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Sun H, Liao F, Tian Y, Lei Y, Fu Y, Wang J. Molecular-Scale Investigations Reveal the Effect of Natural Polyphenols on BAX/Bcl-2 Interactions. Int J Mol Sci 2024; 25:2474. [PMID: 38473728 DOI: 10.3390/ijms25052474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Apoptosis signaling controls the cell cycle through the protein-protein interactions (PPIs) of its major B-cell lymphoma 2-associated x protein (BAX) and B-cell lymphoma 2 protein (Bcl-2). Due to the antagonistic function of both proteins, apoptosis depends on a properly tuned balance of the kinetics of BAX and Bcl-2 activities. The utilization of natural polyphenols to regulate the binding process of PPIs is feasible. However, the mechanism of this modulation has not been studied in detail. Here, we utilized atomic force microscopy (AFM) to evaluate the effects of polyphenols (kaempferol, quercetin, dihydromyricetin, baicalin, curcumin, rutin, epigallocatechin gallate, and gossypol) on the BAX/Bcl-2 binding mechanism. We demonstrated at the molecular scale that polyphenols quantitatively affect the interaction forces, kinetics, thermodynamics, and structural properties of BAX/Bcl-2 complex formation. We observed that rutin, epigallocatechin gallate, and baicalin reduced the binding affinity of BAX/Bcl-2 by an order of magnitude. Combined with surface free energy and molecular docking, the results revealed that polyphenols are driven by multiple forces that affect the orientation freedom of PPIs, with hydrogen bonding, hydrophobic interactions, and van der Waals forces being the major contributors. Overall, our work provides valuable insights into how molecules tune PPIs to modulate their function.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Fenghui Liao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yichen Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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2
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Yu L, Wang R, Li S, Kara UI, Boerner EC, Chen B, Zhang F, Jian Z, Li S, Liu M, Wang Y, Liu S, Yang Y, Wang C, Zhang W, Yao Y, Wang X, Wang C. Experimental Insights into Conformational Ensembles of Assembled β-Sheet Peptides. ACS CENTRAL SCIENCE 2023; 9:1480-1487. [PMID: 37521785 PMCID: PMC10375872 DOI: 10.1021/acscentsci.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Indexed: 08/01/2023]
Abstract
Deciphering the conformations and interactions of peptides in their assemblies offers a basis for guiding the rational design of peptide-assembled materials. Here we report the use of scanning tunneling microscopy (STM), a single-molecule imaging method with a submolecular resolution, to distinguish 18 types of coexisting conformational substates of the β-strand of the 8-37 segment of human islet amyloid polypeptide (hIAPP 8-37). We analyzed the pairwise peptide-peptide interactions in the hIAPP 8-37 assembly and found 82 interconformation interactions within a free energy difference of 3.40 kBT. Besides hIAPP 8-37, this STM method validates the existence of multiple conformations of other β-sheet peptide assemblies, including mutated hIAPP 8-37 and amyloid-β 42. Overall, the results reported in this work provide single-molecule experimental insights into the conformational ensemble and interpeptide interactions in the β-sheet peptide assembly.
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Affiliation(s)
- Lanlan Yu
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Ruonan Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shucong Li
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts, 02138, United States
| | - Ufuoma I. Kara
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eric C. Boerner
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Boyuan Chen
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Feiyi Zhang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
- Institute
for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, People’s
Republic of China
| | - Zhongyi Jian
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shuyuan Li
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Mingwei Liu
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Yang Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Shuli Liu
- Department
of Clinical Laboratory, Peking University
Civil Aviation School of Clinical Medicine, Beijing 100123, People’s Republic of China
| | - Yanlian Yang
- CAS Key Laboratory
of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory
of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience,
CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology, Beijing 100190, People’s Republic
of China
| | - Chen Wang
- CAS Key Laboratory
of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory
of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience,
CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology, Beijing 100190, People’s Republic
of China
| | - Wenbo Zhang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
| | - Yuxing Yao
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xiaoguang Wang
- William
G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Sustainability
Institute, The Ohio State University, Columbus, Ohio, 43210, United
States
| | - Chenxuan Wang
- State
Key Laboratory of Common Mechanism Research for Major Diseases, Haihe
Laboratory of Cell Ecosystem, Department of Biophysics and Structural
Biology, Institute of Basic Medical Sciences,
Chinese Academy of Medical Sciences, School of Basic Medicine Peking
Union Medical College, Beijing 100005, People’s
Republic of China
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3
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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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4
