1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
Collapse
Affiliation(s)
- Heng Sun
- 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.
| |
Collapse
|
3
|
Hu X, Dinu CZ. A bio-pen for direct writing of single molecules on user-functionalized surfaces. NANOSCALE ADVANCES 2020; 2:156-165. [PMID: 36133986 PMCID: PMC9417116 DOI: 10.1039/c9na00379g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/30/2019] [Indexed: 06/16/2023]
Abstract
Advancing ultrahigh resolution (below 10 nm) direct writing technologies could lead to impacts in areas as diverse as disease detection, genetic analysis and nanomanufacturing. Current methods based on electron-beams and photo- or dip-pen nanolithography are laborious and lack flexibility when aiming to create single molecule patterns for application specific integration. We hypothesize that a novel strategy could be developed to allow for writing of parallel and yet individually addressable patterns of single molecules on user-controlled surfaces. The strategy is based on using in vitro self-recognition of tubulin protein to assemble rigid protofilaments of microtubules, with one such microtubule to be subsequently used as a "bio-pen" capable of writing "inks" of single kinesin molecules in user-defined environments. Our results show that single kinesin inks could be written under the energy of adenosine triphosphate hydrolysis and observed by both atomic force and optical microscopy. Upon extending ink functionalities, the integration of soft and hard materials for nanostructure assembly and complex single molecule pattern formation is envisioned.
Collapse
Affiliation(s)
- Xiao Hu
- Department of Chemical and Biomedical Engineering, West Virginia University, Benjamin M. Statler College of Engineering and Mineral Resources PO Box 6102 Morgantown WV 26506 USA +1 304 293 4139 +1 304 293 9338
| | - Cerasela Zoica Dinu
- Department of Chemical and Biomedical Engineering, West Virginia University, Benjamin M. Statler College of Engineering and Mineral Resources PO Box 6102 Morgantown WV 26506 USA +1 304 293 4139 +1 304 293 9338
| |
Collapse
|
4
|
Duan L, Yao H, Xie Y, Pan K. Label-free fluorescence detection of protein–ligand interactions based on binding-induced enzymatic cleavage protection. NEW J CHEM 2020. [DOI: 10.1039/d0nj03316b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Label-free fluorescence monitoring protein–ligand interaction based on binding induced enzymatic cleavage protection.
Collapse
Affiliation(s)
- Lunxi Duan
- Department of General Surgery
- The Second Xiangya Hospital
- Central South University
- Changsha
- People's Republic of China
| | - Hongliang Yao
- Department of General Surgery
- The Second Xiangya Hospital
- Central South University
- Changsha
- People's Republic of China
| | - Yong Xie
- Department of General Surgery
- The Second Xiangya Hospital
- Central South University
- Changsha
- People's Republic of China
| | - Ke Pan
- Department of General Surgery
- The Second Xiangya Hospital
- Central South University
- Changsha
- People's Republic of China
| |
Collapse
|
5
|
Hu X, Guiseppi-Elie A, Dinu CZ. Biomolecular interfaces based on self-assembly and self-recognition form biosensors capable of recording molecular binding and release. NANOSCALE 2019; 11:4987-4998. [PMID: 30839012 DOI: 10.1039/c8nr10090j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This research proposed to create the next generation of versatile electrochemical-based biosensors capable of monitoring target capture and release as dictated by molecular binding or unbinding. The biosensor integrates cellular machines (i.e., microtubules, structural elements of cells and kinesin molecular motors involved in cellular transport) as functional units; its assembly is based on molecular self-assembly and self-recognition. Our results demonstrate that the designed biosensor was capable of allowing detection of binding and unbinding events based on redox reactions at user-controlled electrode interfaces. The analysis also showed that the sensitivity of the designed biosensor or its ability to record such events could be user-controlled at any given time by adjusting the energy source that "fuels" the system.
