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Wahia H, Zhang L, Zhou C, Mustapha AT, Fakayode OA, Amanor-Atiemoh R, Ma H, Dabbour M. Pulsed multifrequency thermosonication induced sonoporation in Alicyclobacillus acidoterrestris spores and vegetative cells. Food Res Int 2022; 156:111087. [DOI: 10.1016/j.foodres.2022.111087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 11/04/2022]
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2
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Yılmaz İ, Korkmaz F. Investigations of pH-dependent dynamic properties of OmpG-16SL, an outer membrane protein G mutant by ATR-FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140780. [PMID: 35405324 DOI: 10.1016/j.bbapap.2022.140780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
In this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 β-strands in its structure, the mutant is designed to have 16 β-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the 1H/2H exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.
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Affiliation(s)
- İrem Yılmaz
- Physics Unit, Biophysics Laboratory, Atilim University, 06836 Ankara, Turkey
| | - Filiz Korkmaz
- Physics Unit, Biophysics Laboratory, Atilim University, 06836 Ankara, Turkey.
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Song R, Li H, Kang Z, Zhong R, Wang Y, Zhang Y, Qu G, Wang T. Surface plasma induced elimination of antibiotic-resistant Escherichia coli and resistance genes: Antibiotic resistance, horizontal gene transfer, and mechanisms. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.119185] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Li H, Kang Z, Jiang E, Song R, Zhang Y, Qu G, Wang T, Jia H, Zhu L. Plasma induced efficient removal of antibiotic-resistant Escherichia coli and antibiotic resistance genes, and inhibition of gene transfer by conjugation. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126465. [PMID: 34214852 DOI: 10.1016/j.jhazmat.2021.126465] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic-resistant bacteria (ARB) and their resistance genes (ARGs) are emerging environmental pollutants that pose great threats to human health. In this study, a novel strategy using plasma was developed to simultaneously remove antibiotic-resistant Escherichia coli (AR bio-56954 E. coli) and its ARGs, aiming to inhibit gene transfer by conjugation. Approximately 6.6 log AR bio-56954 E. coli was inactivated within 10 min plasma treatment, and the antibiotic resistance to tested antibiotics (tetracycline, gentamicin, and amoxicillin) significantly decreased. Reactive oxygen and nitrogen species (RONS) including •OH, 1O2, O2•-, NO2-, and NO3- contributed to ARB and ARGs elimination; their attacks led to destruction of cell membrane, accumulation of excessive intracellular reactive oxygen substances, deterioration of conformational structures of proteins, and destroy of nucleotide bases of DNA. As a result, the ARGs (tet(C), tet(W), blaTEM-1, aac(3)-II), and integron gene intI1), and conjugative transfer frequency of ARGs significantly decreased after plasma treatment. The results demonstrated that plasma has great prospective application in removing ARB and ARGs in water, inhibiting gene transfer by conjugation.
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Affiliation(s)
- Hu Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Zhao Kang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Enli Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Ruiying Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Ying Zhang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Guangzhou Qu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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Yılmaz İ, Yıldız Ö, Korkmaz F. Structural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy. J Biomol Struct Dyn 2019; 38:2104-2115. [PMID: 31157607 DOI: 10.1080/07391102.2019.1624617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The structural and functional differences between wild type (WT) outer membrane protein G and its two mutants are investigated with Fourier transform infrared spectroscopy. Both mutants have a long extension to the primary sequence to increase the number of β-strands from 14 (wild type) to 16 in an attempt to enlarge the pore diameter. The comparison among proteins is made in terms of pH-dependent conformational changes and thermal stability. Results show that all proteins respond to pH change but at different degrees. At acidic environment, all proteins contain the same number of residues participated in β-sheet structure. However, at neutral pH, the mutants have less ordered structure compared to WT porin. Thermal stability tests show that mutants differ significantly from WT porin at neutral pH. Although the transition temperature is directly proportional with the amount of β-sheet content, the changes in the pre-transition phase that pave the way to structural breakdown are shown to involve interactions among charged residues by two-dimensional correlation spectroscopy analysis. Results of the analysis show that side chain interactions play an active role under increasing temperature. Both mutants have more unordered secondary structure but they respond to pH change in tertiary structure level. Findings of this study provided deeper insight on the active players in structural stability of the WT porin.Communicated by Ramaswamy H. Sarma [Formula: see text].
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Affiliation(s)
- İrem Yılmaz
- Department of Physics, Middle East Technical University, Ankara, Turkey
| | - Özkan Yıldız
- Department of Structural Biology, Max Planck Institute for Biophysics, Frankfurt am Main, Germany
| | - Filiz Korkmaz
- Physics Unit, Biophysics Laboratory, Atilim University, Ankara, Turkey
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Henke K, Welte W, Hauser K. Direct Monitoring of β-Sheet Formation in the Outer Membrane Protein TtoA Assisted by TtOmp85. Biochemistry 2016; 55:4333-43. [PMID: 27400268 DOI: 10.1021/acs.biochem.6b00691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy was applied to investigate the folding of an outer membrane protein, TtoA, assisted by TtOmp85, both from the thermophilic eubacterium Thermus thermophilus. To directly monitor the formation of β-sheet structure in TtoA and to analyze the function of TtOmp85, we immobilized unfolded TtoA on an ATR crystal. Interaction with TtOmp85 initiated TtoA folding as shown by time-dependent spectra recorded during the folding process. Our ATR-FTIR experiments prove that TtOmp85 possesses specific functionality to assist β-sheet formation of TtoA. We demonstrate the potential of this spectroscopic approach to study the interaction of outer membrane proteins in vitro and in a time-resolved manner.
