1
|
Sun NN, Xu QF, Yang MD, Li YN, Liu H, Tantai W, Shu GW, Li GL. A high-throughput differential scanning fluorimetry method for rapid detection of thermal stability and iron saturation in lactoferrin. Int J Biol Macromol 2024; 267:131285. [PMID: 38583841 DOI: 10.1016/j.ijbiomac.2024.131285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/09/2024]
Abstract
Thermal stability and iron saturation of lactoferrin (LF) are of great significance not only for the evaluation of the biological activities of LF but also for the optimization of the isolation and drying process parameters. Differential scanning calorimetry (DSC) is a well-established and efficient method for thermal stability and iron saturation detection in LF. However, multiple DSC measurements are typically performed sequentially, thus time-consuming and low throughput. Herein, we introduced the differential scanning fluorimetry (DSF) approach to overcome such limitations. The DSF can monitor LF thermal unfolding with a commonly available real-time PCR instrument and a fluorescent dye (SYPRO orange or Glomelt), and the measured melting temperature of LF is consistent with that determined by DSC. On the basis of that, a new quantification method was established for determination of iron saturation levels using the linear correlation of the degree of ion saturation of LF with DSF measurements. Such DSF method is simple, inexpensive, rapid (<15 min), and high throughput (>96 samples per experiment), and provides a valuable alternative tool for thermal stability detection of LF and other whey proteins.
Collapse
Affiliation(s)
- Na-Na Sun
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Qin-Feng Xu
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China.
| | - Meng-di Yang
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Yan-Ni Li
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Hao Liu
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Wei Tantai
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guo-Wei Shu
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guo-Liang Li
- School of Food Science and Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| |
Collapse
|
2
|
Zheng L, Zhou B, Yang Y, Zan B, Zhong B, Wu B, Feng Y, Liu Q, Hong L. Mn 2+-induced structural flexibility enhances the entire catalytic cycle and the cleavage of mismatches in prokaryotic argonaute proteins. Chem Sci 2024; 15:5612-5626. [PMID: 38638240 PMCID: PMC11023060 DOI: 10.1039/d3sc06221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/01/2024] [Indexed: 04/20/2024] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicate that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.
Collapse
Affiliation(s)
- Lirong Zheng
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Department of Cell and Developmental Biology & Michigan Neuroscience Institute, University of Michigan Medical School 48105 Ann Arbor MI USA
| | - Bingxin Zhou
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
| | - Yu Yang
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bing Zan
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bozitao Zhong
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Banghao Wu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Feng
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Liu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
| |
Collapse
|
3
|
Niidome Y, Wakabayashi R, Goto M, Fujigaya T, Shiraki T. Protein-structure-dependent spectral shifts of near-infrared photoluminescence from locally functionalized single-walled carbon nanotubes based on avidin-biotin interactions. NANOSCALE 2022; 14:13090-13097. [PMID: 35938498 DOI: 10.1039/d2nr01440h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) emit photoluminescence (PL) in the near-infrared (NIR) region (>900 nm). To enhance their PL properties, defect doping via local chemical functionalization has been developed. The locally functionalized SWCNTs (lf-SWCNTs) emit red-shifted and bright E11* PL originating from the excitons localized at the defect-doped sites. Here, we observe the E11* PL energy shifts induced by protein adsorption via the avidin-biotin interactions at the doped sites of lf-SWCNTs. We establish that the difference in the structures of the avidin derivatives notably influences the energy shifts. First, lf-SWCNT-tethering biotin groups (lf-SWCNTs-b) are synthesized based on diazonium chemistry, followed by post-modification. The responsiveness of the lf-SWCNTs-b to different microenvironments is investigated, and a correlation between the E11* PL energy shift and the induction-polarity parameters of surrounding solvents is established. The adsorption of neutravidin onto the lf-SWCNTs-b induces an increase in the induction-polarity parameters around the biotin-doped sites, resulting in the red-shift of the E11* PL peak. The E11* PL shift behaviors of the lf-SWCNTs-b change noticeably when avidin and streptavidin are introduced compared to the case with neutravidin. This is due to the different microenvironments formed at the biotin-doped sites, attributed to the difference in the structural features of the introduced avidin derivatives. Moreover, we successfully enhance the detection signals of lf-SWCNTs-b (>three fold) for streptavidin detection using a fabricated film device. Therefore, lf-SWCNTs exhibit significant promise for application in advanced protein detection/recognition devices based on NIR PL.
