, Belgium
- Polymer Technology, Department of Mechanical Engineering, TU Eindhoven , Box 513, 5600 MB Eindhoven, The Netherlands
| |
Collapse
|
14
|
Bouaziz Z, Soussan L, Janot JM, Lepoitevin M, Bechelany M, Djebbi MA, Amara ABH, Balme S. Structure and antibacterial activity relationships of native and amyloid fibril lysozyme loaded on layered double hydroxide. Colloids Surf B Biointerfaces 2017; 157:10-17. [DOI: 10.1016/j.colsurfb.2017.05.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 11/29/2022]
|
15
|
Choi S, Attri P, Lee I, Oh J, Yun JH, Park JH, Choi EH, Lee W. Structural and functional analysis of lysozyme after treatment with dielectric barrier discharge plasma and atmospheric pressure plasma jet. Sci Rep 2017; 7:1027. [PMID: 28432354 PMCID: PMC5430822 DOI: 10.1038/s41598-017-01030-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/28/2017] [Indexed: 11/09/2022] Open
Abstract
The variation in the biological function of proteins plays an important role in plasma medicine and sterilization. Several non-thermal plasma sources with different feeding gases are used worldwide for plasma treatment, including dielectric barrier discharge (DBD) and atmospheric-pressure plasma jet (APPJ) as the most commonly used sources. Therefore, in the present work, we used both DBD and APPJ plasma sources with N2 and air as feeding gases to evaluate the effects on the structural, thermodynamic, and activity changes of enzymes. In the current work, we used lysozyme as a model enzyme and verified the structural changes using circular dichroism (CD), fluorescence, and X-ray crystallography. In addition, we investigated the lysozyme thermodynamics using CD thermal analysis and changes in the B-factor from X-ray crystallography. The results showed that lysozyme activity decreased after the plasma treatment. From these analyses, we concluded that N2-feeding gas plasma disturbs the structure and activity of lysozyme more than Air feeding gas plasma in our experimental studies. This study provides novel fundamental information on the changes to enzymes upon plasma treatment, which has been absent from the literature until now.
Collapse
Affiliation(s)
- Sooho Choi
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Pankaj Attri
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 139-701, Korea
| | - Inhwan Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Jeongmin Oh
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Ji Hoon Park
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 139-701, Korea
| | - Eun Ha Choi
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 139-701, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 120-749, Korea.
| |
Collapse
|
16
|
Nabavi Zadeh PS, Åkerman B. Immobilization of Enzymes in Mesoporous Silica Particles: Protein Concentration and Rotational Mobility in the Pores. J Phys Chem B 2017; 121:2575-2583. [DOI: 10.1021/acs.jpcb.7b00562] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pegah S. Nabavi Zadeh
- Department of Chemistry and
Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Björn Åkerman
- Department of Chemistry and
Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| |
Collapse
|
17
|
Antonov YA, Moldenaers P, Cardinaels R. Complexation of lysozyme with sodium caseinate and micellar casein in aqueous buffered solutions. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2016.07.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
18
|
Chaari A, Fahy C, Chevillot-Biraud A, Rholam M. Insights into Kinetics of Agitation-Induced Aggregation of Hen Lysozyme under Heat and Acidic Conditions from Various Spectroscopic Methods. PLoS One 2015; 10:e0142095. [PMID: 26571264 PMCID: PMC4646502 DOI: 10.1371/journal.pone.0142095] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 01/28/2023] Open
Abstract
Protein misfolding and amyloid formation are an underlying pathological hallmark in a number of prevalent diseases of protein aggregation ranging from Alzheimer’s and Parkinson’s diseases to systemic lysozyme amyloidosis. In this context, we have used complementary spectroscopic methods to undertake a systematic study of the self-assembly of hen egg-white lysozyme under agitation during a prolonged heating in acidic pH. The kinetics of lysozyme aggregation, monitored by Thioflavin T fluorescence, dynamic light scattering and the quenching of tryptophan fluorescence by acrylamide, is described by a sigmoid curve typical of a nucleation-dependent polymerization process. Nevertheless, we observe significant differences between the values deduced for the kinetic parameters (lag time and aggregation rate). The fibrillation process of lysozyme, as assessed by the attenuated total reflection-Fourier transform infrared spectroscopy, is accompanied by an increase in the β-sheet conformation at the expense of the α-helical conformation but the time-dependent variation of the content of these secondary structures does not evolve as a gradual transition. Moreover, the tryptophan fluorescence-monitored kinetics of lysozyme aggregation is described by three phases in which the temporal decrease of the tryptophan fluorescence quantum yield is of quasilinear nature. Finally, the generated lysozyme fibrils exhibit a typical amyloid morphology with various lengths (observed by atomic force microscopy) and contain exclusively the full-length protein (analyzed by highly performance liquid chromatography). Compared to the data obtained by other groups for the formation of lysozyme fibrils in acidic pH without agitation, this work provides new insights into the structural changes (local, secondary, oligomeric/fibrillar structures) undergone by the lysozyme during the agitation-induced formation of fibrils.
