1
|
Savarino P, Demeyer M, Decroo C, Colson E, Gerbaux P. Mass spectrometry analysis of saponins. MASS SPECTROMETRY REVIEWS 2023; 42:954-983. [PMID: 34431118 DOI: 10.1002/mas.21728] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 05/26/2023]
Abstract
Saponins are amphiphilic molecules of pharmaceutical interest and most of their biological activities (i.e., cytotoxic, hemolytic, fungicide, etc.) are associated to their membranolytic properties. These molecules are secondary metabolites present in numerous plants and in some marine animals, such as sea cucumbers and starfishes. Structurally, all saponins correspond to the combination of a hydrophilic glycan, consisting of sugar chain(s), linked to a hydrophobic triterpenoidic or steroidic aglycone, named the sapogenin. Saponins present a high structural diversity and their structural characterization remains extremely challenging. Ideally, saponin structures are best established using nuclear magnetic resonance experiments conducted on isolated molecules. However, the extreme structural diversity of saponins makes them challenging from a structural analysis point of view since, most of the time, saponin extracts consist in a huge number of congeners presenting only subtle structural differences. In the present review, we wish to offer an overview of the literature related to the development of mass spectrometry for the study of saponins. This review will demonstrate that most of the past and current mass spectrometry methods, including electron, electrospray and matrix-assisted laser desorption/ionization ionizations, gas/liquid chromatography coupled to (tandem) mass spectrometry, collision-induced dissociation including MS3 experiments, multiple reaction monitoring based quantification, ion mobility experiments, and so forth, have been used for saponin investigations with great success on enriched extracts but also directly on tissues using imaging methods.
Collapse
Affiliation(s)
- Philippe Savarino
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Marie Demeyer
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Corentin Decroo
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Emmanuel Colson
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| |
Collapse
|
2
|
Du Y, Du Y, Cui M, Liu Z. Characterization of the Noncovalent Interactions between Lysozyme and Panaxadiol Glycosides by Intensity-Fading – Matrix-Assisted Laser Desorption Ionization – Mass Spectrometry (IF-MALDI-MS). ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1867995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yonggang Du
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Yang Du
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Science and Technology of China, Hefei, Anhui, China
| |
Collapse
|
3
|
Yang S, Guo Q, Wu F, Chu Y, Wang Y, Zhou M, Ding CF. Investigation of noncovalent interactions between peptides with potential intrinsic sequence patterns by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8736. [PMID: 32040870 DOI: 10.1002/rcm.8736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE The conformation of a protein largely depends on the interactions between peptides. Specific and intrinsic sequence peptide patterns, such as DNA double helix backbones, may be present in proteins. A computational statistical deep learning method has supported this assumption, but it has not been experimentally proven. Mass spectrometry, as a fast and accurate experimental method, could be used to evaluate the interaction of biomolecules. The results would be of great value for further study of the mechanism of protein folding. METHODS Several potential intrinsic peptides were chosen by the deep learning method, including seven groups of pentapeptides and five groups of nonapeptides. The noncovalent interactions between mixed polypeptides were investigated by electrospray ionization mass spectrometry (ESI-MS) in full-scan and collision-induced dissociation (CID) modes. Molecular dynamics and molecular mechanics Poisson-Boltzmann surface area (MD-MM/PBSA) analyses were also performed to support the results. RESULTS The ESI-MS spectra showed that 11 of the 12 groups of mixed polypeptides formed binary and ternary complexes with relatively high stability. The binding between nonapeptide groups was stronger than that between pentapeptide groups according to the relative intensity. The binding energies calculated by the MM/PBSA binding energy tool also provided strong evidence for the combination of the complexes. Electrostatic interactions, hydrophobic interactions, and van der Waals forces were thought to stabilize the complexes according to the binding models. CONCLUSIONS The results implied the formation of stable complexes between polypeptides and identified their noncovalent interactions, proving that specific sequences and combinations with relatively strong binding ability exist in potential intrinsic sequences of peptides in protein structures.
