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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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Sobiepanek A, Kowalska PD, Szota M, Grzywa TM, Nowak J, Włodarski PK, Galus R, Jachimska B, Kobiela T. Novel diagnostic and prognostic factors for the advanced melanoma based on the glycosylation-related changes studied by biophysical profiling methods. Biosens Bioelectron 2022; 203:114046. [PMID: 35121451 DOI: 10.1016/j.bios.2022.114046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/28/2022]
Abstract
Melanoma is a life-threatening disease due to the early onset of metastasis and frequent resistance to the applied treatment. For now, no single histological, immunohistochemical or serological biomarker was able to provide a precise predictive value for the aggressive behavior in melanoma patients. Thus, the search for quantifying methods allowing a simultaneous diagnosis and prognosis of melanoma patients is highly desirable. By investigating specific molecular interactions with some biosensor-based techniques, one can determine novel prognostic factors for this tumor. In our previous study, we have shown the possibility of a qualitative in vitro distinguishing the commercially available melanoma cells at different progression stages based on the measurements of the lectin Concanavalin A interacting with surface glycans present on cells. Here, we present the results of the quantitative diagnostic and prognostic study of both commercial and patient-derived melanoma cells based on the evaluation of two novel factors: lectin affinity and glycan viscoelastic index obtained from the quartz crystal microbalance with dissipation monitoring (QCM-D) measurements. Two approaches to the QCM-D measurements were applied, the first uses the ability of melanoma cells to grow as a monolayer of cells on the sensor (cell-based sensors), and the second shortens the time of the analysis (suspension cell based-sensors). The results were confirmed by the complementary label-free (atomic force microscopy, AFM; and surface plasmon resonance, SPR) and labeling (lectin-ELISA; and microscale thermophoresis, MST) techniques. This new approach provides additional quantitative diagnosis and a personalized prognosis which can be done simultaneously to the traditional histopathological analysis.
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Affiliation(s)
- Anna Sobiepanek
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland.
| | - Patrycja D Kowalska
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland; Polish Stem Cell Bank, Warsaw, Poland
| | - Magdalena Szota
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Krakow, Poland
| | - Tomasz M Grzywa
- Department of Methodology, Centre for Preclinical Research, Medical University of Warsaw, Poland; Department of Immunology, Medical University of Warsaw, Warsaw, Poland; Doctoral School, Medical University of Warsaw, Warsaw, Poland
| | - Jakub Nowak
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł K Włodarski
- Department of Methodology, Centre for Preclinical Research, Medical University of Warsaw, Poland
| | - Ryszard Galus
- Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Krakow, Poland
| | - Tomasz Kobiela
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland.
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