Collapse
Affiliation(s)
- Ali Chaari
- ITODYS, UMR CNRS 7086, Univ. Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
- Laboratoire de Génétique et Biologie Cellulaire, Université de Versailles Saint-Quentin-en-Yvelines, 78035, Versailles, France
| | - Christine Fahy
- ITODYS, UMR CNRS 7086, Univ. Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | | | - Mohamed Rholam
- ITODYS, UMR CNRS 7086, Univ. Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
- * E-mail:
| |
Collapse
|
19
|
Relaxation Photoprocesses in a Crowned Styryl Dye and its Metal Complex. J Fluoresc 2015; 25:1739-47. [DOI: 10.1007/s10895-015-1660-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
|
20
|
Sun Y, Filho PLO, Bozelli JC, Carvalho J, Schreier S, Oliveira CLP. Unfolding and folding pathway of lysozyme induced by sodium dodecyl sulfate. SOFT MATTER 2015; 11:7769-7777. [PMID: 26308474 DOI: 10.1039/c5sm01231g] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteins may exhibit an unfolding or folding state in the presence of a surfactant. In the present study, the unfolding and folding pathway of hen egg white lysozyme (HEWL) induced by sodium dodecyl sulfate (SDS) is studied. The stoichiometry obtained from isothermal titration calorimetry (ITC) provides guidelines for other techniques. The fluorescence spectra and circular dichroism show that the fluorescence properties and secondary structure of proteins undergo a two-step change upon binding with SDS, in which the intensity decreases, the emission blue shifts and the helical conformation decreases at low ratios of SDS to HEWL, while all of them return to the native-like state upon the addition of SDS at higher ratios. At the end of the binding, HEWL presents a higher α-helical content but its tertiary structure is lost compared to its native state, which is namely a molten globule state. Small angle X-ray scattering (SAXS) analysis and the derived model reveal that the complexes possess a decorated core-shell structure, with the core composed of dodecyl chains and the shell consisting of SDS head groups with a protein in molten globule state. Five binding steps, including the individual details involved in the denaturation, were obtained to describe the unfolding and folding pathway of HEWL induced by SDS. The results of this study not only present details about the denaturation of protein induced by SDS and the structure of the complexes involved in each binding step, but also provide molecular insights into the mechanism of the higher helical conformation of proteins in the presence of surfactant micelles.
Collapse
Affiliation(s)
- Yang Sun
- Instituto de Física, Universidade de São Paulo, Rua do Matão 187, São Paulo-SP, 05314-970, Brasil.
| | | | | | | | | | | |
Collapse
|
21
|
Maurya JK, Mir MUH, Singh UK, Maurya N, Dohare N, Patel S, Ali A, Patel R. Molecular investigation of the interaction between ionic liquid type gemini surfactant and lysozyme: A spectroscopic and computational approach. Biopolymers 2015; 103:406-15. [DOI: 10.1002/bip.22647] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Jitendra Kumar Maurya
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Muzaffar Ul Hassan Mir
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Upendra Kumar Singh
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Neha Maurya
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Neeraj Dohare
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Seema Patel
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Anwar Ali
- Department of Chemistry; Jamia Millia Islamia (A Central University); New Delhi 110025 India
| | - Rajan Patel
- Biophysical Chemistry Laboratory; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University); New Delhi 110025 India
| |
Collapse
|
22
|
Jaganathan M, Dhathathreyan A, Selvaraju C, Miller R. Jones-Ray effect on the organization of lysozyme in the presence of NaNO3 at an air/water interface: is it a cause or consequence? RSC Adv 2015. [DOI: 10.1039/c5ra15444h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Interfacial rheology confirms the Jones-Ray effect resulting from a synergy between lysozyme and NaNO3 at an air/fluid interface.