Collapse
Affiliation(s)
- Shutong Yang
- Laser Chemistry Institute, Department of Chemistry, Fudan University, Handan Road No. 220, Shanghai, 200433, China
| | - Qi Guo
- Laser Chemistry Institute, Department of Chemistry, Fudan University, Handan Road No. 220, Shanghai, 200433, China
| | - Fangling Wu
- Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, No 818 Fenghua Rd, Ningbo, Zhejiang, 315211, China
| | - Yanqiu Chu
- Laser Chemistry Institute, Department of Chemistry, Fudan University, Handan Road No. 220, Shanghai, 200433, China
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Bethesda, MD, 20850, USA
| | - Mingfei Zhou
- Laser Chemistry Institute, Department of Chemistry, Fudan University, Handan Road No. 220, Shanghai, 200433, China
| | - Chuan-Fan Ding
- Laser Chemistry Institute, Department of Chemistry, Fudan University, Handan Road No. 220, Shanghai, 200433, China
- Institute of Mass Spectrometry, School of Materials Science & Chemical Engineering, Ningbo University, No 818 Fenghua Rd, Ningbo, Zhejiang, 315211, China
| |
Collapse
|
4
|
Chi Q, Zhang W, Wang L, Huang J, Yuan M, Xiao H, Wang X. Evaluation of structurally different brominated flame retardants interacting with the transthyretin and their toxicity on HepG2 cells. CHEMOSPHERE 2020; 246:125749. [PMID: 31927367 DOI: 10.1016/j.chemosphere.2019.125749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 05/03/2023]
Abstract
Brominated flame retardants (BFRs) are found at quantifiable levels in both humans and wildlife and may potentially cause a health risk. For BFRs and their derivatives, limited information regarding the relationship among the structure, binding affinity to the target protein and toxicity is currently available. In the present work, representative BFRs with different hydroxyl- or bromo-substituents, namely 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47), 3-hydroxy-2, 2', 4, 4'-tetrabromodiphenyl ether (3-OH-BDE-47) and tetrabromobisphenol A (TBBPA), were selected to investigate the interactions with transthyretin (TTR) by electrospray ionization mass spectrometry (ESI-MS) and cytotoxicity on HepG2 cells. It was noted that BDE-47 had a weak binding affinity to TTR, while 3-OH-BDE-47 and TBBPA had a stronger binding affinity than BDE-47 and thyroxine (T4). Hence, 3-OH-BDE-47 and TBBPA could affect the binding of TTR with its native ligand T4 by competitive binding to TTR, even at equal concentrations, which might be associated with BFR toxicity of endocrine disruption. Negative cooperativity was found for 3-OH-BDE-47 and TBBPA binding to TTR, similar to T4 with a well-established negatively cooperative binding mechanism. The tendency of toxic effects on HepG2 cells for these three BFRs was, 3-OH-BDE-47 > TBBPA > BDE-47, and this order was in good agreement with the binding ability explored by ESI-MS experiments and molecular docking simulation. The observations obtained by this study demonstrate that the binding properties of these BFRs to TTR and their cytotoxicity are correlated with structure differentials and functional substituents.
Collapse
Affiliation(s)
- Quan Chi
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Wenxiang Zhang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Lang Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Juan Huang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Ming Yuan
- College of Life Science and Technology, Huazhong University of Science and Technology, China
| | - Huaming Xiao
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China.
| |
Collapse
|
5
|
Chi Q, Liu YZ, Wang X. Study on the Structural Effect of Maltoligosaccharides on Cytochrome c Complexes Stabilities by Native Mass Spectrometry. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:57-61. [PMID: 29380206 PMCID: PMC5803145 DOI: 10.1007/s13659-017-0150-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/13/2017] [Indexed: 05/05/2023]
Abstract
Noncovalent interactions between ligands and targeting proteins are essential for understanding molecular mechanisms of proteins. In this work, we investigated the interaction of Cytochrome c (Cyt c) with maltoligosaccharides, namely maltose (Mal II), maltotriose (Mal III), maltotetraose (Mal IV), maltopentaose (Mal V), maltohexaose (Mal VI) and maltoheptaose (Mal VII). Using electrospray ionization mass spetrometry (ESI-MS) assay, the 1:1 and 1:2 complexes formed by Cyt c with maltoligosaccharide ligand were observed. The corresponding association constants were calculated according to the deconvoluted spectra. The order of the relative binding affinities of the selected oligosaccharides with Cyt c were as Mal III > Mal IV > Mal II > Mal V > Mal VI > Mal VII. The results indicated that the stability of noncovalent protein complexes was intimately correlated to the molecular structure of bound ligand. The relevant functional groups that could form H-bonds, electrostatic or hydrophobic forces with protein's amino residues played an important role for the stability of protein complexes. In addition, the steric structure of ligand was also critical for an appropriate interaction with the binding pocket of proteins.
