1
|
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
|
2
|
Choi JK, Naffouje SA, Goto M, Wang J, Christov K, Rademacher DJ, Green A, Stecenko AA, Chakrabarty AM, Das Gupta TK, Yamada T. Cross-talk between cancer and Pseudomonas aeruginosa mediates tumor suppression. Commun Biol 2023; 6:16. [PMID: 36609683 PMCID: PMC9823004 DOI: 10.1038/s42003-022-04395-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
Microorganisms living at many sites in the human body compose a complex and dynamic community. Accumulating evidence suggests a significant role for microorganisms in cancer, and therapies that incorporate bacteria have been tried in various types of cancer. We previously demonstrated that cupredoxin azurin secreted by the opportunistic pathogen Pseudomonas aeruginosa, enters human cancer cells and induces apoptotic death1-4. However, the physiological interactions between P. aeruginosa and humans and their role in tumor homeostasis are largely unknown. Here, we show that P. aeruginosa upregulated azurin secretion in response to increasing numbers of and proximity to cancer cells. Conversely, cancer cells upregulated aldolase A secretion in response to increasing proximity to P. aeruginosa, which also correlated with enhanced P. aeruginosa adherence to cancer cells. Additionally, we show that cancer patients had detectable P. aeruginosa and azurin in their tumors and exhibited increased overall survival when they did, and that azurin administration reduced tumor growth in transgenic mice. Our results suggest host-bacterial symbiotic mutualism acting as a diverse adjunct to the host defense system via inter-kingdom communication mediated by the evolutionarily conserved proteins azurin and human aldolase A. This improved understanding of the symbiotic relationship of bacteria with humans indicates the potential contribution to tumor homeostasis.
Collapse
Affiliation(s)
- Juliana K Choi
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.,Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Samer A Naffouje
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.,General Surgery, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Masahide Goto
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Jing Wang
- Department of Mathematics, Statistics and Computer Science, University of Illinois College of Liberal Arts and Sciences, Chicago, IL, 60607, USA
| | - Konstantin Christov
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - David J Rademacher
- Department of Microbiology and Immunology and Core Imaging Facility, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Albert Green
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Arlene A Stecenko
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ananda M Chakrabarty
- Department of Microbiology & Immunology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Tapas K Das Gupta
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA. .,Richard & Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering, Chicago, IL, 60607, USA.
| |
Collapse
|
3
|
Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
Collapse
Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| |
Collapse
|
4
|
Moscetti I, Cannistraro S, Bizzarri AR. Surface Plasmon Resonance Sensing of Biorecognition Interactions within the Tumor Suppressor p53 Network. SENSORS 2017; 17:s17112680. [PMID: 29156626 PMCID: PMC5713020 DOI: 10.3390/s17112680] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
Abstract
Surface Plasmon Resonance (SPR) is a powerful technique to study the kinetics of biomolecules undergoing biorecognition processes, particularly suited for protein-protein interactions of biomedical interest. The potentiality of SPR was exploited to sense the interactions occurring within the network of the tumor suppressor p53, which is crucial for maintaining genome integrity and whose function is inactivated, mainly by down regulation or by mutation, in the majority of human tumors. This study includes p53 down-regulators, p53 mutants and also the p53 family members, p63 and p73, which could vicariate p53 protective function. Furthermore, the application of SPR was extended to sense the interaction of p53 with anti-cancer drugs, which might restore p53 function. An extended review of previous published work and unpublished kinetic data is provided, dealing with the interaction between the p53 family members, or their mutants and two anticancer molecules, Azurin and its cell-penetrating peptide, p28. All the kinetic results are discussed in connection with those obtained by a complementary approach operating at the single molecule level, namely Atomic Force Spectroscopy and the related literature data. The overview of the SPR kinetic results may significantly contribute to a deeper understanding of the interactions within p53 network, also in the perspective of designing suitable anticancer drugs.
