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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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Sun H, Tian Y, Fu Y, Lei Y, Wang Y, Yan X, Wang J. Single-molecule scale quantification reveals interactions underlying protein-protein interface: from forces to non-covalent bonds. Phys Chem Chem Phys 2023; 25:31791-31803. [PMID: 37966041 DOI: 10.1039/d3cp04351g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Protein-protein interactions (PPIs) between the B-cell lymphoma 2 (Bcl-2) family are considered a major driving force in cell cycle regulation and signaling. However, how this interfacial noncovalent interaction is achieved molecularly remains poorly understood. Herein, anti-apoptotic protein (Bcl-2) and pro-apoptotic protein (BAX) were used as models and their PPIs were explored for the first time using atomic force microscopy-based single-molecule force spectroscopy (SMFS) and in silico approaches. In addition, we used advanced analytical models, including multiple kinetic models, thermodynamic models, Poisson distributions, and contact angle molecular recognition to fully reveal the complexity of the BAX/Bcl-2 interaction interfaces. We propose that the binding kinetics between BAX/Bcl-2 are mainly mediated by specific (hydrogen bonding) and non-specific forces (hydrophobic interactions and electrostatic interactions) and show that the complicated multivalent binding interaction induces stable BAX/Bcl-2 complexes. This study enriches our understanding of the molecular mechanisms by which BAX interacts with Bcl-2. It provides valuable insights into the physical factors that need to be considered when designing PPI inhibitors.
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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.
| | - Yichen Tian
- 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.
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yani Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Xinrui Yan
- 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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Maiolo D, Del Pino P, Metrangolo P, Parak WJ, Baldelli Bombelli F. Nanomedicine delivery: does protein corona route to the target or off road? Nanomedicine (Lond) 2015; 10:3231-47. [PMID: 26470748 DOI: 10.2217/nnm.15.163] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nanomedicine aims to find novel solutions for urgent biomedical needs. Despite this, one of the most challenging hurdles that nanomedicine faces is to successfully target therapeutic nanoparticles to cells of interest in vivo. As for any biomaterials, once in vivo, nanoparticles can interact with plasma biomolecules, forming new entities for which the name protein coronas (PCs) have been coined. The PC can influence the in vivo biological fate of a nanoparticle. Thus for guaranteeing the desired function of an engineered nanomaterial in vivo, it is crucial to dissect its PC in terms of formation and evolution within the body. In this contribution we will review the 'good' and 'bad' sides of the PC, starting from the scientific aspects to the technological applications.
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Affiliation(s)
- Daniele Maiolo
- Fondazione Centro Europeo Nanomedicina c/o Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials, & Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy
| | - Pablo Del Pino
- CIC Biomagune, San Sebastian, Spain.,Fachbereich Physik, Philipps Universität Marburg, Marburg, Germany
| | - Pierangelo Metrangolo
- Fondazione Centro Europeo Nanomedicina c/o Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials, & Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy.,VTT-Technical Research Centre of Finland, FI-02044 VTT, Espoo, Finland
| | - Wolfgang J Parak
- CIC Biomagune, San Sebastian, Spain.,Fachbereich Physik, Philipps Universität Marburg, Marburg, Germany
| | - Francesca Baldelli Bombelli
- Fondazione Centro Europeo Nanomedicina c/o Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials, & Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy
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Angiogenic growth factors interactome and drug discovery: The contribution of surface plasmon resonance. Cytokine Growth Factor Rev 2014; 26:293-310. [PMID: 25465594 DOI: 10.1016/j.cytogfr.2014.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 11/21/2022]
Abstract
Angiogenesis is implicated in several pathological conditions, including cancer, and in regenerative processes, including the formation of collateral blood vessels after stroke. Physiological angiogenesis is the outcome of a fine balance between the action of angiogenic growth factors (AGFs) and anti-angiogenic molecules, while pathological angiogenesis occurs when this balance is pushed toward AGFs. AGFs interact with multiple endothelial cell (EC) surface receptors inducing cell proliferation, migration and proteases upregulation. On the contrary, free or extracellular matrix-associated molecules inhibit angiogenesis by sequestering AGFs (thus hampering EC stimulation) or by interacting with specific EC receptors inducing apoptosis or decreasing responsiveness to AGFs. Thus, angiogenesis results from an intricate network of interactions among pro- and anti-angiogenic molecules, EC receptors and various modulators. All these interactions represent targets for the development of pro- or anti-angiogenic therapies. These aims call for suitable technologies to study the countless interactions occurring during neovascularization. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time. It has become the golden standard technology for interaction analysis in biomedical research, including angiogenesis. From a survey of the literature it emerges that SPR has already contributed substantially to the better understanding of the neovascularization process, laying the basis for the decoding of the angiogenesis "interactome" and the identification of "hub molecules" that may represent preferential targets for an efficacious modulation of angiogenesis. Here, the still unexploited full potential of SPR is enlightened, pointing to improvements in its use for a deeper understanding of the mechanisms of neovascularization and the identification of novel anti-angiogenic drugs.