Collapse
Affiliation(s)
- Yoshiaki Niidome
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
- Center for Future Chemistry (CFC), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tsuyohiko Fujigaya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Center for Molecular Systems (CMS), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomohiro Shiraki
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
4
|
Andrade UMS, Castro ASB, Oliveira PHF, da Silva LHM, Rocha MS. Imidazolium-based ionic liquids binding to DNA: Mechanical effects and thermodynamics of the interactions. Int J Biol Macromol 2022; 214:500-511. [PMID: 35714872 DOI: 10.1016/j.ijbiomac.2022.06.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
We performed a robust characterization of the molecular interactions between the DNA molecule and two imidazolium-based ionic liquids (ILs): 1-Butyl-3-methylimidazolium chloride ([bmim]Cl) and 1-Octyl-3-methylimidazolium chloride ([omim]Cl), using single molecule approaches (optical and magnetic tweezers) and bulk techniques (isothermal titration calorimetry and conductivity measurements). Optical and magnetic tweezers allowed us to obtain the changes on the mechanical properties of the DNA complexes formed with both ILs, as well as the relevant physicochemical (binding) parameters of the interaction. Despite the weak binding measured between DNA and the two ILs, we identify a transition on the regime of polymer elasticity of the complexes formed, which results in a relevant DNA compaction for high IL concentrations. In addition, isothermal titration calorimetry and conductivity complemented the single molecule investigation, giving a complete thermodynamic characterization of the interactions and allowing the identification of the most relevant driving forces at various different concentration ranges of the ILs. Based on the results obtained with all the employed techniques, we propose a model for the binding schemes involving DNA and both [bmim]Cl and [omim]Cl.
Collapse
Affiliation(s)
- U M S Andrade
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Departamento de Formação Geral, Centro Federal de Educação Tecnológica de Minas Gerais, Curvelo, Minas Gerais, Brazil.
| | - A S B Castro
- Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - P H F Oliveira
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - L H M da Silva
- Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
5
|
de Castro ASB, de Paula HMC, Coelho YL, Hudson EA, Pires ACS, da Silva LHM. Kinetic and thermodynamic of lactoferrin - Ethoxylated-nonionic surfactants supramolecular complex formation. Int J Biol Macromol 2021; 187:325-331. [PMID: 34280448 DOI: 10.1016/j.ijbiomac.2021.07.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 11/19/2022]
Abstract
Understanding nonionic surfactant-protein interactions is fundamental from both technological and scientific points of view. However, there is a complete absence of kinetic data for such interactions. We employed surface plasmon resonance (SPR) to determine the kinetic and thermodynamic parameters of bovine lactoferrin-Brij58 interactions at various temperatures under physiological conditions (pH 7.4). The adsorption process was accelerated with increasing temperature, while the desorption rate decreased, resulting in a more thermodynamically stable complex. The kinetic energetic parameters obtained for the formation of the activated complex, [bLF-Brij58]‡, indicated that the potential energy barrier for [bLF-Brij58]‡ formation arises primarily from the reduction in system entropy. [bLF-Brij58]○ formation was entropically driven, indicating that hydrophobic interactions play a fundamental role in bLF interactions with Brij58.
Collapse
Affiliation(s)
- Alan Stampini Benhame de Castro
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Hauster Maximiler Campos de Paula
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Yara Luiza Coelho
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil; Colloid Chemistry Group, Chemistry Institute, Federal University of Alfenas (UNIFAL-MG), Rua Gabriel Monteiro da Silva, 700, 37130-000 Alfenas, MG, Brazil
| | - Eliara Acipreste Hudson
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Ana Clarissa S Pires
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Luis Henrique M da Silva
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil.
| |
Collapse
|
6
|
Hu L, Wu L, Lai C, Li M, Yang W. The influence of pH and concentration on the zeta potential, hydrophobicity of OVT and the relationship between its structure and interfacial behaviors. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2021.1880431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Linfang Hu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Leiyan Wu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Chanjuan Lai
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Mingliang Li
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Wuying Yang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
7
|
Lactoferrin-phenothiazine dye interactions: Thermodynamic and kinetic approach. Int J Biol Macromol 2019; 136:559-569. [DOI: 10.1016/j.ijbiomac.2019.06.097] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/31/2019] [Accepted: 06/13/2019] [Indexed: 01/12/2023]
|
8
|
Srivastava R, Alam MS. Role of (single/double chain surfactant) micelles on the protein aggregation. Int J Biol Macromol 2019; 122:72-81. [DOI: 10.1016/j.ijbiomac.2018.10.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022]
|