Collapse
Affiliation(s)
- Ilaria Moscetti
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| |
Collapse
|
5
|
Signorelli S, Cannistraro S, Bizzarri AR. Structural Characterization of the Intrinsically Disordered Protein p53 Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2017; 71:823-832. [PMID: 27340212 DOI: 10.1177/0003702816651891] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The intrinsically disordered protein p53 has attracted a strong interest for its important role in genome safeguarding and potential therapeutic applications. However, its disordered character makes difficult a full characterization of p53 structural architecture. A deep knowledge of p53 structural motifs could significantly help the understanding of its functional properties, in connection with its complex binding network. We have applied Raman spectroscopy to investigate the structural composition and the conformational heterogeneity of both full-length p53 and its DNA binding domain (DBD), in different solvent environments. In particular, a careful analysis of the Amide I Raman band, which is highly sensitive to protein secondary structure elements such as α-helices, β-sheets and random coils, has revealed the presence of extended random coils in p53 and predominant β-sheet regions in its DBD. In addition, this analysis has allowed us to explore the ensemble of interchanging conformations in both p53 and its DBD, highlighting a higher conformational heterogeneity in p53 than in its DBD. Furthermore, by applying a principal components analysis, we have identified the principal spectral markers in both p53 and DBD samples. The combination of the two approaches could be insightful for the study of intrinsically disordered proteins, by offering increased versatility and wide application as a label-free, real-time and non-invasive detection method.
Collapse
Affiliation(s)
- Sara Signorelli
- 1 Biophysics and Nanoscience Centre, Università della Tuscia, Italy
- 2 Department of Science, University Roma Tre, Italy
| | | | | |
Collapse
|
6
|
Signorelli S, Santini S, Yamada T, Bizzarri AR, Beattie CW, Cannistraro S. Binding of Amphipathic Cell Penetrating Peptide p28 to Wild Type and Mutated p53 as studied by Raman, Atomic Force and Surface Plasmon Resonance spectroscopies. Biochim Biophys Acta Gen Subj 2017; 1861:910-921. [PMID: 28126403 DOI: 10.1016/j.bbagen.2017.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/21/2016] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Mutations within the DNA binding domain (DBD) of the tumor suppressor p53 are found in >50% of human cancers and may significantly modify p53 secondary structure impairing its function. p28, an amphipathic cell-penetrating peptide, binds to the DBD through hydrophobic interaction and induces a posttranslational increase in wildtype and mutant p53 restoring functionality. We use mutation analyses to explore which elements of secondary structure may be critical to p28 binding. METHODS Molecular modeling, Raman spectroscopy, Atomic Force Spectroscopy (AFS) and Surface Plasmon Resonance (SPR) were used to identify which secondary structure of site-directed and naturally occurring mutant DBDs are potentially altered by discrete changes in hydrophobicity and the molecular interaction with p28. RESULTS We show that specific point mutations that alter hydrophobicity within non-mutable and mutable regions of the p53 DBD alter specific secondary structures. The affinity of p28 was positively correlated with the β-sheet content of a mutant DBD, and reduced by an increase in unstructured or random coil that resulted from a loss in hydrophobicity and redistribution of surface charge. CONCLUSIONS These results help refine our knowledge of how mutations within p53-DBD alter secondary structure and provide insight on how potential structural alterations in p28 or similar molecules improve their ability to restore p53 function. GENERAL SIGNIFICANCE Raman spectroscopy, AFS, SPR and computational modeling are useful approaches to characterize how mutations within the p53DBD potentially affect secondary structure and identify those structural elements prone to influence the binding affinity of agents designed to increase the functionality of p53.
Collapse
Affiliation(s)
- Sara Signorelli
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy; Department of Science, University Roma Tre, Rome, Italy
| | - Simona Santini
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy.