Collapse
Affiliation(s)
| | | | | | - Reinhard Miller
- Max-Planck-Institut fuer Kolloid-und Grenzflaechenforschung
- Potsdam
- Germany
| |
Collapse
|
23
|
Babcock JJ, Brancaleon L. The effect of local dynamics of Atto 390-labeled lysozyme on fluorescence anisotropy modeling. Biopolymers 2014; 103:285-95. [PMID: 25431279 DOI: 10.1002/bip.22596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 11/07/2022]
Abstract
Fluorescence anisotropy decay is a popular optical technique to study the structure, size, shape, and even functions of biomolecules. The method measures the time dependence of the depolarization of a fluorophore and is therefore sensitive to the changes in the rotational motion (e.g., aggregation and binding) or changes in the mobility of segments of biopolymers (such as the ones associated with tertiary structure changes). Fluorescence anisotropy decay often requires the use of fluorescent dyes that need to be covalently attached to the biomolecule. The location of the attachment on the biomolecule (e.g., a protein) and the linker used, affect the mobility of the dye and its anisotropy decay. With this study we have combined the experimental data with molecular dynamic simulations to offer a more correct interpretation of the fluorescence anisotropy decay of a popular fluorescent dye (Atto 390) attached to the N-terminus of Hen Egg White Lysozyme (HEWL). Our model showed how the use of relatively simple molecular dynamics computation to simulate the motion of the dye, provide a model to interpret the experimental fluorescence anisotropy decay that yields a better estimate of the hydrodynamic radius of HEWL. The improvement is provided by a more detailed description of the segmental motion of the dye attached to the protein.
Collapse
Affiliation(s)
- Jeremiah J Babcock
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78242
| | | |
Collapse
|
24
|
Nakashima H, Fukunaga Y, Ueno R, Nishimoto E. Sugar binding effects on the enzymatic reaction and conformation near the active site of pokeweed antiviral protein revealed by fluorescence spectroscopy. J Fluoresc 2014; 24:951-8. [PMID: 24696383 DOI: 10.1007/s10895-014-1378-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 03/19/2014] [Indexed: 11/29/2022]
Abstract
In various trials for elucidating the physiological function of pokeweed antiviral protein (PAP), studies on the interaction with sugar are essential. The fluorescence titration curves showed that PAP retained the strong affinity against N-acetylglucosamine (NAG) and two sites in one PAP molecule co-operatively participated in the binding. In the complex of PAP with NAG, Trp208 located at the entrance lid site of substrate came closer to Tyr72 about 0.3 Å. Furthermore, the fluorescence anisotropy decay measurement demonstrated that the segmental rotation of Trp208 was enlarged by the binding of PAP with NAG. Such conformational changes around the active site closely correlate with the enzymatic activity of PAP. The N-glycosidase activity of PAP was enhanced more than two times in the presence of NAG. The obtained results consistently suggested the enzymatic activity of PAP would be regulated through the conformation change near the active site induced by the binding with NAG.
Collapse
Affiliation(s)
- Hiromichi Nakashima
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | | | | | | |
Collapse
|
25
|
Ravi VK, Swain T, Chandra N, Swaminathan R. On the characterization of intermediates in the isodesmic aggregation pathway of hen lysozyme at alkaline pH. PLoS One 2014; 9:e87256. [PMID: 24489883 PMCID: PMC3904990 DOI: 10.1371/journal.pone.0087256] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 12/25/2013] [Indexed: 12/24/2022] Open
Abstract
Protein aggregation leading to formation of amyloid fibrils is a symptom of several diseases like Alzheimer’s, type 2 diabetes and so on. Elucidating the poorly understood mechanism of such phenomena entails the difficult task of characterizing the species involved at each of the multiple steps in the aggregation pathway. It was previously shown by us that spontaneous aggregation of hen-eggwhite lysozyme (HEWL) at room temperature in pH 12.2 is a good model to study aggregation. Here in this paper we investigate the growth kinetics, structure, function and dynamics of multiple intermediate species populating the aggregation pathway of HEWL at pH 12.2. The different intermediates were isolated by varying the HEWL monomer concentration in the 300 nM—0.12 mM range. The intermediates were characterized using techniques like steady-state and nanosecond time-resolved fluorescence, atomic force microscopy and dynamic light scattering. Growth kinetics of non-fibrillar HEWL aggregates were fitted to the von Bertalanffy equation to yield a HEWL concentration independent rate constant (k = (6.6±0.6)×10−5 s−1). Our results reveal stepwise changes in size, molecular packing and enzymatic activity among growing HEWL aggregates consistent with an isodesmic aggregation model. Formation of disulphide bonds that crosslink the monomers in the aggregate appear as a unique feature of this aggregation. AFM images of multiple amyloid fibrils emanating radially from amorphous aggregates directly confirmed that on-pathway fibril formation was feasible under isodesmic polymerization. The isolated HEWL aggregates are revealed as polycationic protein nanoparticles that are robust at neutral pH with ability to take up non-polar molecules like ANS.