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Affiliation(s)
- Katharina Henke
- Department of Chemistry, ‡Department of Biology, and §Konstanz Research School Chemical Biology, University of Konstanz , 78457 Konstanz, Germany
| | - Wolfram Welte
- Department of Chemistry, ‡Department of Biology, and §Konstanz Research School Chemical Biology, University of Konstanz , 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, ‡Department of Biology, and §Konstanz Research School Chemical Biology, University of Konstanz , 78457 Konstanz, Germany
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IR-spectroscopic characterization of an elongated OmpG mutant. Arch Biochem Biophys 2015; 576:73-9. [DOI: 10.1016/j.abb.2015.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/10/2015] [Accepted: 04/27/2015] [Indexed: 11/22/2022]
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Korkmaz F, Erdogan DA, Özalp-Yaman Ş. Interaction of a novel platinum drug with bovine serum albumin: FTIR and UV-Vis spectroscopy analysis. NEW J CHEM 2015. [DOI: 10.1039/c5nj00785b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Platinum-Blue docks at a hydrophobic cavity at low concentrations with a binding constant comparable to that of cisplatin.
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Affiliation(s)
- Filiz Korkmaz
- Atilim University
- Faculty of Engineering
- Biophysics Laboratory
- Ankara
- Turkey
| | - Deniz Altunoz Erdogan
- Atilim University
- Faculty of Engineering
- Department of Chemical Engineering and Applied Chemistry
- Ankara
- Turkey
| | - Şeniz Özalp-Yaman
- Atilim University
- Faculty of Engineering
- Department of Chemical Engineering and Applied Chemistry
- Ankara
- Turkey
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Li Y, Maurer J, Roth A, Vogel V, Winter E, Mäntele W. A setup for simultaneous measurement of infrared spectra and light scattering signals: watching amyloid fibrils grow from intact proteins. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:084302. [PMID: 25173287 DOI: 10.1063/1.4891704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A setup for the simultaneous measurement of mid-infrared spectra and static light scattering is described that can be used for the analysis of the formation of nanoscale and microscopic aggregates from smaller molecules to biopolymers. It can be easily integrated into sample chambers of infrared spectrometers or combined with laser beams from tunable infrared lasers. Here, its use for the analysis of the formation of amyloid fibrils from intact proteins is demonstrated. The formation of amyloid fibrils or plaques from proteins is a widespread and pathogenetic relevant process, and a number of diseases are caused and correlated with the deposition of amyloid fibrils in cells and tissues. The molecular mechanisms of these transformations, however, are still unclear. We report here the simultaneous measurement of infrared spectra and static light scattering for the analysis of fibril formation from egg-white lysozyme. The transformation of the native form into non-native forms rich in β-sheet structure is measured by analysis of the amide I spectral region in the infrared spectra, which is sensitive for local structures. At the same time, light scattering signals at forward direction as well as the forward/backward ratio, which are sensitive for the number of scattering centers and their approximate sizes, respectively, are collected for the analysis of fibril growth. Thermodynamic and kinetic parameters as well as mechanistic information are deduced from the combination of the two complementary techniques.
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Affiliation(s)
- Yang Li
- Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main, Germany
| | - Jürgen Maurer
- Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main, Germany
| | - Andreas Roth
- Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main, Germany
| | - Vitali Vogel
- Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main, Germany
| | - Ernst Winter
- Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main, Germany
| | - Werner Mäntele
- Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main, Germany
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Zhuang T, Chisholm C, Chen M, Tamm LK. NMR-based conformational ensembles explain pH-gated opening and closing of OmpG channel. J Am Chem Soc 2013; 135:15101-13. [PMID: 24020969 DOI: 10.1021/ja408206e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The outer membrane protein G (OmpG) is a monomeric 33 kDa 14-stranded β-barrel membrane protein functioning as a nonspecific porin for the uptake of oligosaccharides in Escherichia coli. Two different crystal structures of OmpG obtained at different values of pH suggest a pH-gated pore opening mechanism. In these structures, extracellular loop 6 extends away from the barrel wall at neutral pH but is folded back into the pore lumen at low pH, blocking transport through the pore. Loop 6 was invisible in a previously published solution NMR structure of OmpG in n-dodecylphosphocholine micelles, presumably due to conformational exchange on an intermediate NMR time scale. Here we present an NMR paramagnetic relaxation enhancement (PRE)-based approach to visualize the conformational dynamics of loop 6 and to calculate conformational ensembles that explain the pH-gated opening and closing of the OmpG channel. The different loop conformers detected by the PRE ensemble calculations were validated by disulfide cross-linking of strategically engineered cysteines and electrophysiological single channel recordings. The results indicate a more dynamically regulated channel opening and closing than previously thought and reveal additional membrane-associated conformational ensembles at pH 6.3 and 7.0. We anticipate this approach to be generally applicable to detect and characterize functionally important conformational ensembles of membrane proteins.
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Affiliation(s)
- Tiandi Zhuang
- Department of Molecular Physiology and Biological Physics and Center for Membrane Biology, University of Virginia , Charlottesville, Virginia 22903, United States
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Yu M, Sun P, He Y, Xiao L, Sun D, Zhang L, Tian C. Mutation of the critical pH-gating residues histidine 231 to glutamate increase open probability of outer membrane protein G in planar lipid bilayer. Protein Cell 2013; 4:803-6. [PMID: 24018649 DOI: 10.1007/s13238-013-3070-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Mu Yu
- High Magnetic Field Laboratory, Chinese Academic of Sciences, Hefei, 230031, China
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Korkmaz F, Ressl S, Ziegler C, Mäntele W. K+-induced conformational changes in the trimeric betaine transporter BetP monitored by ATR-FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1181-91. [DOI: 10.1016/j.bbamem.2013.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/10/2012] [Accepted: 01/08/2013] [Indexed: 11/28/2022]
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