| | - Craig W Beattie
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, USA
| | | |
Collapse
|
7
|
Yamada T, Das Gupta TK, Beattie CW. p28, an Anionic Cell-Penetrating Peptide, Increases the Activity of Wild Type and Mutated p53 without Altering Its Conformation. Mol Pharm 2013; 10:3375-83. [DOI: 10.1021/mp400221r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tohru Yamada
- Department of Surgery, Division of
Surgical Oncology,
University of Illinois at Chicago College of Medicine, 840 South Wood
Street, Suite 618, Chicago, Illinois 60612, United States
| | - Tapas K. Das Gupta
- Department of Surgery, Division of
Surgical Oncology,
University of Illinois at Chicago College of Medicine, 840 South Wood
Street, Suite 618, Chicago, Illinois 60612, United States
| | - Craig W. Beattie
- Department of Surgery, Division of
Surgical Oncology,
University of Illinois at Chicago College of Medicine, 840 South Wood
Street, Suite 618, Chicago, Illinois 60612, United States
| |
Collapse
|
8
|
Yamada T, Christov K, Shilkaitis A, Bratescu L, Green A, Santini S, Bizzarri AR, Cannistraro S, Gupta TKD, Beattie CW. p28, a first in class peptide inhibitor of cop1 binding to p53. Br J Cancer 2013; 108:2495-504. [PMID: 23736031 PMCID: PMC3694247 DOI: 10.1038/bjc.2013.266] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 05/08/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND A 28 amino-acid (aa) cell-penetrating peptide (p28) derived from azurin, a redox protein secreted from the opportunistic pathogen Pseudomonas aeruginosa, produces a post-translational increase in p53 in cancer cells by inhibiting its ubiquitination. METHODS In silico computational simulations were used to predict motifs within the p53 DNA-binding domain (DBD) as potential sites for p28 binding. In vitro direct and competitive pull-down studies as well as western blot and RT-PCR analyses were used to validate predictions. RESULTS The L1 loop (aa 112-124), a region within the S7-S8 loop (aa 214-236) and T140, P142, Q144, W146, R282 and L289 of the p53DBD were identified as potential sites for p28 binding. p28 decreased the level of the E3 ligase COP1 >80%, in p53wt and p53mut cells with no decrease in COP1 in p53dom/neg or p53null cells. Brief increases in the expression of the E3 ligases, TOPORS, Pirh2 and HDM2 (human double minute 2) in p53wt and p53mut cells were in response to sustained increases in p53. CONCLUSION These data identify the specific motifs within the DBD of p53 that bind p28 and suggest that p28 inhibition of COP1 binding results in the sustained, post-translational increase in p53 levels and subsequent inhibition of cancer cell growth independent of an HDM2 pathway.
Collapse
Affiliation(s)
- T Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - K Christov
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - A Shilkaitis
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - L Bratescu
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - A Green
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - S Santini
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Viterbo, Italy
| | - A R Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Viterbo, Italy
| | - S Cannistraro
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Viterbo, Italy
| | - T K D Gupta
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - C W Beattie
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| |
Collapse
|
9
|
Bizzarri AR, Santini S, Coppari E, Bucciantini M, Di Agostino S, Yamada T, Beattie CW, Cannistraro S. Interaction of an anticancer peptide fragment of azurin with p53 and its isolated domains studied by atomic force spectroscopy. Int J Nanomedicine 2011; 6:3011-9. [PMID: 22162658 PMCID: PMC3230568 DOI: 10.2147/ijn.s26155] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
p28 is a 28-amino acid peptide fragment of the cupredoxin azurin derived from Pseudomonas aeruginosa that preferentially penetrates cancerous cells and arrests their proliferation in vitro and in vivo. Its antitumor activity reportedly arises from post-translational stabilization of the tumor suppressor p53 normally downregulated by the binding of several ubiquitin ligases. This would require p28 to specifically bind to p53 to inhibit specific ligases from initiating proteosome-mediated degradation. In this study, atomic force spectroscopy, a nanotechnological approach, was used to investigate the interaction of p28 with full-length p53 and its isolated domains at the single molecule level. Analysis of the unbinding forces and the dissociation rate constant suggest that p28 forms a stable complex with the DNA-binding domain of p53, inhibiting the binding of ubiquitin ligases other than Mdm2 to reduce proteasomal degradation of p53.
Collapse
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Viterbo, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Santini S, Bizzarri AR, Cannistraro S. Modelling the interaction between the p53 DNA-binding domain and the p28 peptide fragment of Azurin. J Mol Recognit 2011; 24:1043-55. [DOI: 10.1002/jmr.1153] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simona Santini
- Biophysics and Nanoscience Centre; CNISM; Facoltà di Scienze; Università della Tuscia; 01100; Viterbo; Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre; CNISM; Facoltà di Scienze; Università della Tuscia; 01100; Viterbo; Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre; CNISM; Facoltà di Scienze; Università della Tuscia; 01100; Viterbo; Italy
| |
Collapse
|