Collapse
Affiliation(s)
- Vijay Kumar Ravi
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Tulsi Swain
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Nividh Chandra
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Rajaram Swaminathan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- * E-mail:
| |
Collapse
|
26
|
Cao J, Zhang H, Wang Y, Yang J, Jiang F. Investigation on the interaction behavior between curcumin and PAMAM dendrimer by spectral and docking studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 108:251-255. [PMID: 23501936 DOI: 10.1016/j.saa.2013.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 11/03/2012] [Accepted: 02/07/2013] [Indexed: 06/01/2023]
Abstract
The interactions between PAMAM-C12 25% and curcumin were studied by UV/vis, fluorescence spectroscopy, and molecular modeling methods. The experimental results showed that the formation of PAMAM-C12 25%@curcumin non-covalent adduct induced the fluorescence quenching of PAMAM-C12 25%; Curcumin entered the interface of PAMAM-C12 25% with mainly five classes of binding sites by hydrophobic, hydrogen bonds, and van der Waals forces interactions. The bigger values of binding constants indicated that PAMAM-C12 25% hold the curcumin tightly.
Collapse
Affiliation(s)
- Jian Cao
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China.
| | | | | | | | | |
Collapse
|
27
|
Matsumoto S, Taniguchi Y, Fukunaga Y, Nakashima H, Watanabe K, Yamashita S, Nishimoto E. Structural characteristic of folding/unfolding intermediate of pokeweed anti-viral protein revealed by time-resolved fluorescence. J Fluoresc 2013; 23:407-15. [PMID: 23319009 DOI: 10.1007/s10895-013-1155-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/07/2013] [Indexed: 11/25/2022]
Abstract
The structural feature of unfolding intermediate of pokeweed anti-viral protein (PAP) was characterized using time-resolved fluorescence spectroscopic methods to elucidate protein folding/unfolding process. CD and fluorescence spectra consistently demonstrated that the unfolding of PAP completed at 4 M of guanidine hydrochloride (GuHCl). The fluorescence resonance energy transfer (FRET) and time-resolve fluorescence depolarization analysis of Trp208 and Trp237 located in the C-terminal domain of PAP suggested that peculiar unfolding intermediate populated before reaching to the unfolding state. The FRET distance of Trp237 to Tyr182 was extended to more than 28 Å with keeping the compact conformation in the unfolding intermediate state populated in the presence of 2 M GuHCl. On the other hand, Trp208 maintained the energy transfer pair with Tyr72 near the active site, although the rotational freedom was increased a little. There results suggest that the most distinguished structural feature of the unfolding intermediate of PAP is the separation of C-terminal domain from N-terminal domain. FRET and fluorescence depolarization studies also showed that C-terminal domain would be more separated to liberate the segmental motions of Trp208 and Trp237 distinctly at the unfolding state.
Collapse
Affiliation(s)
- Shuzo Matsumoto
- Industrial Technology Center of Nagasaki, Ohmura, Nagasaki, Japan
| | | | | | | | | | | | | |
Collapse
|
28
|
Raccosta S, Martorana V, Manno M. Thermodynamic versus conformational metastability in fibril-forming lysozyme solutions. J Phys Chem B 2012; 116:12078-87. [PMID: 22984801 DOI: 10.1021/jp303430g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of intermolecular interaction in fibril-forming protein solutions and its relation with molecular conformation is a crucial aspect for the control and inhibition of amyloid structures. Here, we study the fibril formation and the protein-protein interactions of lysozyme at acidic pH and low ionic strength. The amyloid formation occurs after a long lag time and is preceded by the formation of oligomers, which seems to be off-pathway with respect to fibrillation. By measuring the osmotic isothermal compressibility and the collective diffusion coefficient of lysozyme in solution, we observe that the monomeric solution is kept in a thermodynamically metastable state by strong electrostatic repulsion, even in denaturing conditions. The measured repulsive interaction between monomers is satisfactorily accounted for by classical polyelectrolyte theory. Further, we observe a slow conformational change involving both secondary and tertiary structure, which drives the proteins toward a more hydrophobic conformation. Denatured proteins are driven out of metastability through conformational substates, which are kinetically populated and experience a lower activation energy for fibril formation. Thus, our results highlight the role of electrostatic repulsion, which hinders the aggregation of partially denatured proteins and operates as a gatekeeper favoring the association of those monomers whose conformation is capable of forming amyloid structure.