Collapse
Affiliation(s)
- Quan Chi
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, People's Republic of China
| | - Ying-Zhi Liu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, People's Republic of China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, People's Republic of China.
| |
Collapse
|
6
|
Wang B, Qin Q, Chang M, Li S, Shi X, Xu G. Molecular interaction study of flavonoids with human serum albumin using native mass spectrometry and molecular modeling. Anal Bioanal Chem 2017; 410:827-837. [PMID: 28840311 DOI: 10.1007/s00216-017-0564-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/30/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022]
Abstract
Noncovalent interactions between proteins and small-molecule ligands widely exist in biological bodies and play significant roles in many physiological and pathological processes. Native mass spectrometry (MS) has emerged as a new powerful tool to study noncovalent interactions by directly analyzing the ligand-protein complexes. In this work, an ultrahigh-resolution native MS method based on a 15-T SolariX XR Fourier transform ion cyclotron resonance mass spectrometer was firstly used to investigate the interaction between human serum albumin (HSA) and flavonoids. Various flavonoids with similar structure were selected to unravel the relationship between the structure of flavonoids and their binding affinity for HSA. It was found that the position of the hydroxyl groups and double bond of flavonoids could influence the noncovalent interaction. Through a competitive experiment between HSA binding site markers and apigenin, the subdomain IIA (site 1) of HSA was determined as the binding site for flavonoids. Moreover, a cooperative allosteric interaction between apigenin and ibuprofen was found from their different HSA binding sites, which was further verified by circular dichroism spectroscopy and molecular docking studies. These results show that native MS is a useful tool to investigate the molecular interaction between a protein and its ligands. Graphical abstract Unravel the relationship between the structure of flavonoids and their binding affinity to HSA by native MS.
Collapse
Affiliation(s)
- Bohong Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengmeng Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyan Li
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| |
Collapse
|
7
|
Abstract
Using high-resolution mass spectrometry, we have studied the synthesis of isoquinoline in a charged electrospray droplet and the complexation between cytochrome c and maltose in a fused droplet to investigate the feasibility of droplets to drive reactions (both covalent and noncovalent interactions) at a faster rate than that observed in conventional bulk solution. In both the cases we found marked acceleration of reaction, by a factor of a million or more in the former and a factor of a thousand or more in the latter. We believe that carrying out reactions in microdroplets (about 1–15 μm in diameter corresponding to 0·5 pl – 2 nl) is a general method for increasing reaction rates. The mechanism is not presently established but droplet evaporation and droplet confinement of reagents appear to be two important factors among others. In the case of fused water droplets, evaporation has been shown to be almost negligible during the flight time from where droplet fusion occurs and the droplets enter the heated capillary inlet of the mass spectrometer. This suggests that (1) evaporation is not responsible for the acceleration process in aqueous droplet fusion and (2) the droplet–air interface may play a significant role in accelerating the reaction. We argue that this ‘microdroplet chemistry’ could be a remarkable alternative to accelerate slow and difficult reactions, and in conjunction with mass spectrometry, it may provide a new arena to study chemical and biochemical reactions in a confined environment.
Collapse
|
8
|
Luo H, Li C, Fang H, Wang X. Comparative study of the interactions between bisphenol analogues and serum albumins by electrospray mass spectrometry and fluorescence spectroscopy. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30 Suppl 1:162-167. [PMID: 27539432 DOI: 10.1002/rcm.7633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RATIONALE Bisphenol A and its alternatives are widely used in common consumer products and are known as environmental endocrine disrupting chemicals. Five bisphenol analogues, namely, tetrabromobisphenol A (TBBPA), tetrachlorobisphenol A (TCBPA), 4,4'-sulfonyldiphenol (BPS), bisphenol A (BPA) and 4,4'-hexafluoroisopropylidenediphenol (BPAF), were selected to study their interactions with serum albumins, aiming at a better understanding of the toxicological mechanisms of bisphenol compounds. METHODS The interactions between human and bovine serum albumins (HSA and BSA) with these five compounds were investigated by electrospray ionization mass spectrometry (ESI-MS). Fluorescence spectroscopy and molecular docking confirmed the ESI-MS observations and provided complementary information with respect to thermodynamic properties and binding modes. RESULTS TBBPA showed the highest binding ability with HSA and BSA, followed by TBBPA and BPS, whereas BPA and BPAF exhibited little or no binding with these serum albumins. The calculated thermodynamic parameters suggested that hydrogen bonds and electrostatic forces played important roles for these interactions. Binding energies of TBBPA, TCBPA, and BPS calculated by molecular docking were -35.18, -34.39, and -25.89 kJ mol(-1) , respectively, in good agreement with ESI-MS measurements. CONCLUSIONS The results of this study showed that halogenated substituents on the phenolic rings of bisphenol could enhance the binding ability with serum albumins. This work could provide useful information for further research on the relationship between molecular structures and toxicities of bisphenols. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Huangshi Luo
- Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Chunya Li
- Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Huaifang Fang
- Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| | - Xian Wang
- Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, China
| |
Collapse
|
9
|
Tang J, Fu Q, Cui M, Xing J, Liu Z, Liu S. Study of the non-covalent interactions of ginsenosides and lysozyme using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2031-8. [PMID: 26443403 DOI: 10.1002/rcm.7366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/18/2015] [Accepted: 08/18/2015] [Indexed: 05/21/2023]
Abstract
RATIONALE Ginsenosides are an important class of natural products extracted from ginseng that possess various important biological activities. Studies of interactions of ginsenosides with proteins are essential for comprehensive understanding of the biological activities of ginsenosides. In this study, the interactions of ginsenosides with lysozyme were investigated by electrospray ionization mass spectrometry (ESI-MS). METHODS Both protopanaxadiol-type and protopanaxatriol-type ginsenosides were chosen to explore the interactions of ginsenosides towards lysozyme near the physiological conditions by direct ESI-MS, respectively. Comparative experiments were conducted to confirm the interactions were specific. In addition, the dissociation constants of ginsenoside-lysozyme complexes were determined by a ESI-MS titration strategy. RESULTS The results showed ginsenosides bound to lysozyme at the stoichiometries of 1:1 and 2:1. The association constants of ginsenosides to lysozyme were in the order of Re>Rd>Rf>Rg2 >Rg3 . According to their structures, the binding affinities associated with the type of aglycone and the type and the number of sugar moieties linked on the aglycone. CONCLUSIONS It has been demonstrated that ESI-MS is a powerful tool to probe the non-covalent interactions between lysozyme and ginsenosides. These results provide insights into the interaction of ginsenosides with lysozyme at the molecular level. The developed strategy could be applied to determine the interactions of proteins with other natural products.
Collapse
Affiliation(s)
- Jun Tang
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Qiang Fu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Meng Cui
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
| | - Junpeng Xing
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
| | - Shuying Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- Changchun University of Chinese Medicine, Changchun, 130117, China
| |
Collapse
|
10
|
Buth SA, Menin L, Shneider MM, Engel J, Boudko SP, Leiman PG. Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4. Viruses 2015; 7:4676-706. [PMID: 26295253 PMCID: PMC4576200 DOI: 10.3390/v7082839] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 12/22/2022] Open
Abstract
Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.
Collapse
Affiliation(s)
- Sergey A Buth
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
| | - Laure Menin
- Service de Spectrométrie de Masse, ISIC, EPFL, BCH 1520, 1015 Lausanne, Switzerland.
| | - Mikhail M Shneider
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Jürgen Engel
- Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
| | - Sergei P Boudko
- Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
- The Research Department, Shriner's Hospital for Children, 3101 Sam Jackson Park Road, Portland, OR 97239, USA.
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Petr G Leiman
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
| |
Collapse
|
11
|
Darabi F, Marzo T, Massai L, Scaletti F, Michelucci E, Messori L. Reactions of model proteins with aurothiomalate, a clinically established gold(I) drug: The comparison with auranofin. J Inorg Biochem 2015; 149:102-7. [DOI: 10.1016/j.jinorgbio.2015.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/20/2015] [Accepted: 03/24/2015] [Indexed: 12/18/2022]
|
12
|
Sharon M, Horovitz A. Probing allosteric mechanisms using native mass spectrometry. Curr Opin Struct Biol 2015; 34:7-16. [PMID: 26005781 DOI: 10.1016/j.sbi.2015.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 11/16/2022]
Abstract
Native mass spectrometry (MS) and ion mobility MS provide a way to discriminate between various allosteric mechanisms that cannot be distinguished using ensemble measurements of ligand binding in bulk protein solutions. Native MS, which yields mass measurements of intact assemblies, can be used to determine the values of ligand binding constants of multimeric allosteric proteins, thereby providing a way to distinguish, for example, between concerted and sequential allosteric models. Native MS can also be employed to study cooperativity owing to ligand-modulated protein oligomerization. The rotationally averaged cross-section areas of complexes obtained by ion mobility MS can be used to distinguish between induced fit and conformational selection. Native MS and its allied techniques are, therefore, becoming increasingly powerful tools for dissecting allosteric mechanisms.
Collapse
Affiliation(s)
- Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
13
|
Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
| | | |
Collapse
|
14
|
Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
15
|
Wang X, Liu Y, Wang H. A structure-differential binding method for elucidating the interactions between flavonoids and cytochrome-c by ESI-MS and molecular docking. Talanta 2013; 116:368-75. [DOI: 10.1016/j.talanta.2013.05.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/06/2013] [Accepted: 05/28/2013] [Indexed: 01/26/2023]
|