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Lu Y, Sarshar MA, Du K, Chou T, Choi CH, Sukhishvili SA. Large-amplitude, reversible, pH-triggered wetting transitions enabled by layer-by-layer films. ACS APPLIED MATERIALS & INTERFACES 2013; 5:12617-12623. [PMID: 24191775 DOI: 10.1021/am403944m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report on the use of layer-by-layer (LbL) hydrogels, composed of amphiphilic polymers that undergo reversible collapse-dissolution transition in solutions as a function of pH, to induce sharp, large-amplitude wetting transition at microstructured surfaces. Surface hydrogels were composed of poly(2-alkylacrylic acids) (PaAAs) of varied hydrophobicity, i.e., poly(methacrylic acid) (PMAA), poly(2-ethylacrylic acid) (PEAA), poly(2-n-propylacrylic acid) (PPAA) and poly(2-n-butylacrylic acid) (PBAA). When deposited at a micropillar-patterned silicon substrate, hydrophilic PMAA LbL hydrogels supported complete surface wetting (contact angle, CA, of 0°), whereas PEAA, PPAA, and PBAA ultrathin coatings supported large-amplitude wetting transitions, with CA changes from 110 to 125° at acidic to 0° at basic pH values, and the transition pH increasing from 6.2 to 8.4 with increased polyacid hydrophobicity. At acidic pHs, droplets showed a large hysteresis in CA (a "sticky droplet" behavior), and remained in the Wenzel state. The fact that CA changes for wetting-nonwetting transitions occurred at values close to physiologic pH makes these coatings promising for controlling flow and bioadhesion using external stimuli. Finally, we show that the surface wettability transitions can be used to detect positively charged analytes (such as gentamicin) in solution via large changes in CA associated with adsorption of analytes within the hydrogels.
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Affiliation(s)
- Yiming Lu
- Department of Chemistry, Chemical Biology and Biomedical Engineering, ‡Department of Mechanical Engineering, and §Department of Chemical Engineering and Material Science, Stevens Institute of Technology , Hoboken, New Jersey 07030, United States
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Nanomechanics of surface DNA switches probed by captive contact angle. J Colloid Interface Sci 2013; 402:334-9. [PMID: 23647692 DOI: 10.1016/j.jcis.2013.03.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 01/09/2023]
Abstract
Self-assembled monolayers of Thrombin Binding Aptamers (TBA) were prepared on gold surfaces with typical surface densities of close-packed ssDNA (4×10(12) and 8×10(12)molecules/cm(2)). CONtact Angle MOlecular REcognition (CONAMORE) in captive bubble geometry was then assessed to scan the surface work triggered by TBAs when switching from the elongated to the G-quadruplex conformation upon binding with Na(+) or K(+) cations. We found Na(+) and K(+) could induce comparable linear to G-quadruplex strokes, and resulted in values for surface work of ~-70 pN nm/molecule (~18 kBT). The strokes change the in-plane van der Waals and weak electrostatic interactions and accumulate to result in macroscopic surface work. Micro- to macroscopic translation strongly depends on the nature of the cation and TBA surface density. In particular, the K(+) stimulus triggers a macroscopic surface work of -2.2±0.2 and -5.3±0.2 mN/m for low and high packed monolayers, respectively, while Na(+) triggers up to -6.7±1.0 mN/m in the highly packed monolayer, but creates negligible work for the low packed monolayer. These results show that CONAMORE can contribute important information for the development of devices based on DNA switches, and ultimately help address some of the open challenges for DNA-based nanomachinery.