Collapse
Affiliation(s)
- Samuele Raccosta
- Institute of Biophysics, National Research Council of Italy, via U. La Malfa 153, I-90146 Palermo, Italy
| | | | | |
Collapse
|
29
|
The effect of lysozyme amyloid fibrils on cytochrome c–lipid interactions. Chem Phys Lipids 2012; 165:769-76. [DOI: 10.1016/j.chemphyslip.2012.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/21/2022]
|
30
|
Qin P, Su B, Liu R. Probing the binding of two fluoroquinolones to lysozyme: a combined spectroscopic and docking study. MOLECULAR BIOSYSTEMS 2012; 8:1222-9. [DOI: 10.1039/c2mb05423j] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
Takahashi D, Yamashita S, Prakash O, Nishimoto E. Rotational Diffusion Analysis of Polyethylene Glycol Induced Protein Interactions. J Phys Chem B 2011; 115:11786-92. [DOI: 10.1021/jp205279k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daisuke Takahashi
- Institute of Biophysics, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
- Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Shoji Yamashita
- Institute of Biophysics, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Om Prakash
- Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Etsuko Nishimoto
- Institute of Biophysics, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| |
Collapse
|
32
|
Zhang HM, Xu YQ, Zhou QH, Wang YQ. Investigation of the interaction between chlorophenols and lysozyme in solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2011; 104:405-13. [DOI: 10.1016/j.jphotobiol.2011.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/17/2011] [Accepted: 04/20/2011] [Indexed: 11/25/2022]
|
33
|
D'Amico M, Raccosta S, Cannas M, Martorana V, Manno M. Existence of metastable intermediate lysozyme conformation highlights the role of alcohols in altering protein stability. J Phys Chem B 2011; 115:4078-87. [PMID: 21425817 DOI: 10.1021/jp106748g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alcohols have a manifold effect on the conformational and thermodynamic stability of native proteins. Here, we study the effect of moderate concentrations of trifluoroethanol (TFE) on the thermal stability of hen egg-white lysozyme (HEWL), by far-UV circular dichroism and by steady-state and time-resolved photoluminescence of intrinsic tryptophans. Our results highlight that TFE affects lysozyme stability by preferential solvation of the protein molecule. Furthermore, we discovered the existence at 20% TFE of an equilibrium partially folded state of lysozyme, intermediate between the native and the unfolded state. A three-state model is therefore used to interpolate the thermal denaturation data. Our analysis explains how the stabilization of the intermediate conformation enhances the entropic contribution to unfolding, and thus decreases the unfolding temperature, while, at the same time, TFE enhances the conformational stability of the native fold at room temperature. Eventually, we challenged the ability of these intermediate structures to form supramolecular aggregates by heating experiments at different TFE concentrations.
Collapse
Affiliation(s)
- Michele D'Amico
- Institute of Biophysics at Palermo (IBF), National Research Council of Italy (CNR), via U. La Malfa 153, I-90146 Palermo, Italy
| | | | | | | | | |
Collapse
|
34
|
Zhang HM, Chen J, Zhou QH, Shi YQ, Wang YQ. Study on the interaction between cinnamic acid and lysozyme. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.11.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
35
|
Tryptophan-Tryptophan Energy Transfer and Classification of Tryptophan Residues in Proteins Using a Therapeutic Monoclonal Antibody as a Model. J Fluoresc 2010; 21:275-88. [DOI: 10.1007/s10895-010-0715-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
|
36
|
Weinreis SA, Ellis JP, Cavagnero S. Dynamic fluorescence depolarization: a powerful tool to explore protein folding on the ribosome. Methods 2010; 52:57-73. [PMID: 20685617 PMCID: PMC2934862 DOI: 10.1016/j.ymeth.2010.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/25/2022] Open
Abstract
Protein folding is a fundamental biological process of great significance for cell function and life-related processes. Surprisingly, very little is presently known about how proteins fold in vivo. The influence of the cellular environment is of paramount importance, as molecular chaperones, the ribosome, and the crowded medium affect both folding pathways and potentially even equilibrium structures. Studying protein folding in physiologically relevant environments, however, poses a number of technical challenges due to slow tumbling rates, low concentrations and potentially non-homogenous populations. Early work in this area relied on biological assays based on antibody recognition, proteolysis, and activity studies. More recently, it has been possible to directly observe the structure and dynamics of nascent polypeptides at high resolution by spectroscopic and microscopic techniques. The fluorescence depolarization decay of nascent polypeptides labeled with a small extrinsic fluorophore is a particularly powerful tool to gain insights into the dynamics of newly synthesized proteins. The fluorophore label senses both its own local mobility and the motions of the macromolecule to which it is attached. Fluorescence anisotropy decays can be measured both in the time and frequency domains. The latter mode of data collection is extremely convenient to capture the nanosecond motions in ribosome-bound nascent proteins, indicative of the development of independent structure and folding on the ribosome. In this review, we discuss the theory of fluorescence depolarization and its exciting applications to the study of the dynamics of nascent proteins in the cellular environment.
