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Zhu Y, Tian J, Liu S, Li M, Zhao L, Liu W, Zhao G, Liang D, Ma Y, Tu Q. Rapid capture and quantification of food-borne spores based on the double-enhanced Fe 3O 4@PEI@Ag@PEI core-shell structure SERS sensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123512. [PMID: 37864975 DOI: 10.1016/j.saa.2023.123512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 10/08/2023] [Indexed: 10/23/2023]
Abstract
To realize rapid capture and quantification of food-borne spores and prevent their potential harm, Fe3O4@PEI@Ag@PEI core-shell structure nanoparticles were combined with flower-like AgNPs for double enhancement and efficient capture of spores. The developed sensor showed excellent reproducibility and SERS enhancement factor (AEF) is 4.6 × 104. Orthogonal partial least-squares discrimination analysis and linear discriminant analysis accurately identified the three spores (Bacillus subtilis, Bacillus cereus, and Clostridium perfringens), and the qualitative identification accuracy of linear discriminant analysis was 100 %. Efficient enrichment of B. subtilis spores was realized within 5 min, with a detection limit of 3 cfu/mL. Spiked tests revealed that this sensor was effective in detecting spores in milk, orange juice, and water samples, with recovery ratio of 95.2-103.9 % and relative standard deviation of 3.1-7.7 %. Thus, the developed sensor was accurate and reliable, and could achieve rapid identification and quantitative detection of food-borne spores.
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Affiliation(s)
- Yaodi Zhu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China; Henan Jiuyuquan Food Co., LTD., Postdoctoral Innovation Base, Henan Province, Yuanyang 453500, PR China
| | - Jiaqi Tian
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Shijie Liu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Miaoyun Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China.
| | - Lijun Zhao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Weijia Liu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Gaiming Zhao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Dong Liang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China; Henan Jiuyuquan Food Co., LTD., Postdoctoral Innovation Base, Henan Province, Yuanyang 453500, PR China
| | - Yangyang Ma
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Qiancheng Tu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou 450002, PR China
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Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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Zheng X, Yang N, Hou Y, Cai K. Dissecting amide-I vibrations in histidine dipeptide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122424. [PMID: 36750008 DOI: 10.1016/j.saa.2023.122424] [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: 09/27/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The amide-I vibrational characteristics and conformational preferences of the model compound - histidine dipeptide (Ac-His-NHCH3, HISD) in gas phase and solution have been revealed with the help of ab initio calculations and wavefunction analyses. The Gibbs free energy surfaces (FESs) of solvated HISD were smoothed by solvent effect to exhibit different structural populations concerning various external environments. It was shown that the most stable conformations of HISD in CHCl3 and gas phase are C7eq, while those in DMSO and water are β and PPII, respectively. Compared with ALAD, the number of accessible conformational states on these FESs was predicted to be reduced due to the steric effect of imidazole group. The two amide-I normal modes of HISD were found to have intrinsically secondary structural dependencies, and be sensitive to surrounding environments. The average amide-Ia frequencies of HISD isomers in these environments were predicted to be almost the same as those of ALAD, while the amide-Ib mean frequencies were estimated to be lower than ALAD due to the intramolecular interactions between the imidazole group and amino-terminal amide unit. The good linear correlations between amide-I frequencies and the atomic electrostatic potentials (ESPs) of amide groups were also found to interpret the solvent-induced amide-I frequency shifts of HISD at the electronic structure level. These results allow us to gain a deep understanding of amide-I vibrations of HISD, and would be helpful for the site-specific conformational monitoring and spectral interpretation of solvated polypeptides.
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Affiliation(s)
- Xuan Zheng
- College of Chemistry, Chemical Engineering and Environment, Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, PR China.
| | - Nairong Yang
- College of Chemistry, Chemical Engineering and Environment, Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, PR China
| | - Yanjun Hou
- College of Chemistry, Chemical Engineering and Environment, Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, PR China
| | - Kaicong Cai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China; Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, PR China.
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Kamnev AA, Dyatlova YA, Kenzhegulov OA, Fedonenko YP, Evstigneeva SS, Tugarova AV. Fourier Transform Infrared (FTIR) Spectroscopic Study of Biofilms Formed by the Rhizobacterium Azospirillum baldaniorum Sp245: Aspects of Methodology and Matrix Composition. Molecules 2023; 28:molecules28041949. [PMID: 36838937 PMCID: PMC9962177 DOI: 10.3390/molecules28041949] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Biofilms represent the main mode of existence of bacteria and play very significant roles in many industrial, medical and agricultural fields. Analysis of biofilms is a challenging task owing to their sophisticated composition, heterogeneity and variability. In this study, biofilms formed by the rhizobacterium Azospirillum baldaniorum (strain Sp245), isolated biofilm matrix and its macrocomponents have for the first time been studied in detail, using Fourier transform infrared (FTIR) spectroscopy, with a special emphasis on the methodology. The accompanying novel data of comparative chemical analyses of the biofilm matrix, its fractions and lipopolysaccharide isolated from the outer membrane of the cells of this strain, as well as their electrophoretic analyses (SDS-PAGE) have been found to be in good agreement with the FTIR spectroscopic results.
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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Kamnev AA, Dyatlova YA, Kenzhegulov OA, Vladimirova AA, Mamchenkova PV, Tugarova AV. Fourier Transform Infrared (FTIR) Spectroscopic Analyses of Microbiological Samples and Biogenic Selenium Nanoparticles of Microbial Origin: Sample Preparation Effects. Molecules 2021; 26:1146. [PMID: 33669948 PMCID: PMC7924863 DOI: 10.3390/molecules26041146] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/14/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022] Open
Abstract
To demonstrate the importance of sample preparation used in Fourier transform infrared (FTIR) spectroscopy of microbiological materials, bacterial biomass samples with and without grinding and after different drying periods (1.5-23 h at 45 °C), as well as biogenic selenium nanoparticles (SeNPs; without washing and after one to three washing steps) were comparatively studied by transmission FTIR spectroscopy. For preparing bacterial biomass samples, Azospirillum brasilense Sp7 and A. baldaniorum Sp245 (earlier known as A. brasilense Sp245) were used. The SeNPs were obtained using A. brasilense Sp7 incubated with selenite. Grinding of the biomass samples was shown to result in slight downshifting of the bands related to cellular poly-3-hydroxybutyrate (PHB) present in the samples in small amounts (under ~10%), reflecting its partial crystallisation. Drying for 23 h was shown to give more reproducible FTIR spectra of bacterial samples. SeNPs were shown to contain capping layers of proteins, polysaccharides and lipids. The as-prepared SeNPs contained significant amounts of carboxylated components in their bioorganic capping, which appeared to be weakly bound and were largely removed after washing. Spectroscopic characteristics and changes induced by various sample preparation steps are discussed with regard to optimising sample treatment procedures for FTIR spectroscopic analyses of microbiological specimens.
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Affiliation(s)
- Alexander A. Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia; (Y.A.D.); (O.A.K.); (A.A.V.); (P.V.M.); (A.V.T.)
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