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2020; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease. Methods to study structure, toxicity, and kinetics of transient amyloid oligomers. NMR and single particle methods can characterize lowly-populated oligomers. Chemical tools/antibodies stabilize oligomers for structural and toxicity studies A combination of methods is needed to fully characterize amyloid assembly pathways.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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5
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Karanji AK, Beasely M, Sharif D, Ranjbaran A, Legleiter J, Valentine SJ. Investigating the interactions of the first 17 amino acid residues of Huntingtin with lipid vesicles using mass spectrometry and molecular dynamics. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4470. [PMID: 31756784 PMCID: PMC7342490 DOI: 10.1002/jms.4470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/04/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
The first 17 amino acid residues of Huntingtin protein (Nt17 of htt) are thought to play an important role in the protein's function; Nt17 is one of two membrane binding domains in htt. In this study the binding ability of Nt17 peptide with vesicles comprised of two subclasses of phospholipids is studied using electrospray ionization - mass spectrometry (ESI-MS) and molecular dynamics (MD) simulations. Overall, the peptide is shown to have a greater propensity to interact with vesicles of phosphatidylcholine (PC) rather than phosphatidylethanolamine (PE) lipids. Mass spectra show an increase in lipid-bound peptide adducts where the ordering of the number of such specie is 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) > 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) > 1-palmitoyl-2-oleoyl-sn-glycero-3 phosphoethanolamine (POPE). MD simulations suggest that the compactness of the bilayer plays a role in governing peptide interactions. The peptide shows greater disruption of the DOPC bilayer order at the surface and interacts with the hydrophobic tails of lipid molecules via hydrophobic residues. Conversely, the POPE vesicle remains ordered and lipids display transient interactions with the peptide through the formation of hydrogen bonds with hydrophilic residues. The POPC system displays intermediate behavior with regard to the degree of peptide-membrane interaction. Finally, the simulations suggest a helix stabilizing effect resulting from the interactions between hydrophobic residues and the lipid tails of the DOPC bilayer.
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Affiliation(s)
- Ahmad Kiani Karanji
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26506
| | - Maryssa Beasely
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26506
| | - Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26506
| | - Ali Ranjbaran
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown WV 26506
| | - Justin Legleiter
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26506
- Blanchette Rockefeller Neurosciences Institute, Robert C. Byrd Health Sciences Center, P.O. Box 9304, West Virginia University, Morgantown, West Virginia 26506, United States
- NanoSAFE, P.O. Box 6223, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26506
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6
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Kakinen A, Xing Y, Arachchi NH, Javed I, Feng L, Faridi A, Douek AM, Sun Y, Kaslin J, Davis TP, Higgins MJ, Ding F, Ke PC. Single-Molecular Heteroamyloidosis of Human Islet Amyloid Polypeptide. NANO LETTERS 2019; 19:6535-6546. [PMID: 31455083 PMCID: PMC6742555 DOI: 10.1021/acs.nanolett.9b02771] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Human amyloids and plaques uncovered post mortem are highly heterogeneous in structure and composition, yet literature concerning the heteroaggregation of amyloid proteins is extremely scarce. This knowledge deficiency is further exacerbated by the fact that peptide delivery is a major therapeutic strategy for targeting their full-length counterparts associated with the pathologies of a range of human diseases, including dementia and type 2 diabetes (T2D). Accordingly, here we examined the coaggregation of full-length human islet amyloid polypeptide (IAPP), a peptide associated with type 2 diabetes, with its primary and secondary amyloidogenic fragments 19-29 S20G and 8-20. Single-molecular aggregation dynamics was obtained by high-speed atomic force microscopy, augmented by transmission electron microscopy, X-ray diffraction, and super-resolution stimulated emission depletion microscopy. The coaggregation significantly prolonged the pause phase of fibril elongation, increasing its dwell time by 3-fold. Surprisingly, unidirectional elongation of mature fibrils, instead of protofilaments, was observed for the coaggregation, indicating a new form of tertiary protein aggregation unknown to existing theoretical models. Further in vivo zebrafish embryonic assay indicated improved survival and hatching, as well as decreased frequency and severity of developmental abnormalities for embryos treated with the heteroaggregates of IAPP with 19-29 S20G, but not with 8-20, compared to the control, indicating the therapeutic potential of 19-29 S20G against T2D.
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Affiliation(s)
- Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Nuwan Hegoda Arachchi
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Innovation Campus, Squires Way, NSW 2522, Australia
| | - Ibrahim Javed
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Lei Feng
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Innovation Campus, Squires Way, NSW 2522, Australia
| | - Ava Faridi
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Alon M. Douek
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J. Higgins
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Innovation Campus, Squires Way, NSW 2522, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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