Collapse
Affiliation(s)
- Xiao Hu
- Department of Chemical and Biomedical Engineering, West Virginia University, WV, USA.
| | | | | |
Collapse
|
6
|
Hu X, Fagone P, Dong C, Su R, Xu Q, Dinu CZ. Biological Self-Assembly and Recognition Used to Synthesize and Surface Guide Next Generation of Hybrid Materials. ACS APPLIED MATERIALS & INTERFACES 2018; 10:28372-28381. [PMID: 29939708 DOI: 10.1021/acsami.8b09421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Free-standing, high aspect ratio sulfur-doped carbon nanodot-based hybrid nanowires with a microtubular aspect were synthesized using self-recognition and self-assembly processes of tubulin, a biological molecule precursor of the cytoskeletal microtubule. Physicochemical characterizations (e.g., morphology, diameter, spectral characteristics, etc.) of such user-synthesized hybrid bionanowires were performed using classical atomic and spectroscopic techniques, whereas bioactivity and functionality testing was demonstrated by mimicking cellular transport based on kinesin, a motor protein capable to recognize, and move on the microtubules. Our results indicate that user-synthesized hybrid nanowires could be manipulated in vitro under constant chemical energy of adenosine triphosphate and have the potential to be implemented in the next generation of synthetic applications from drug delivery to diagnosis systems, and photocatalytic to optical devices.
Collapse
Affiliation(s)
| | | | | | - Rigu Su
- State Key Laboratory of Heavy Oil Processing , China University of Petroleum (Beijing) , Beijing 102249 , China
| | - Quan Xu
- State Key Laboratory of Heavy Oil Processing , China University of Petroleum (Beijing) , Beijing 102249 , China
| | | |
Collapse
|
7
|
Hossain A, Nandi U, Fule R, Nokhodchi A, Maniruzzaman M. Advanced surface chemical analysis of continuously manufactured drug loaded composite pellets. J Colloid Interface Sci 2016; 492:157-166. [PMID: 28086118 DOI: 10.1016/j.jcis.2016.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/02/2016] [Accepted: 11/06/2016] [Indexed: 01/01/2023]
Abstract
The aim of the present study was to develop and characterise polymeric composite pellets by means of continuous melt extrusion techniques. Powder blends of a steroid hormone (SH) as a model drug and either ethyl cellulose (EC N10 and EC P7 grades) or hydroxypropyl methylcellulose (HPMC AS grade) as polymeric carrier were extruded using a Pharma 11mm twin screw extruder in a continuous mode of operation to manufacture extruded composite pellets of 1mm length. Molecular modelling study using commercial Gaussian 09 software outlined a possible drug-polymer interaction in the molecular level to develop solid dispersions of the drug in the pellets. Solid-state analysis conducted via a differential scanning calorimetry (DSC), hot stage microscopy (HSM) and X-ray powder diffraction (XRPD) analyses revealed the amorphous state of the drug in the polymer matrices. Surface analysis using SEM/energy dispersive X-ray (EDX) of the produced pellets arguably showed a homogenous distribution of the C and O atoms in the pellet matrices. Moreover, advanced chemical surface analysis conducted via atomic force microscopy (AFM) showed a homogenous phase system having the drug molecule dispersed onto the amorphous matrices while Raman mapping confirmed the homogenous single-phase drug distribution in the manufactured composite pellets. Such composite pellets are expected to deliver multidisciplinary applications in drug delivery and medical sciences by e.g. modifying drug solubility/dissolutions or stabilizing the unstable drug (e.g. hormone, protein) in the composite network.
Collapse
Affiliation(s)
- Akter Hossain
- Faculty of Engineering and Science, University of Greenwich, Central Avenue, Chatham Maritime, Chatham, Kent ME4 4TB, UK
| | - Uttom Nandi
- Faculty of Engineering and Science, University of Greenwich, Central Avenue, Chatham Maritime, Chatham, Kent ME4 4TB, UK
| | - Ritesh Fule
- Faculty of Pharmaceutics Department, H.K. College of Pharmacy, Relief Road, Oshiwara, Jogeshwari West, Mumbai 400102, Maharashtra, India
| | - Ali Nokhodchi
- Department of Pharmacy (Chemistry), School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK; Drug Applied Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammed Maniruzzaman
- Department of Pharmacy (Chemistry), School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK.
| |
Collapse
|