Collapse
Affiliation(s)
- Sarah A. Weinreis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | | | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| |
Collapse
|
37
|
Wang YQ, Chen TT, Zhang HM. Investigation of the interactions of lysozyme and trypsin with biphenol A using spectroscopic methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:1130-1137. [PMID: 20093070 DOI: 10.1016/j.saa.2009.12.071] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 12/19/2009] [Accepted: 12/31/2009] [Indexed: 05/28/2023]
Abstract
The interaction between bisphenol A (BPA) and lysozyme (or trypsin) was investigated by UV-vis absorption, fluorescence, synchronous fluorescence, and three-dimensional fluorescence spectra techniques under physiological pH 7.40. BPA effectively quenched the intrinsic fluorescence of lysozyme and trypsin via static quenching. H-bonds and van der Waals interactions played a major role in stabilizing the BPA-proteinase complex. The distance r between donor and acceptor was obtained to be 1.65 and 2.26 nm for BPA-lysozyme and BPA-trypsin complexes, respectively. The effect of BPA on the conformation of lysozyme and trypsin was analyzed using synchronous fluorescence and three-dimensional fluorescence spectra.
Collapse
Affiliation(s)
- Yan-Qing Wang
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province, People's Republic of China.
| | | | | |
Collapse
|
38
|
Ruta J, Perrier S, Ravelet C, Fize J, Peyrin E. Noncompetitive fluorescence polarization aptamer-based assay for small molecule detection. Anal Chem 2009; 81:7468-73. [PMID: 19630421 DOI: 10.1021/ac9014512] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this paper, a new fluorescence polarization (FP) assay strategy is described reporting the first demonstration of a noncompetitive FP technique dedicated to the small molecule sensing. This approach was based on the unique induced-fit binding mechanism of nucleic acid aptamers which was exploited to convert the small target binding event into a detectable fluorescence anisotropy signal. An anti-L-tyrosinamide DNA aptamer, labeled by a single fluorescent dye at its extremity, was employed as a model functional nucleic acid probe. The DNA conformational change generated by the L-tyrosinamide binding was able to induce a significant increase in the fluorescence anisotropy signal. The method allowed enantioselective sensing of tyrosinamide and analysis in practical samples. The methodology was also applied to the L-argininamide detection, suggesting the potential generalizability of the direct FP-based strategy. Such aptamer-based assay appeared to be a sensitive analytical system of remarkable simplicity and ease of use.
Collapse
Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble cedex 9, France
| | | | | | | | | |
Collapse
|
39
|
Zhang HM, Tang BP, Wang YQ. The interaction of lysozyme with caffeine, theophylline and theobromine in solution. Mol Biol Rep 2009; 37:3127-36. [DOI: 10.1007/s11033-009-9891-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 10/02/2009] [Indexed: 11/30/2022]
|
40
|
Otosu T, Nishimoto E, Yamashita S. Fluorescence Decay Characteristics of Indole Compounds Revealed by Time-Resolved Area-Normalized Emission Spectroscopy. J Phys Chem A 2009; 113:2847-53. [DOI: 10.1021/jp8078937] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takuhiro Otosu
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Etsuko Nishimoto
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Shoji Yamashita
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| |
Collapse
|
41
|
Doi-Kawano K, Nishimoto E, Kouzuma Y, Takahashi D, Yamashita S, Kimura M. Steady-State and Time-Resolved Fluorescence Spectroscopic Studies on Interaction of the N-terminal Region with the Hairpin Loop of the Phytocystain Scb. J Fluoresc 2008; 19:631-9. [DOI: 10.1007/s10895-008-0454-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 12/09/2008] [Indexed: 10/21/2022]
|
42
|
Fukunaga Y, Nishimoto E, Otosu T, Murakami Y, Yamashita S. The Unfolding of -Momorcharin Proceeds Through the Compact Folded Intermediate. J Biochem 2008; 144:457-66. [DOI: 10.1093/jb/mvn088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
43
|
Heterogeneous packing in the folding/unfolding intermediate state of bitter gourd trypsin inhibitor. Biosci Biotechnol Biochem 2008; 72:1498-505. [PMID: 18540100 DOI: 10.1271/bbb.80009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The conformation and dynamics of a protein are essential in characterizing the protein folding/unfolding intermediate state. They are closely involved in the packing and site-specific interactions of peptide elements to build and stabilize the tertiary structure of the protein. In this study, it was confirmed that trypsin inhibitor obtained from seeds of bitter gourd (BGTI) adopted a peculiar but plausible conformation and dynamics in the unfolding intermediate state. The fluorescence spectrum of one of two tryptophan residues of BGTI, Trp9, shifted to the blue side in the presence of 2-3 M guanidine hydrochloride, although the other, Trp54, did not show this spectral shift. At the same time, the motional freedom of Trp9 revealed by a time-resolved fluorescence study decreased, suggesting that the segmental motion of this residue was more restricted. These results indicate that BGTI takes such a conformation state that the hydrophobic core and loop domains arranging Trp9 and Trp54 respectively are heterogeneously packed in the unfolding intermediate state.