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Mielecki M, Wojtasik J, Zborowska M, Kurzątkowska K, Grzelak K, Dehaen W, Radecki J, Radecka H. Oriented immobilization of His-tagged kinase RIO1 protein on redox active N-(IDA-like)-Cu(II) monolayer deposited on gold electrode—The base of electrochemical biosensor. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.02.085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Yin TI, Zhao Y, Horak J, Bakirci H, Liao HH, Tsai HH, Juang YZ, Urban G. A micro-cantilever sensor chip based on contact angle analysis for a label-free troponin I immunoassay. LAB ON A CHIP 2013; 13:834-842. [PMID: 23282576 DOI: 10.1039/c2lc40767a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cantilever sensors have been extensively explored as a promising technique for real-time and label-free analyses in biological systems. A major sensing principle utilized by state-of-the-art cantilever sensors is based on analyte-induced surface stress changes, which result in static bending of a cantilever. The sensor performance, however, suffers from the intrinsically small change in surface stress induced by analytes, especially for molecular recognition such as antigen-antibody binding. Through the contact angle change on a tailored solid surface, it is possible to convert a tiny surface stress into a capillary force-a much larger physical quantity needed for a practical sensor application. In this work, a micro-cantilever sensor based on contact angle analysis (CAMCS) was proposed to effectively enhance the sensitivity of a sensor in proportion to the square of the length to thickness ratio of the cantilever structure. CAMCS chips were fabricated using a standard complementary-metal-oxide-semiconductor (CMOS) process to demonstrate a 1250-fold enhancement in the sensitivity of surface stress to bioanalyte adsorption using a piezoresistive sensing method. A real-time and label-free troponin I (cTnI) immunoassay, which is now widely used in clinics and considered a gold standard for the early diagnosis and prognosis of cardiovascular disease, was performed to demonstrate cTnI detection levels as low as 1 pg mL(-1). The short detection time of this assay was within several minutes, which matches the detection time of commercially available instruments that are based on fluorescence-labeling techniques.
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Affiliation(s)
- Tsung-I Yin
- Department for Microsystems Engineering (IMTEK), University of Freiburg, 79110 Freiburg, Germany.
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Maiolo D, Mitola S, Leali D, Oliviero G, Ravelli C, Bugatti A, Depero LE, Presta M, Bergese P. Role of nanomechanics in canonical and noncanonical pro-angiogenic ligand/VEGF receptor-2 activation. J Am Chem Soc 2012; 134:14573-9. [PMID: 22860754 DOI: 10.1021/ja305816p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR2) is an endothelial cell receptor that plays a pivotal role in physiologic and pathologic angiogenesis and is a therapeutic target for angiogenesis-dependent diseases, including cancer. By leveraging on a dedicated nanomechanical biosensor, we investigated the nanoscale mechanical phenomena intertwined with VEGFR2 surface recognition by its prototypic ligand VEGF-A and its noncanonical ligand gremlin. We found that the two ligands bind the immobilized extracellular domain of VEGFR2 (sVEGFR2) with comparable binding affinity. Nevertheless, they interact with sVEGFR2 with different binding kinetics and drive different in-plane piconewton intermolecular forces, suggesting that the binding of VEGF-A or gremlin induces different conformational changes in sVEGFR2. These behaviors can be effectively described in terms of a different "nanomechanical affinity" of the two ligands for sVEGFR2, about 16-fold higher for VEGF-A with respect to gremlin. Such nanomechanical differences affect the biological activity driven by the two angiogenic factors in endothelial cells, as evidenced by a more rapid VEGFR2 clustering and a more potent mitogenic response triggered by VEGF-A in respect to gremlin. Together, these data point to surface intermolecular interactions on cell membrane between activated receptors as a key modulator of the intracellular signaling cascade.
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Affiliation(s)
- Daniele Maiolo
- Chemistry for Technologies Laboratory and INSTM, School of Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
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Federici S, Oliviero G, Maiolo D, Depero LE, Colombo I, Bergese P. On the thermodynamics of biomolecule surface transformations. J Colloid Interface Sci 2012; 375:1-11. [DOI: 10.1016/j.jcis.2012.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 02/06/2023]
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Dionisio M, Oliviero G, Menozzi D, Federici S, Yebeutchou RM, Schmidtchen FP, Dalcanale E, Bergese P. Nanomechanical Recognition of N-Methylammonium Salts. J Am Chem Soc 2012; 134:2392-8. [DOI: 10.1021/ja210567k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Dionisio
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Giulio Oliviero
- Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123 Brescia,
Italy
| | - Daniela Menozzi
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Stefania Federici
- Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123 Brescia,
Italy
| | - Roger M. Yebeutchou
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | | | - Enrico Dalcanale
- Department of Organic and Industrial
Chemistry, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Paolo Bergese
- Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123 Brescia,
Italy
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