Collapse
|
44
|
Volchkov VV, Uzhinov BM. Structural relaxation of excited molecules of heteroaromatic compounds. HIGH ENERGY CHEMISTRY 2008. [DOI: 10.1134/s0018143908030016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
45
|
Gorbenko GP, Ioffe VM, Molotkovsky JG, Kinnunen PK. Resonance energy transfer study of lysozyme–lipid interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1213-21. [DOI: 10.1016/j.bbamem.2007.09.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 09/06/2007] [Accepted: 09/17/2007] [Indexed: 11/24/2022]
|
46
|
Protein-protein interaction on lysozyme crystallization revealed by rotational diffusion analysis. Biophys J 2008; 94:4484-92. [PMID: 18310245 DOI: 10.1529/biophysj.107.111872] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intermolecular interactions between protein molecules diffusing in various environments underlie many biological processes as well as control protein crystallization, which is a crucial step in x-ray protein structure determinations. Protein interactions were investigated through protein rotational diffusion analysis. First, it was confirmed that tetragonal lysozyme crystals containing fluorescein-tagged lysozyme were successfully formed with the same morphology as that of native protein. Using this nondisruptive fluorescent tracer system, we characterized the effects of sodium chloride and ammonium sulfate concentrations on lysozyme-lysozyme interactions by steady-state and time-resolved fluorescence anisotropy measurements and the introduction of a novel interaction parameter, k(rot). The results suggested that the specific attractive interaction, which was reflected in the retardation of the protein rotational diffusion, was induced depending on the salt type and its concentration. The change in the attractive interactions also correlated with the crystallization/precipitation behavior of lysozyme. Moreover, we discuss the validity of our rotational diffusion analysis through comparison with the osmotic second virial coefficient, B(22), previously reported for lysozyme and those estimated from k(rot).
Collapse
|
47
|
Scognamiglio V, Scirè A, Aurilia V, Staiano M, Crescenzo R, Palmucci C, Bertoli E, Rossi M, Tanfani F, D'Auria S. A strategic fluorescence labeling of D-galactose/D-glucose-binding protein from Escherichia coli helps to shed light on the protein structural stability and dynamics. J Proteome Res 2007; 6:4119-26. [PMID: 17924684 DOI: 10.1021/pr070439r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The D-glucose/D-galactose-binding protein (GGBP) of Escherichia coli serves as an initial component for both chemotaxis toward D-galactose and D-glucose and high-affinity active transport of the two sugars. GGBP is a monomer with a molecular weight of about 32 kDa that binds glucose with micromolar affinity. The sugar-binding site is located in the cleft between the two lobes of the bilobate protein. In this work, the local and global structural features of GGBP were investigated by a strategic fluorescence labeling procedure and spectroscopic methodologies. A mutant form of GGBP containing the amino acid substitution Met to Cys at position 182 was realized and fluorescently labeled to probe the effect of glucose binding on the local and overall structural organization of the protein. The labeling of the N-terminus with a fluorescence probe as well as the protein intrinsic fluorescence were also used to obtain a complete picture of the GGBP structure and dynamics. Our results showed that the binding of glucose to GGBP resulted in no stabilizing effect on the N-terminus portion of GGBP and in a moderate stabilization of the protein matrix in the vicinity of the ligand-binding site. On the contrary, it was observed that the binding of glucose has a strong stabilization effect on the C-terminal domain of the GGBP structure.
Collapse
Affiliation(s)
- Viviana Scognamiglio
- Institute of Protein Biochemistry, National Research Council of Italy (CNR), Via P. Castellino, 111 80131, Naples, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Pastor I, Ferrer ML, Lillo MP, Gómez J, Mateo CR. Structure and Dynamics of Lysozyme Encapsulated in a Silica Sol−Gel Matrix. J Phys Chem B 2007; 111:11603-10. [PMID: 17850137 DOI: 10.1021/jp074790b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Proteins entrapped in sol-gel matrices have been extensively studied during the last 15 years, showing that most of them can be encapsulated with retention of their native structure and functionality and with enhanced stability. However, relatively little is known about the structural and dynamical details of the biomolecule-matrix interactions. To achieve this goal, the model protein hen egg white lysozyme (HEWL) has been entrapped in sol-gel matrices prepared from tetraethyl orthosilicate through an alcohol-free sol-gel route, and the photophysical properties of its fluorescent tryptophans have been determined using both steady-state and time-resolved fluorescence techniques. By combining fluorescence spectra, quenching experiments, lifetimes, and time-resolved fluorescence anisotropy measurements, we have obtained information on the structure, dynamics, and solvation properties of the entrapped protein. Our results show that the environment of HEWL within the silica pore as well as its internal dynamics is similar to that in aqueous solution, except that the protein showed no or, depending on conditions, very much slower global motion but retained its internal angularly restricted (hindered) segmental rotation upon entrapment. The experiments carried out at different experimental conditions indicate that, below the isoelectric point of the protein, a strong electrostatic interaction is established between the protein molecule and the negatively charged sol-gel walls, which is ultimately responsible for the total arrest of the overall rotation of the protein, but without significant effect upon its segmental rotational relaxation. The electrostatic nature of the interaction is clearly established since either reducing the positive charge of the protein (by increasing the pH toward its isoelectric point) or increasing the ionic strength of the solution (shielding against the attractive interaction) leads to a situation in which the protein freely rotates within the matrix pore, albeit an order of magnitude more slowly than that in free solution under similar macroscopic solution conditions, and still retains its segmental rotational properties.
Collapse
Affiliation(s)
- Isabel Pastor
- Instituto de Biología Molecular y Celular, Universidad Miguel HernAndez, 03202-Elche, Spain
| | | | | | | | | |
Collapse
|
49
|
Chowdhury P, Gondry M, Genet R, Martin JL, Ménez A, Négrerie M, Petrich JW. Picosecond Dynamics of a Peptide from the Acetylcholine Receptor Interacting with a Neurotoxin Probed by Tailored Tryptophan Fluorescence¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0770151pdoapf2.0.co2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
50
|
Gorbenko GP, Ioffe VM, Kinnunen PKJ. Binding of lysozyme to phospholipid bilayers: evidence for protein aggregation upon membrane association. Biophys J 2007; 93:140-53. [PMID: 17434939 PMCID: PMC1914450 DOI: 10.1529/biophysj.106.102749] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Biological functions of lysozyme, including its antimicrobial, antitumor, and immune-modulatory activities have been suggested to be largely determined by the lipid binding properties of this protein. To gain further insight into these interactions on a molecular level the association of lysozyme to liposomes composed of either 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine or its mixtures with 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-glycerol, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-phosphatidylserine, or bovine heart cardiolipin was studied by a combination of fluorescence techniques. The characteristics of the adsorption of lysozyme to lipid bilayers were investigated using fluorescein 5'-isothiocyanate labeled protein, responding to membrane association by a decrease in fluorescence. Upon increasing the content of anionic phospholipids in lipid vesicles, the binding isotherms changed from Langmuir-like to sigmoidal. Using adsorption models based on scaled particle and double-layer theories, this finding was rationalized in terms of self-association of the membrane-bound protein. The extent of quenching of lysozyme tryptophan fluorescence by acrylamide decreased upon membrane binding, revealing a conformational transition for the protein upon its surface association, resulting in a diminished access of the fluorophore to the aqueous phase. Steady-state fluorescence anisotropy of bilayer-incorporated probe 1,6-diphenyl-1,3,5-hexatriene was measured at varying lipid-to-protein molar ratios. Lysozyme was found to increase acyl-chain order for liposomes with the content of acidic phospholipid exceeding 10 mol %. Both electrostatic and hydrophobic protein-lipid interactions can be concluded to modulate the aggregation behavior of lysozyme when bound to lipid bilayers. Modulation of lysozyme aggregation propensity by membrane binding may have important implications for protein fibrillogenesis in vivo. Disruption of membrane integrity by the aggregated protein species is likely to be the mechanism responsible for the cytotoxicity of lysozyme.
Collapse
Affiliation(s)
- Galyna P Gorbenko
- Department of Biological and Medical Physics, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | | | | |
Collapse
|